Setup

FastQC Summary

Summary statistics for all libraries
Filename Total Flagged As Poor Quality Sequence Length %GC
10_MORGAN_6P_PH2-55220212_R1.combined.fastq.gz 30,104,052 0 62-76 43
11_MORGAN_6P_PH3-55214290_R1.combined.fastq.gz 48,869,955 0 61-76 43
12_MORGAN_6P_PH4-55264337_R1.combined.fastq.gz 36,665,915 0 61-76 42
13_MORGAN_6Q_PH1-55263325_R1.combined.fastq.gz 50,464,316 0 61-76 43
14_MORGAN_6Q_PH2-55278258_R1.combined.fastq.gz 35,944,820 0 60-76 42
15_MORGAN_6Q_PH3-55266315_R1.combined.fastq.gz 39,338,114 0 61-76 43
16_MORGAN_6Q_PH4-55261347_R1.combined.fastq.gz 38,706,052 0 61-76 43
17_MORGAN_24P_PN1-55274270_R1.combined.fastq.gz 41,991,090 0 61-76 43
18_MORGAN_24P_PN2-55270301_R1.combined.fastq.gz 39,930,253 0 41-76 44
19_MORGAN_24P_PN3-55268329_R1.combined.fastq.gz 38,508,128 0 59-76 44
1_MORGAN_6P_PN1-55208326_R1.combined.fastq.gz 26,302,897 0 35-76 44
20_MORGAN_24P_PN4-55261353_R1.combined.fastq.gz 41,087,938 0 61-76 43
21_MORGAN_24Q_PN1-55275281_R1.combined.fastq.gz 40,319,737 0 35-76 43
22_MORGAN_24Q_PN2-55327522_R1.combined.fastq.gz 33,326,737 0 35-76 43
23_MORGAN_24Q_PN3-55331438_R1.combined.fastq.gz 39,011,465 0 35-76 43
24_MORGAN_24Q_PN4-55332434_R1.combined.fastq.gz 36,731,786 0 35-76 43
25_MORGAN_24P_PH1-55343298_R1.combined.fastq.gz 36,518,384 0 35-76 43
26_MORGAN_24P_PH2-55330437_R1.combined.fastq.gz 35,306,089 0 35-76 44
27_MORGAN_24P_PH3-55334388_R1.combined.fastq.gz 37,603,755 0 35-76 44
28_MORGAN_24P_PH4-55339325_R1.combined.fastq.gz 35,080,360 0 35-76 43
29_MORGAN_24Q_PH1-55339326_R1.combined.fastq.gz 30,928,083 0 35-76 42
2_MORGAN_6P_PN2-55205326_R1.combined.fastq.gz 45,259,313 0 60-76 44
30_MORGAN_24Q_PH2-55342306_R1.combined.fastq.gz 32,400,816 0 35-76 43
31_MORGAN_24Q_PH3-55327525_R1.combined.fastq.gz 34,285,350 0 35-76 43
32_MORGAN_24Q_PH4-55324604_R1.combined.fastq.gz 29,889,388 0 35-76 42
3_MORGAN_6P_PN3-55218254_R1.combined.fastq.gz 29,287,775 0 61-76 44
4_MORGAN_6P_PN4-55210343_R1.combined.fastq.gz 32,052,087 0 61-76 43
5_MORGAN_6Q_PN1-55205328_R1.combined.fastq.gz 27,397,157 0 62-76 43
6_MORGAN_6Q_PN2-55206333_R1.combined.fastq.gz 24,012,323 0 62-76 43
7_MORGAN_6Q_PN3-55220220_R1.combined.fastq.gz 31,072,166 0 61-76 43
8_MORGAN_6Q_PN4-55212303_R1.combined.fastq.gz 24,046,785 0 60-76 43
9_MORGAN_6P_PH1-55210349_R1.combined.fastq.gz 30,645,100 0 62-76 43

Read Totals

Library Sizes ranged between 24,012,323 and 50,464,316 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

