Marsh wren quality control
Devon DeRaad
7/28/2022
library(gridExtra)
library(knitr)
library(ggplot2)
library(fastqcr)
#must run this if fastqc is not already installed locally
#fastqc_install()###ONLY THIS CHUNK REQUIRES MODIFICATION###
###assign your directory locations here:
#specify full path to directory containing a .fastq.gz file for each sample
fq.dir<-"/home/d669d153/scratch/marsh.wren.rad/fastq"
#specify full path to the output directory where you want
qc.dir<-"/home/d669d153/scratch/marsh.wren.rad/qc"#run fastqc on all .fastq.gz files, through r
#This only needs to be run once, if only tweaking downstream visualizations, you can comment out this step
fastqc(fq.dir = fq.dir, # FASTQ files directory
qc.dir = qc.dir, # Results directory
threads = 4 # Number of threads
)# List of files in the output directory to ensure fastqc worked
list.files(qc.dir)[1] “25369_fastqc.html” “25369_fastqc.zip” “25370_fastqc.html” [4] “25370_fastqc.zip” “25371_fastqc.html” “25371_fastqc.zip”
[7] “25372_fastqc.html” “25372_fastqc.zip” “25373_fastqc.html” [10] “25373_fastqc.zip” “25374_fastqc.html” “25374_fastqc.zip”
[13] “25375_fastqc.html” “25375_fastqc.zip” “25376_fastqc.html” [16] “25376_fastqc.zip” “25377_fastqc.html” “25377_fastqc.zip”
[19] “25378_fastqc.html” “25378_fastqc.zip” “25379_fastqc.html” [22] “25379_fastqc.zip” “25380_fastqc.html” “25380_fastqc.zip”
[25] “25381_fastqc.html” “25381_fastqc.zip” “25382_fastqc.html” [28] “25382_fastqc.zip” “25383_fastqc.html” “25383_fastqc.zip”
[31] “31445_fastqc.html” “31445_fastqc.zip” “31446_fastqc.html” [34] “31446_fastqc.zip” “31897_fastqc.html” “31897_fastqc.zip”
[37] “31898_fastqc.html” “31898_fastqc.zip” “B00907_fastqc.html” [40] “B00907_fastqc.zip” “B00908_fastqc.html” “B00908_fastqc.zip” [43] “B00909_fastqc.html” “B00909_fastqc.zip” “B00910_fastqc.html” [46] “B00910_fastqc.zip” “B00911_fastqc.html” “B00911_fastqc.zip” [49] “B00912_fastqc.html” “B00912_fastqc.zip” “B00913_fastqc.html” [52] “B00913_fastqc.zip” “B00914_fastqc.html” “B00914_fastqc.zip” [55] “B00915_fastqc.html” “B00915_fastqc.zip” “B00916_fastqc.html” [58] “B00916_fastqc.zip” “B00922_fastqc.html” “B00922_fastqc.zip” [61] “B00927_fastqc.html” “B00927_fastqc.zip” “B00928_fastqc.html” [64] “B00928_fastqc.zip” “B00929_fastqc.html” “B00929_fastqc.zip” [67] “B00930_fastqc.html” “B00930_fastqc.zip” “B00931_fastqc.html” [70] “B00931_fastqc.zip” “B00932_fastqc.html” “B00932_fastqc.zip” [73] “B00933_fastqc.html” “B00933_fastqc.zip” “B00934_fastqc.html” [76] “B00934_fastqc.zip” “B00935_fastqc.html” “B00935_fastqc.zip” [79] “B00936_fastqc.html” “B00936_fastqc.zip” “B00937_fastqc.html” [82] “B00937_fastqc.zip” “B00938_fastqc.html” “B00938_fastqc.zip” [85] “B00939_fastqc.html” “B00939_fastqc.zip” “B00940_fastqc.html” [88] “B00940_fastqc.zip” “B00941_fastqc.html” “B00941_fastqc.zip” [91] “B00942_fastqc.html” “B00942_fastqc.zip” “B00943_fastqc.html” [94] “B00943_fastqc.zip” “B00944_fastqc.html” “B00944_fastqc.zip” [97] “B00945_fastqc.html” “B00945_fastqc.zip” “B00946_fastqc.html” [100] “B00946_fastqc.zip” “B00947_fastqc.html” “B00947_fastqc.zip” [103] “B00948_fastqc.html” “B00948_fastqc.zip” “B00949_fastqc.html” [106] “B00949_fastqc.zip” “B00950_fastqc.html” “B00950_fastqc.zip” [109] “B00951_fastqc.html” “B00951_fastqc.zip” “B00952_fastqc.html” [112] “B00952_fastqc.zip” “B00953_fastqc.html” “B00953_fastqc.zip” [115] “B00954_fastqc.html” “B00954_fastqc.zip” “B00955_fastqc.html” [118] “B00955_fastqc.zip” “B00956_fastqc.html” “B00956_fastqc.zip” [121] “B00957_fastqc.html” “B00957_fastqc.zip” “B00958_fastqc.html” [124] “B00958_fastqc.zip” “B00959_fastqc.html” “B00959_fastqc.zip” [127] “B00960_fastqc.html” “B00960_fastqc.zip” “B00961_fastqc.html” [130] “B00961_fastqc.zip” “B00962_fastqc.html” “B00962_fastqc.zip” [133] “B00963_fastqc.html” “B00963_fastqc.zip” “B00964_fastqc.html” [136] “B00964_fastqc.zip” “B00965_fastqc.html” “B00965_fastqc.zip” [139] “B00966_fastqc.html” “B00966_fastqc.zip” “B00967_fastqc.html” [142] “B00967_fastqc.zip” “B02324_fastqc.html” “B02324_fastqc.zip” [145] “B02325_fastqc.html” “B02325_fastqc.zip” “B02326_fastqc.html” [148] “B02326_fastqc.zip” “B02327_fastqc.html” “B02327_fastqc.zip” [151] “B02328_fastqc.html” “B02328_fastqc.zip” “B02330_fastqc.html” [154] “B02330_fastqc.zip” “B02332_fastqc.html” “B02332_fastqc.zip” [157] “B02333_fastqc.html” “B02333_fastqc.zip” “B02334_fastqc.html” [160] “B02334_fastqc.zip” “B02336_fastqc.html” “B02336_fastqc.zip” [163] “B02337_fastqc.html” “B02337_fastqc.zip” “B02338_fastqc.html” [166] “B02338_fastqc.zip” “B02339_fastqc.html” “B02339_fastqc.zip” [169] “B02340_fastqc.html” “B02340_fastqc.zip” “B02341_fastqc.html” [172] “B02341_fastqc.zip” “B02342_fastqc.html” “B02342_fastqc.zip” [175] “B02343_fastqc.html” “B02343_fastqc.zip” “B02344_fastqc.html” [178] “B02344_fastqc.zip” “B02345_fastqc.html” “B02345_fastqc.zip” [181] “B02346_fastqc.html” “B02346_fastqc.zip” “B02347_fastqc.html” [184] “B02347_fastqc.zip” “B02348_fastqc.html” “B02348_fastqc.zip” [187] “B02349_fastqc.html” “B02349_fastqc.zip” “B02350_fastqc.html” [190] “B02350_fastqc.zip” “B02351_fastqc.html” “B02351_fastqc.zip” [193] “B02352_fastqc.html” “B02352_fastqc.zip” “B02353_fastqc.html” [196] “B02353_fastqc.zip” “B02354_fastqc.html” “B02354_fastqc.zip” [199] “B02355_fastqc.html” “B02355_fastqc.zip” “B02358_fastqc.html” [202] “B02358_fastqc.zip” “B02359_fastqc.html” “B02359_fastqc.zip” [205] “B02360_fastqc.html” “B02360_fastqc.zip” “B02361_fastqc.html” [208] “B02361_fastqc.zip” “B02363_fastqc.html” “B02363_fastqc.zip” [211] “B02364_fastqc.html” “B02364_fastqc.zip” “B02366_fastqc.html” [214] “B02366_fastqc.zip” “B02367_fastqc.html” “B02367_fastqc.zip” [217] “B02368_fastqc.html” “B02368_fastqc.zip” “B02369_fastqc.html” [220] “B02369_fastqc.zip” “B02371_fastqc.html” “B02371_fastqc.zip” [223] “B02372_fastqc.html” “B02372_fastqc.zip” “B02373_fastqc.html” [226] “B02373_fastqc.zip” “B02374_fastqc.html” “B02374_fastqc.zip” [229] “B02375_fastqc.html” “B02375_fastqc.zip” “B02376_fastqc.html” [232] “B02376_fastqc.zip” “B02377_fastqc.html” “B02377_fastqc.zip” [235] “B02378_fastqc.html” “B02378_fastqc.zip” “B02379_fastqc.html” [238] “B02379_fastqc.zip” “B