Setup

FastQC Summary

Summary statistics for all libraries
Filename Total Flagged As Poor Quality Sequence Length %GC
CCR2_2R_S11_R1_001.fastq.gz 19,852,983 0 35-76 50
CCR2_3R_S12_R1_001.fastq.gz 21,415,186 0 35-76 50
CCR2_RB_S10_R1_001.fastq.gz 20,316,690 0 35-76 50
CCR6_2R_S8_R1_001.fastq.gz 19,903,216 0 35-76 50
CCR6_3R_S9_R1_001.fastq.gz 18,613,895 0 35-76 49
CCR6_RB_S7_R1_001.fastq.gz 20,089,874 0 35-76 50
DN_2R_S2_R1_001.fastq.gz 21,864,056 0 35-76 50
DN_3R_S3_R1_001.fastq.gz 20,291,599 0 35-76 50
DN_RB_S1_R1_001.fastq.gz 18,903,819 0 35-76 50
DP_2R_S5_R1_001.fastq.gz 21,752,264 0 35-76 50
DP_3R_S6_R1_001.fastq.gz 19,677,738 0 35-76 50
DP_RB_S4_R1_001.fastq.gz 21,835,911 0 35-76 50
lung_minus_ve_1_S22_R1_001.fastq.gz 20,288,748 0 35-76 50
lung_minus_ve_2_S23_R1_001.fastq.gz 18,872,795 0 35-76 49
lung_minus_ve_3_S24_R1_001.fastq.gz 19,768,164 0 35-76 49
lung_plus_ve_1_S16_R1_001.fastq.gz 22,006,468 0 35-76 50
lung_plus_ve_2_S17_R1_001.fastq.gz 22,373,038 0 35-76 49
lung_plus_ve_3_S18_R1_001.fastq.gz 28,363,583 0 35-76 42
mLN_minus_ve_1_S19_R1_001.fastq.gz 20,012,380 0 35-76 50
mLN_minus_ve_2_S20_R1_001.fastq.gz 2.1e+07 0 35-76 49
mLN_minus_ve_3_S21_R1_001.fastq.gz 21,648,553 0 35-76 49
mLN_plus_ve_1_S13_R1_001.fastq.gz 16,213,624 0 35-76 48
mLN_plus_ve_2_S14_R1_001.fastq.gz 21,201,653 0 35-76 50
mLN_plus_ve_3_S15_R1_001.fastq.gz 22,871,006 0 35-76 50

Read Totals

Library Sizes ranged between 16,213,624 and 28,363,583 reads.

Read totals for each library. Duplicated reads are conventionally an high overestimate at this point.

FastQC Summary

Summary of FastQC flags for each parameter

Per Base Sequence Quality

Heatmap showing mean base qualities for each library

Per Sequence Quality Scores

Heatmap showing mean sequence qualities for each library

Per Base Sequence Content

Heatmap of summed base distributions along each read

Per Sequence GC Content

GC Content Heatmap normalised to theoretical GC content in the Hsapiens Transcriptome

GC Content Distributions for all reads showing theoretical GC content from the Hsapiens Transcriptome

Sequence Length Distribution

Sequence Duplication Levels

Overrepresented Summary

Overrepresented Sequences

## No overrepresented sequences were detected by FastQC

Adapter Content

Universal Adapter Content

Kmer Content

Summary of Overrepresented Kmers in all files. A maximum of 30 Kmers are shown.
Filename Sequence Count PValue Obs/Exp_Max Max_Obs/Exp_Position
lung_plus_ve_3_S18_R1_001 AACGCAG 118,480 0 25.22 6
lung_plus_ve_3_S18_R1_001 ACGCAGA 126,870 0 23.56 7
lung_plus_ve_3_S18_R1_001 AGAGTAC 125,375 0 21.97 11
DN_2R_S2_R1_001 AGAGTAC 56,355 0 22.58 11
mLN_plus_ve_3_S15_R1_001 AGAGTAC 56,090 0 22.2 11
lung_plus_ve_3_S18_R1_001 AGTACGG 68,195 0 21.23 13
lung_plus_ve_3_S18_R1_001 AGTACTT 74,895 0 17.12 13
lung_plus_ve_3_S18_R1_001 ATCAACG 113,075 0 26.4 3
lung_plus_ve_3_S18_R1_001 CAACGCA 115,830 0 25.78 5
lung_plus_ve_3_S18_R1_001 CAGAGTA 130,070 0 21.52 10
DN_2R_S2_R1_001 CAGAGTA 60,080 0 21.34 10
mLN_plus_ve_3_S15_R1_001 CAGAGTA 59,505 0 21.02 10
mLN_plus_ve_1_S13_R1_001 CAGAGTA 55,735 0 23.26 10
lung_plus_ve_3_S18_R1_001 CGCAGAG 128,050 0 23.34 8
DN_2R_S2_R1_001 CGCAGAG 56,750 0 22.5 8
lung_plus_ve_3_S18_R1_001 GAGTACG 67,395 0 21.51 12
lung_plus_ve_3_S18_R1_001 GAGTACT 68,145 0 18.77 12
lung_plus_ve_3_S18_R1_001 GCAGAGT 140,245 0 21.29 9
DN_2R_S2_R1_001 GCAGAGT 65,250 0 19.71 9
mLN_plus_ve_3_S15_R1_001 GCAGAGT 64,620 0 19.4 9
mLN_plus_ve_1_S13_R1_001 GCAGAGT 58,740 0 22.07 9
DP_2R_S5_R1_001 GCAGAGT 57,305 0 18.21 9
CCR2_3R_S12_R1_001 GCAGAGT 57,135 0 18.67 9
DN_RB_S1_R1_001 GCAGAGT 56,280 0 19.2 9
lung_minus_ve_1_S22_R1_001 GCAGAGT 56,120 0 19.54 9
lung_plus_ve_3_S18_R1_001 GTACGGG 71,655 0 20.14 14
lung_plus_ve_3_S18_R1_001 GTATCAA 77,775 0 38.77 1
lung_plus_ve_3_S18_R1_001 TACGGGG 56,680 0 19.72 15
lung_plus_ve_3_S18_R1_001 TATCAAC 111,505 0 26.85 2
lung_plus_ve_3_S18_R1_001 TCAACGC 115,240 0 25.9 4