GC Content Distributions for all reads

Sequence Length Distribution

Sequence Duplication Levels

Overrepresented Sequences

Summary of Overrepresented Sequences in all files. A maximum of 30 seqences are shown.
Filename Sequence Count Percentage Possible_Source
12_MORGAN_6P_PH4-55264337_R1.combined ATTAATTTCATCTATAAGGTATAAAATTCGAAGTGATGGTAAAGCAATCAAAATAAGAATGATGGCCGGAAGGA 37,041 0.101 No Hit
29_MORGAN_24Q_PH1-55339326_R1.combined ATTAATTTCATCTATAAGGTATAAAATTCGAAGTGATGGTAAAGCAATCAAAATAAGAATGATGGCCGGAAGGA 32,699 0.1057 No Hit
15_MORGAN_6Q_PH3-55266315_R1.combined CCGGAACCCAAAGACTCGTGGTTTCCCGCACGCTGCCCGGCGGGTCATGG 46,619 0.1185 No Hit
23_MORGAN_24Q_PN3-55331438_R1.combined CCGGAACCCAAAGACTCGTGGTTTCCCGCACGCTGCCCGGCGGGTCATGG 39,968 0.1025 No Hit
11_MORGAN_6P_PH3-55214290_R1.combined CTCAAATGTGTGGTAGGGGGGAGGGCAGCCGTGTAATCATTCTACATTTGTTGCGGTCAATTCAACTGACAGAA 49,445 0.1012 No Hit
12_MORGAN_6P_PH4-55264337_R1.combined CTCAAATGTGTGGTAGGGGGGAGGGCAGCCGTGTAATCATTCTACATTTGTTGCGGTCAATTCAACTGACAGAA 36,889 0.1006 No Hit
21_MORGAN_24Q_PN1-55275281_R1.combined CTCAAATGTGTGGTAGGGGGGAGGGCAGCCGTGTAATCATTCTACATTTGTTGCGGTCAATTCAACTGACAGAA 40,845 0.1013 No Hit
22_MORGAN_24Q_PN2-55327522_R1.combined CTCAAATGTGTGGTAGGGGGGAGGGCAGCCGTGTAATCATTCTACATTTGTTGCGGTCAATTCAACTGACAGAA 33,458 0.1004 No Hit
24_MORGAN_24Q_PN4-55332434_R1.combined CTCAAATGTGTGGTAGGGGGGAGGGCAGCCGTGTAATCATTCTACATTTGTTGCGGTCAATTCAACTGACAGAA 43,561 0.1186 No Hit
12_MORGAN_6P_PH4-55264337_R1.combined GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAAATCTCGTATGC 61,477 0.1677 TruSeq Adapter, Index 13 (98% over 50bp)
29_MORGAN_24Q_PH1-55339326_R1.combined GTCAACATCCCCCTAGTTCAGGGGTGGGGGCTAAACTTGAATGATAAAAA 37,254 0.1205 No Hit
10_MORGAN_6P_PH2-55220212_R1.combined TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 34,202 0.1136 No Hit
29_MORGAN_24Q_PH1-55339326_R1.combined TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 32,742 0.1059 No Hit
9_MORGAN_6P_PH1-55210349_R1.combined TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 32,145 0.1049 No Hit

Adapter Content

Universal Adapter Content

Kmer Content

Summary of Overrepresented Sequences in all files. A maximum of 30 Kmers are shown.
Filename Sequence Count PValue Obs/Exp_Max Max_Obs/Exp_Position
12_MORGAN_6P_PH4-55264337_R1.combined ACACGTC 18,875 0 28.03 13
12_MORGAN_6P_PH4-55264337_R1.combined ACGTCTG 19,365 0 27.08 15
15_MORGAN_6Q_PH3-55266315_R1.combined ATAACGC 16,530 0 21.88 53
12_MORGAN_6P_PH4-55264337_R1.combined ATCGGAA 15,760 0 32.84 2
12_MORGAN_6P_PH4-55264337_R1.combined ATCTCGT 16,560 0 27.81 40
2_MORGAN_6P_PN2-55205326_R1.combined ATTCTAC 20,930 0 16.5 39
12_MORGAN_6P_PH4-55264337_R1.combined CACACGT 20,275 0 25.97 12
12_MORGAN_6P_PH4-55264337_R1.combined CACGTCT 20,850 0 25.54 14
11_MORGAN_6P_PH3-55214290_R1.combined CCGTGTA 18,030 0 21.23 29
2_MORGAN_6P_PN2-55205326_R1.combined CCGTGTA 15,570 0 21.91 29
12_MORGAN_6P_PH4-55264337_R1.combined CGGAAGA 17,495 0 29.94 4
15_MORGAN_6Q_PH3-55266315_R1.combined CGGGTCG 16,480 0 31.47 70
11_MORGAN_6P_PH3-55214290_R1.combined CGGTCAA 21,140 0 18.14 54
2_MORGAN_6P_PN2-55205326_R1.combined CGGTCAA 18,315 0 18.84 54
17_MORGAN_24P_PN1-55274270_R1.combined CGGTCAA 17,400 0 18.59 54
11_MORGAN_6P_PH3-55214290_R1.combined CGTGTAA 20,950 0 18.59 30
2_MORGAN_6P_PN2-55205326_R1.combined CGTGTAA 17,650 0 19.62 30
17_MORGAN_24P_PN1-55274270_R1.combined CGTGTAA 17,550 0 18.65 30
12_MORGAN_6P_PH4-55264337_R1.combined CTCGTAT 15,475 0 29.94 42
12_MORGAN_6P_PH4-55264337_R1.combined GATCGGA 15,850 0 31.71 1
12_MORGAN_6P_PH4-55264337_R1.combined GCACACG 21,545 0 25.55 11
15_MORGAN_6Q_PH3-55266315_R1.combined GCCGGAT 16,395 0 21.76 61
12_MORGAN_6P_PH4-55264337_R1.combined GCCGTCT 17,975 0 28.07 49
11_MORGAN_6P_PH3-55214290_R1.combined TAGGGGG 20,010 0 19.64 14
2_MORGAN_6P_PN2-55205326_R1.combined TAGGGGG 18,435 0 18.92 14
17_MORGAN_24P_PN1-55274270_R1.combined TAGGGGG 17,040 0 19.67 14
12_MORGAN_6P_PH4-55264337_R1.combined TCGGAAG 15,985 0 32.55 3
12_MORGAN_6P_PH4-55264337_R1.combined TCTCGTA 16,320 0 28.3 41
15_MORGAN_6Q_PH3-55266315_R1.combined TGCCCGG 15,885 0 22.62 34
12_MORGAN_6P_PH4-55264337_R1.combined TGCCGTC 19,575 0 26.26 48