02380_fastqc.html” “B02380_fastqc.zip” [241] “B02381_fastqc.html” “B02381_fastqc.zip” “B02382_fastqc.html” [244] “B02382_fastqc.zip” “B02383_fastqc.html” “B02383_fastqc.zip” [247] “B02385_fastqc.html” “B02385_fastqc.zip” “B02386_fastqc.html” [250] “B02386_fastqc.zip” “B02387_fastqc.html” “B02387_fastqc.zip” [253] “B02388_fastqc.html” “B02388_fastqc.zip” “B02389_fastqc.html” [256] “B02389_fastqc.zip” “B02390_fastqc.html” “B02390_fastqc.zip” [259] “B02391_fastqc.html” “B02391_fastqc.zip” “B02392_fastqc.html” [262] “B02392_fastqc.zip” “B02393_fastqc.html” “B02393_fastqc.zip” [265] “B02394_fastqc.html” “B02394_fastqc.zip” “B02395_fastqc.html” [268] “B02395_fastqc.zip” “B02397_fastqc.html” “B02397_fastqc.zip” [271] “B02438_fastqc.html” “B02438_fastqc.zip” “B02439_fastqc.html” [274] “B02439_fastqc.zip” “B02440_fastqc.html” “B02440_fastqc.zip” [277] “B02441_fastqc.html” “B02441_fastqc.zip” “B02449_fastqc.html” [280] “B02449_fastqc.zip” “B02456_fastqc.html” “B02456_fastqc.zip” [283] “B02458_fastqc.html” “B02458_fastqc.zip” “B02459_fastqc.html” [286] “B02459_fastqc.zip” “B02460_fastqc.html” “B02460_fastqc.zip” [289] “B02461_fastqc.html” “B02461_fastqc.zip” “B02464_fastqc.html” [292] “B02464_fastqc.zip” “B02478_fastqc.html” “B02478_fastqc.zip” [295] “B02546_fastqc.html” “B02546_fastqc.zip” “B02569_fastqc.html” [298] “B02569_fastqc.zip” “B02578_fastqc.html” “B02578_fastqc.zip” [301] “B02588_fastqc.html” “B02588_fastqc.zip” “B02594_fastqc.html” [304] “B02594_fastqc.zip” “B02609_fastqc.html” “B02609_fastqc.zip” [307] “B02620_fastqc.html” “B02620_fastqc.zip” “B03553_fastqc.html” [310] “B03553_fastqc.zip” “B03554_fastqc.html” “B03554_fastqc.zip” [313] “B03555_fastqc.html” “B03555_fastqc.zip” “B03556_fastqc.html” [316] “B03556_fastqc.zip” “B03557_fastqc.html” “B03557_fastqc.zip” [319] “B03558_fastqc.html” “B03558_fastqc.zip” “B03559_fastqc.html” [322] “B03559_fastqc.zip” “B03560_fastqc.html” “B03560_fastqc.zip” [325] “B03561_fastqc.html” “B03561_fastqc.zip” “B03562_fastqc.html” [328] “B03562_fastqc.zip”
#create a character vector where each value is the full path to the .zip created by fastqc() for a given sample
samps<-list.files(qc.dir, full.names = T, pattern = "*.zip")
#plot qc test results for each sample
for (i in samps){
#read info for given sample from the .zip file generated in the previous step
samp.info <- qc_read(i)
#open blank list to hold qc visualizations for the given sample
plot<-list()
#do qc for the given sample
plot[[1]]<-qc_plot(samp.info, "Basic statistics")
plot[[2]]<-qc_plot(samp.info, "Per sequence quality scores")
plot[[3]]<-qc_plot(samp.info, "Sequence duplication levels")
#visualize tables
print(paste0("QC results for sample ", gsub(".*/", "", i)))
cat('\n')
print(kable(plot[[1]]))
cat('\n')
#visualize plots
grid.arrange(plot[[2]],plot[[3]],
ncol=2)
#clear plot to hold info for next sample
rm(plot)
}[1] “QC results for sample 25369_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | 25369.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2350156 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample 25370_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | 25370.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2653101 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample 25371_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | 25371.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 628213 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 40 |
[1] “QC results for sample 25372_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | 25372.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3245280 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 43 |
[1] “QC results for sample 25373_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | 25373.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 242485 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 40 |
[1] “QC results for sample 25374_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | 25374.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2696071 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample 25375_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | 25375.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1157194 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 40 |
[1] “QC results for sample 25376_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | 25376.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 4143095 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample 25377_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | 25377.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3098561 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample 25378_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | 25378.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 159223 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample 25379_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | 25379.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 7025552 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample 25380_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | 25380.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 515899 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample 25381_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | 25381.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 575000 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample 25382_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | 25382.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1619620 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample 25383_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | 25383.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 848170 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample 31445_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | 31445.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1826306 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample 31446_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | 31446.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1842219 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample 31897_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | 31897.