FastQCFastQC Report
Thu 24 Oct 2013
mysample1_R1.fastq

Summary

[OK] Basic Statistics

Measure Value
Filename mysample1_R1.fastq
File type Conventional base calls
Encoding Sanger / Illumina 1.9
Total Sequences 1810387
Filtered Sequences 0
Sequence length 32-151
%GC 47

[OK] Per base sequence quality

Per base quality graph

[OK] Per sequence quality scores

Per Sequence quality graph

[FAIL] Per base sequence content

Per base sequence content

[FAIL] Per base GC content

Per base GC content graph

[WARN] Per sequence GC content

Per sequence GC content graph

[OK] Per base N content

N content graph

[WARN] Sequence Length Distribution

Sequence length distribution

[FAIL] Sequence Duplication Levels

Duplication level graph

[OK] Overrepresented sequences

No overrepresented sequences

[WARN] Kmer Content

Kmer graph

Sequence Count Obs/Exp Overall Obs/Exp Max Max Obs/Exp Position
TTTTT 923495 3.3427355 4.4745975 145-147
CAGCA 678230 2.9933293 7.2701044 4
TGCTG 635130 2.8486948 7.7340355 2
GCAGC 567430 2.725728 5.429261 8
AGCAG 623830 2.6689231 5.8500257 7
CCTGG 536685 2.6396506 7.957445 3
CCAGG 542260 2.6048205 8.740774 3
CTGCT 557360 2.5788538 6.6141624 9
GGAGG 561325 2.5337825 5.005335 6
GCTGC 507165 2.4944584 5.6050067 8
CCCAG 497635 2.4659762 7.8031945 2
CTGGG 513915 2.4502513 8.857077 4
AGGAG 565260 2.3442855 6.3883934 5
GCTGG 491485 2.3433092 7.331573 3
CAGCC 457995 2.2695441 5.508094 9
GGCTG 472485 2.2527208 8.6054735 7
CAGGG 476860 2.2205138 9.378212 4
GGCAG 474225 2.208244 6.295689 7
AGAAG 576800 2.197833 5.052427 5
CCCTG 430120 2.1823497 7.087998 2
CTGCA 477410 2.1573756 6.393377 4
GCAGG 460425 2.1439838 7.7856693 3
TCCAG 470855 2.127754 5.295399 2
CCTGC 419265 2.1272733 5.16862 8
TGCAG 485410 2.1263528 7.6062 2
CTGGA 479145 2.0989087 8.2049265 4
CTGCC 408830 2.074328 5.500767 9
CAGAG 484530 2.072958 7.5618796 4
CTCTG 442815 2.0488646 6.460589 2
TGGGG 442305 2.0442479 6.2672615 5
CAGGA 469840 2.01011 8.287774 4
CACAG 451010 1.9905068 7.954073 7
TGGAG 466135 1.9793864 6.7027454 5
CTGTG 437980 1.9644345 10.833825 9
AGCTG 439720 1.9262064 5.4923854 7
AGAGG 461145 1.9124925 5.518508 5
GGGAG 420960 1.9001845 5.017396 7
GCCTG 385285 1.8949995 6.6760693 7
CAGGC 394240 1.8937861 5.2463603 4
GGAGA 456225 1.8920877 5.2137704 6
CAGAA 479795 1.8859614 5.343325 4
CCAGA 401800 1.7733213 5.109149 3
GCAGA 411290 1.7596163 5.4956827 3
GGGCC 336510 1.7593855 5.3609467 6
TGGCC 357085 1.7562996 5.4111643 5
CACTG 386165 1.745047 7.9570074 7
TCTGG 384940 1.7265387 5.530794 3
CTGAG 391560 1.7152401 6.0278707 9
CAGTG 387525 1.6975645 7.037392 9
GGGCA 363825 1.6941628 5.3178725 1
ACCTG 371665 1.6795228 5.638729 7
GGCCT 331815 1.6320107 5.358597 6
GAGAG 389100 1.6137024 5.5794554 7
TGGGC 337625 1.6097333 6.4302187 5
ACAGC 361305 1.5945989 6.058421 8
GGGCT 333570 1.5903997 6.223203 6
AGGGC 337965 1.573745 6.6222935 5
ACAGA 399405 1.5699673 6.385733 8
GCTGT 348290 1.5621556 5.815391 8
CCTGT 334640 1.5483488 6.6605234 8
ACAGG 359490 1.5380011 5.5871034 8
AACAG 370750 1.457331 5.1437707 7
ACACA 354215 1.4363216 6.749986 6
GACAG 332510 1.422573 7.8933907 7
CTGTC 307335 1.422011 6.1011004 9
CACAC 305700 1.3918121 6.5569825 5
GAGCA 323765 1.3851594 5.1089034 1
AGGCT 314180 1.3762747 5.422158 6
AGACA 348850 1.3712475 5.6820426 6
AGAGC 317015 1.3562812 5.321324 5
GGACA 311955 1.3346328 6.7445335 6
ACTGG 297205 1.3019152 5.0593143 8
GTGCT 286870 1.2866737 6.2701545 1
AGCAC 290150 1.2805604 6.0937986 5
ACTGC 271915 1.228761 5.16481 8
GCACA 277915 1.2265619 5.44226 6
AGGAC 270940 1.1591591 6.584495 5
TGGAC 258270 1.1313592 6.753556 5
ACTGT 271660 1.1194798 7.9498296 8
AAGAC 275230 1.0818645 5.122765 5
ACAGT 266745 1.0735693 6.446932 8
GACTG 237520 1.0404633 6.5896916 7
GCACT 227985 1.0302448 5.243293 6
GTGCA 234445 1.0269932 5.7637553 1
TGCAC 226755 1.0246867 5.961718 5
ACACT 227525 0.94464916 5.449719 6
AGACT 229745 0.92465544 5.358105 6
GGACT 203095 0.8896635 5.1763606 6
TACAC 151790 0.63020897 5.2223005 5