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 62132 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample 31898_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | 31898.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 83668 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample B00907_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00907.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 198262 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00908_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00908.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1057448 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00909_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00909.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 119066 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00910_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00910.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1163248 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00911_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00911.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2220095 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00912_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00912.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1010252 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00913_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00913.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 4849192 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00914_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00914.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2956334 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00915_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00915.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1516604 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00916_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00916.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 755637 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00922_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00922.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 113581 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00927_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00927.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 5336172 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00928_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00928.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1461301 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00929_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00929.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3400437 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00930_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00930.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3109911 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00931_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00931.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 4076776 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00932_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00932.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3008916 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00933_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00933.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 241245 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00934_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00934.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2246609 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00935_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00935.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1031381 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00936_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00936.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 383229 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00937_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00937.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 708625 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00938_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00938.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 290966 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00939_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00939.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1389321 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00940_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00940.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 657861 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00941_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00941.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2484177 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00942_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00942.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2219774 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00943_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00943.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2621156 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00944_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00944.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1120457 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00945_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00945.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 612055 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00946_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00946.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1441428 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00947_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00947.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1217087 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00948_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00948.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 762077 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00949_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00949.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1427344 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00950_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00950.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 338531 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00951_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00951.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1872818 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00952_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00952.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 272789 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00953_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00953.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1807253 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00954_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00954.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3381446 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00955_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00955.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1747898 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00956_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00956.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2912843 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00957_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00957.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1660079 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00958_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00958.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1927429 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00959_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00959.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3592914 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00960_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00960.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2550156 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00961_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00961.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 4600197 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00962_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00962.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2292868 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00963_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00963.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2874987 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00964_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00964.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1739355 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00965_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00965.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 542090 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00966_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00966.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2367372 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B00967_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B00967.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 662378 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02324_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02324.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1308386 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02325_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02325.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3999381 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02326_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02326.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2423060 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02327_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02327.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 5642982 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02328_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02328.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1387953 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02330_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02330.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 6091426 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02332_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02332.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1111129 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02333_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02333.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2788873 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02334_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02334.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3772349 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02336_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02336.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 337231 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02337_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02337.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 4065226 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02338_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02338.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2629232 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02339_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02339.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 625724 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02340_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02340.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2337980 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02341_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02341.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2569767 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02342_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02342.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2261935 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02343_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02343.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1129564 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02344_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02344.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 390697 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02345_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02345.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3648003 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02346_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02346.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1180170 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02347_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02347.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3929724 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02348_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02348.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2603752 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02349_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02349.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 202652 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample B02350_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02350.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 5990515 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02351_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02351.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 744882 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02352_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02352.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 931015 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02353_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02353.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1905923 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 36 |
[1] “QC results for sample B02354_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02354.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1047117 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 37 |
[1] “QC results for sample B02355_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02355.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 316787 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02358_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02358.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1443208 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02359_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02359.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 164640 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample B02360_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02360.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1361064 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02361_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02361.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3031759 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02363_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02363.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 997999 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02364_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02364.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 5655221 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 43 |
[1] “QC results for sample B02366_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02366.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 4084448 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02367_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02367.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2080252 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample B02368_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02368.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1187944 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample B02369_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02369.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 162808 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample B02371_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02371.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 7688801 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample B02372_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02372.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1489265 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample B02373_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02373.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3474638 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample B02374_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02374.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3433272 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02375_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02375.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 5205011 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02376_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02376.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 4309853 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 43 |
[1] “QC results for sample B02377_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02377.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 260413 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02378_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02378.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2069449 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample B02379_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02379.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2478518 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 39 |
[1] “QC results for sample B02380_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02380.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 244932 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 40 |
[1] “QC results for sample B02381_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02381.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2897405 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02382_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02382.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3101725 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02383_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02383.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 881074 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02385_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02385.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1052275 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02386_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02386.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3775790 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample B02387_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02387.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2684945 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample B02388_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02388.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3972448 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 43 |
[1] “QC results for sample B02389_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02389.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1382797 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample B02390_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02390.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 635972 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02391_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02391.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1953511 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02392_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02392.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1521745 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02393_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02393.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1095468 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 40 |
[1] “QC results for sample B02394_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02394.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1921118 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02395_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02395.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 430893 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample B02397_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02397.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1962086 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 43 |
[1] “QC results for sample B02438_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02438.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 306591 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample B02439_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02439.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1607926 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02440_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02440.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 4741502 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02441_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02441.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2142984 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02449_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02449.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2339694 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample B02456_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02456.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1480293 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02458_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02458.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2130420 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02459_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02459.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3667463 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02460_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02460.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2111917 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 44 |
[1] “QC results for sample B02461_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02461.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 4178821 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B02464_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02464.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1945419 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample B02478_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02478.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1361032 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 40 |
[1] “QC results for sample B02546_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02546.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1275803 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample B02569_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02569.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 352272 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 40 |
[1] “QC results for sample B02578_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02578.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 2375676 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample B02588_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02588.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 384623 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 40 |
[1] “QC results for sample B02594_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02594.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 892139 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample B02609_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02609.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1109850 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 40 |
[1] “QC results for sample B02620_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B02620.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1344206 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 40 |
[1] “QC results for sample B03553_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B03553.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 4461379 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 41 |
[1] “QC results for sample B03554_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B03554.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1891500 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 42 |
[1] “QC results for sample B03555_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B03555.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 3216115 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 40 |
[1] “QC results for sample B03556_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B03556.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 539917 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 39 |
[1] “QC results for sample B03557_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B03557.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 1932241 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 40 |
[1] “QC results for sample B03558_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B03558.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 73993 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample B03559_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B03559.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 162840 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 39 |
[1] “QC results for sample B03560_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B03560.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 838520 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 39 |
[1] “QC results for sample B03561_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B03561.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 60408 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 38 |
[1] “QC results for sample B03562_fastqc.zip”
| Measure | Value |
|---|---|
| Filename | B03562.fq.gz |
| File type | Conventional base calls |
| Encoding | Sanger / Illumina 1.9 |
| Total Sequences | 848582 |
| Sequences flagged as poor quality | 0 |
| Sequence length | 95 |
| %GC | 43 |
#aggregate the reports by pointing this function to the folder holding output of fastqc()
qc <- qc_aggregate(qc.dir, progressbar = F)
#stats per sample
knitr::kable(qc_stats(qc))| sample | pct.dup | pct.gc | tot.seq | seq.length |
|---|---|---|---|---|
| 25369.fq.gz | 96.15 | 41 | 2350156 | 95 |
| 25370.fq.gz | 96.15 | 42 | 2653101 | 95 |
| 25371.fq.gz | 92.99 | 40 | 628213 | 95 |
| 25372.fq.gz | 97.09 | 43 | 3245280 | 95 |
| 25373.fq.gz | 89.42 | 40 | 242485 | 95 |
| 25374.fq.gz | 96.81 | 41 | 2696071 | 95 |
| 25375.fq.gz | 94.19 | 40 | 1157194 | 95 |
| 25376.fq.gz | 97.16 | 42 | 4143095 | 95 |
| 25377.fq.gz | 97.11 | 42 | 3098561 | 95 |
| 25378.fq.gz | 88.80 | 41 | 159223 | 95 |
| 25379.fq.gz | 97.85 | 42 | 7025552 | 95 |
| 25380.fq.gz | 92.04 | 41 | 515899 | 95 |
| 25381.fq.gz | 93.43 | 41 | 575000 | 95 |
| 25382.fq.gz | 95.21 | 41 | 1619620 | 95 |
| 25383.fq.gz | 94.49 | 41 | 848170 | 95 |
| 31445.fq.gz | 95.32 | 37 | 1826306 | 95 |
| 31446.fq.gz | 96.01 | 42 | 1842219 | 95 |
| 31897.fq.gz | 79.97 | 41 | 62132 | 95 |
| 31898.fq.gz | 78.80 | 38 | 83668 | 95 |
| B00907.fq.gz | 88.14 | 37 | 198262 | 95 |
| B00908.fq.gz | 95.00 | 37 | 1057448 | 95 |
| B00909.fq.gz | 78.48 | 37 | 119066 | 95 |
| B00910.fq.gz | 94.66 | 37 | 1163248 | 95 |
| B00911.fq.gz | 96.39 | 37 | 2220095 | 95 |
| B00912.fq.gz | 93.92 | 37 | 1010252 | 95 |
| B00913.fq.gz | 97.17 | 37 | 4849192 | 95 |
| B00914.fq.gz | 96.17 | 37 | 2956334 | 95 |
| B00915.fq.gz | 94.89 | 37 | 1516604 | 95 |
| B00916.fq.gz | 94.00 | 37 | 755637 | 95 |
| B00922.fq.gz | 83.56 | 37 | 113581 | 95 |
| B00927.fq.gz | 97.29 | 37 | 5336172 | 95 |
| B00928.fq.gz | 95.32 | 37 | 1461301 | 95 |
| B00929.fq.gz | 96.07 | 37 | 3400437 | 95 |
| B00930.fq.gz | 96.02 | 37 | 3109911 | 95 |
| B00931.fq.gz | 96.98 | 37 | 4076776 | 95 |
| B00932.fq.gz | 96.71 | 37 | 3008916 | 95 |
| B00933.fq.gz | 89.16 | 37 | 241245 | 95 |
| B00934.fq.gz | 95.90 | 37 | 2246609 | 95 |
| B00935.fq.gz | 94.83 | 37 | 1031381 | 95 |
| B00936.fq.gz | 92.06 | 37 | 383229 | 95 |
| B00937.fq.gz | 94.06 | 37 | 708625 | 95 |
| B00938.fq.gz | 91.15 | 37 | 290966 | 95 |
| B00939.fq.gz | 95.36 | 37 | 1389321 | 95 |
| B00940.fq.gz | 92.22 | 37 | 657861 | 95 |
| B00941.fq.gz | 96.03 | 37 | 2484177 | 95 |
| B00942.fq.gz | 96.26 | 37 | 2219774 | 95 |
| B00943.fq.gz | 96.30 | 37 | 2621156 | 95 |
| B00944.fq.gz | 94.88 | 37 | 1120457 | 95 |
| B00945.fq.gz | 93.13 | 37 | 612055 | 95 |
| B00946.fq.gz | 94.76 | 37 | 1441428 | 95 |
| B00947.fq.gz | 94.85 | 37 | 1217087 | 95 |
| B00948.fq.gz | 93.26 | 37 | 762077 | 95 |
| B00949.fq.gz | 95.49 | 37 | 1427344 | 95 |
| B00950.fq.gz | 91.60 | 37 | 338531 | 95 |
| B00951.fq.gz | 95.42 | 37 | 1872818 | 95 |
| B00952.fq.gz | 90.37 | 37 | 272789 | 95 |
| B00953.fq.gz | 95.66 | 37 | 1807253 | 95 |
| B00954.fq.gz | 96.55 | 37 | 3381446 | 95 |
| B00955.fq.gz | 96.10 | 37 | 1747898 | 95 |
| B00956.fq.gz | 96.63 | 37 | 2912843 | 95 |
| B00957.fq.gz | 95.13 | 37 | 1660079 | 95 |
| B00958.fq.gz | 95.66 | 37 | 1927429 | 95 |
| B00959.fq.gz | 96.64 | 37 | 3592914 | 95 |
| B00960.fq.gz | 96.11 | 37 | 2550156 | 95 |
| B00961.fq.gz | 97.08 | 37 | 4600197 | 95 |
| B00962.fq.gz | 95.64 | 37 | 2292868 | 95 |
| B00963.fq.gz | 96.00 | 37 | 2874987 | 95 |
| B00964.fq.gz | 95.73 | 37 | 1739355 | 95 |
| B00965.fq.gz | 93.23 | 37 | 542090 | 95 |
| B00966.fq.gz | 96.33 | 37 | 2367372 | 95 |
| B00967.fq.gz | 90.32 | 37 | 662378 | 95 |
| B02324.fq.gz | 93.76 | 37 | 1308386 | 95 |
| B02325.fq.gz | 96.76 | 37 | 3999381 | 95 |
| B02326.fq.gz | 96.11 | 37 | 2423060 | 95 |
| B02327.fq.gz | 97.42 | 37 | 5642982 | 95 |
| B02328.fq.gz | 95.09 | 37 | 1387953 | 95 |
| B02330.fq.gz | 97.52 | 37 | 6091426 | 95 |
| B02332.fq.gz | 94.91 | 37 | 1111129 | 95 |
| B02333.fq.gz | 96.53 | 37 | 2788873 | 95 |
| B02334.fq.gz | 96.79 | 37 | 3772349 | 95 |
| B02336.fq.gz | 91.46 | 37 | 337231 | 95 |
| B02337.fq.gz | 96.90 | 37 | 4065226 | 95 |
| B02338.fq.gz | 96.09 | 37 | 2629232 | 95 |
| B02339.fq.gz | 93.44 | 37 | 625724 | 95 |
| B02340.fq.gz | 96.26 | 37 | 2337980 | 95 |
| B02341.fq.gz | 96.40 | 37 | 2569767 | 95 |
| B02342.fq.gz | 96.12 | 37 | 2261935 | 95 |
| B02343.fq.gz | 94.63 | 37 | 1129564 | 95 |
| B02344.fq.gz | 91.51 | 37 | 390697 | 95 |
| B02345.fq.gz | 96.96 | 37 | 3648003 | 95 |
| B02346.fq.gz | 93.68 | 37 | 1180170 | 95 |
| B02347.fq.gz | 96.97 | 37 | 3929724 | 95 |
| B02348.fq.gz | 96.61 | 37 | 2603752 | 95 |
| B02349.fq.gz | 89.17 | 38 | 202652 | 95 |
| B02350.fq.gz | 97.57 | 37 | 5990515 | 95 |
| B02351.fq.gz | 92.75 | 37 | 744882 | 95 |
| B02352.fq.gz | 94.20 | 37 | 931015 | 95 |
| B02353.fq.gz | 95.27 | 36 | 1905923 | 95 |
| B02354.fq.gz | 94.49 | 37 | 1047117 | 95 |
| B02355.fq.gz | 91.28 | 42 | 316787 | 95 |
| B02358.fq.gz | 95.83 | 42 | 1443208 | 95 |
| B02359.fq.gz | 81.45 | 41 | 164640 | 95 |
| B02360.fq.gz | 95.67 | 42 | 1361064 | 95 |
| B02361.fq.gz | 97.14 | 42 | 3031759 | 95 |
| B02363.fq.gz | 94.80 | 42 | 997999 | 95 |
| B02364.fq.gz | 97.60 | 43 | 5655221 | 95 |
| B02366.fq.gz | 96.57 | 42 | 4084448 | 95 |
| B02367.fq.gz | 95.84 | 41 | 2080252 | 95 |
| B02368.fq.gz | 95.18 | 41 | 1187944 | 95 |
| B02369.fq.gz | 87.54 | 41 | 162808 | 95 |
| B02371.fq.gz | 97.96 | 41 | 7688801 | 95 |
| B02372.fq.gz | 95.55 | 41 | 1489265 | 95 |
| B02373.fq.gz | 96.37 | 41 | 3474638 | 95 |
| B02374.fq.gz | 96.57 | 42 | 3433272 | 95 |
| B02375.fq.gz | 97.40 | 42 | 5205011 | 95 |
| B02376.fq.gz | 97.54 | 43 | 4309853 | 95 |
| B02377.fq.gz | 90.23 | 42 | 260413 | 95 |
| B02378.fq.gz | 96.11 | 41 | 2069449 | 95 |
| B02379.fq.gz | 96.28 | 39 | 2478518 | 95 |
| B02380.fq.gz | 90.46 | 40 | 244932 | 95 |
| B02381.fq.gz | 96.79 | 42 | 2897405 | 95 |
| B02382.fq.gz | 96.77 | 42 | 3101725 | 95 |
| B02383.fq.gz | 95.05 | 42 | 881074 | 95 |
| B02385.fq.gz | 94.18 | 42 | 1052275 | 95 |
| B02386.fq.gz | 96.75 | 41 | 3775790 | 95 |
| B02387.fq.gz | 96.66 | 41 | 2684945 | 95 |
| B02388.fq.gz | 97.10 | 43 | 3972448 | 95 |
| B02389.fq.gz | 95.32 | 41 | 1382797 | 95 |
| B02390.fq.gz | 93.75 | 42 | 635972 | 95 |
| B02391.fq.gz | 95.73 | 42 | 1953511 | 95 |
| B02392.fq.gz | 95.89 | 42 | 1521745 | 95 |
| B02393.fq.gz | 94.37 | 40 | 1095468 | 95 |
| B02394.fq.gz | 96.27 | 42 | 1921118 | 95 |
| B02395.fq.gz | 92.52 | 41 | 430893 | 95 |
| B02397.fq.gz | 96.10 | 43 | 1962086 | 95 |
| B02438.fq.gz | 91.10 | 41 | 306591 | 95 |
| B02439.fq.gz | 95.88 | 42 | 1607926 | 95 |
| B02440.fq.gz | 97.13 | 42 | 4741502 | 95 |
| B02441.fq.gz | 96.52 | 42 | 2142984 | 95 |
| B02449.fq.gz | 96.61 | 41 | 2339694 | 95 |
| B02456.fq.gz | 95.52 | 42 | 1480293 | 95 |
| B02458.fq.gz | 96.15 | 42 | 2130420 | 95 |
| B02459.fq.gz | 96.98 | 42 | 3667463 | 95 |
| B02460.fq.gz | 96.30 | 44 | 2111917 | 95 |
| B02461.fq.gz | 97.12 | 42 | 4178821 | 95 |
| B02464.fq.gz | 95.71 | 41 | 1945419 | 95 |
| B02478.fq.gz | 94.96 | 40 | 1361032 | 95 |
| B02546.fq.gz | 95.35 | 41 | 1275803 | 95 |
| B02569.fq.gz | 91.55 | 40 | 352272 | 95 |
| B02578.fq.gz | 96.46 | 41 | 2375676 | 95 |
| B02588.fq.gz | 88.83 | 40 | 384623 | 95 |
| B02594.fq.gz | 93.36 | 41 | 892139 | 95 |
| B02609.fq.gz | 94.83 | 40 | 1109850 | 95 |
| B02620.fq.gz | 95.20 | 40 | 1344206 | 95 |
| B03553.fq.gz | 97.29 | 41 | 4461379 | 95 |
| B03554.fq.gz | 96.23 | 42 | 1891500 | 95 |
| B03555.fq.gz | 96.73 | 40 | 3216115 | 95 |
| B03556.fq.gz | 93.48 | 39 | 539917 | 95 |
| B03557.fq.gz | 96.37 | 40 | 1932241 | 95 |
| B03558.fq.gz | 84.02 | 38 | 73993 | 95 |
| B03559.fq.gz | 89.20 | 39 | 162840 | 95 |
| B03560.fq.gz | 94.86 | 39 | 838520 | 95 |
| B03561.fq.gz | 83.02 | 38 | 60408 | 95 |
| B03562.fq.gz | 95.27 | 43 | 848582 | 95 |
solid red line = median sample value
dashed red line = 10% of median sample value
#save stats info as an object
stats.info<-qc_stats(qc)
#make tot.seq numeric
stats.info$tot.seq<-as.numeric(stats.info$tot.seq)
#make histogram of number of sequence reads for each sample
ggplot(stats.info, aes(x=tot.seq))+
geom_histogram(color="black", fill="white", bins=20)+
geom_vline(aes(xintercept=median(tot.seq)), color = "red")+
geom_vline(aes(xintercept=median(tot.seq)*.1), color = "red", lty=14)+
theme_classic()+
xlab("Number of sequencing reads")
#solid red line = median sample value
#dashed red line = 10% of median sample value
ggplot(stats.info, aes(x=tot.seq))+
geom_histogram(color="black", fill="white", bins=200)+
geom_vline(aes(xintercept=median(tot.seq)), color = "red")+
geom_vline(aes(xintercept=median(tot.seq)*.1), color = "red", lty=14)+
theme_classic()+
xlab("Number of sequencing reads")
#show me the samples that have less than 10% of the number of reads as the median sample from this experiment (these should be dropped immediately)
print(paste("Median sample contains", median(stats.info$tot.seq), "reads. The following samples contain less than", median(stats.info$tot.seq)*.1, "reads (10% of the median), and should likely be dropped"))[1] “Median sample contains 1699717 reads. The following samples contain less than 169971.7 reads (10% of the median), and should likely be dropped”
knitr::kable(stats.info[stats.info$tot.seq < median(stats.info$tot.seq)*.1,])| sample | pct.dup | pct.gc | tot.seq | seq.length |
|---|---|---|---|---|
| 25378.fq.gz | 88.80 | 41 | 159223 | 95 |
| 31897.fq.gz | 79.97 | 41 | 62132 | 95 |
| 31898.fq.gz | 78.80 | 38 | 83668 | 95 |
| B00909.fq.gz | 78.48 | 37 | 119066 | 95 |
| B00922.fq.gz | 83.56 | 37 | 113581 | 95 |
| B02359.fq.gz | 81.45 | 41 | 164640 | 95 |
| B02369.fq.gz | 87.54 | 41 | 162808 | 95 |
| B03558.fq.gz | 84.02 | 38 | 73993 | 95 |
| B03559.fq.gz | 89.20 | 39 | 162840 | 95 |
| B03561.fq.gz | 83.02 | 38 | 60408 | 95 |