FastQCFastQC Report
Wed 2 Apr 2014
mcf_T1D3_R2.fastq

Summary

[OK] Basic Statistics

Measure Value
Filename mcf_T1D3_R2.fastq
File type Conventional base calls
Encoding Sanger / Illumina 1.9
Total Sequences 5016400
Filtered Sequences 0
Sequence length 19-38
%GC 16

[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

[OK] 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

[OK] Sequence Duplication Levels

Duplication level graph

[OK] Overrepresented sequences

No overrepresented sequences

[FAIL] Kmer Content

Kmer graph

Sequence Count Obs/Exp Overall Obs/Exp Max Max Obs/Exp Position
GGGGG 5 85393.81 2503879.8 2
GGTGG 140 20872.082 218554.92 1
GGCGG 15 5290.1494 111142.93 33
GGGGA 35 4331.613 26736.137 28
GGGAG 30 3712.811 25726.977 27
GGGCG 10 3526.766 54088.13 18
AGGGG 25 3094.009 24684.125 26
GGGTG 20 2981.7263 54949.547 24
GTGGG 20 2981.726 33587.96 29
GGAGG 20 2475.207 21960.064 23
TGGGG 15 2236.2944 30991.668 27
GGGGC 5 1763.383 58421.344 21
CGGGG 5 1763.3829 56731.65 20
GCGGG 5 1763.3829 88567.61 31
GCGCG 205 1492.9688 4922.254 29
GAGCG 510 1303.3829 4832.349 33
GAGGG 10 1237.6036 19908.125 20
GGGGT 5 745.43164 23367.893 19
GGAAG 685 614.3237 2041.929 34
GGTCG 195 600.33356 5417.0625 4
CGGTG 120 369.43604 2707.897 1
GTAGG 290 313.30038 1275.5138 30
CGCCG 2080 312.8099 1543.4302 3
TAGGG 280 302.49695 1356.5359 31
CCGCG 1645 247.39052 396.83734 1
GTGGT 180 234.2565 1907.9906 2
GGGAA 260 233.174 1130.5035 33
AGGGA 255 228.68988 954.7563 32
CGCGA 4280 225.87381 340.58392 11
GGCGC 30 218.48326 3202.8828 1
CGGCG 30 218.48323 2139.8694 6
GAGTG 185 199.86406 1756.9883 34
TCGCG 3140 199.6218 255.66255 20
CGTCG 3040 193.2644 367.2015 31
GTCGG 55 169.32484 1638.754 32
CGCGC 1115 167.68416 293.4974 34
CGACG 2925 154.36469 263.1469 26
GTGCG 50 153.93169 665.0818 28
GCCGG 20 145.65549 2135.7554 4
AGCGG 55 140.5609 1662.523 34
ACGCG 2660 140.37952 224.64629 10
GCGTG 45 138.53851 2319.4104 31
CGCGT 2160 137.31944 214.35274 1
GTGTG 100 130.1425 765.00775 9
GCGAG 50 127.78262 831.2615 34
GGCGT 40 123.14536 1001.3684 34
GTCCG 1885 119.83665 186.10442 34
CGGAG 45 115.00436 1360.3716 32
GGCCG 15 109.241615 1640.7513 29
GCGGC 15 109.241615 1828.922 31
GCGGT 35 107.75219 693.5918 29
GGAGC 40 102.226105 749.47375 4
TCGGG 30 92.35902 970.2044 33
CTGGG 30 92.35902 526.99493 22
GAGAG 90 80.71407 875.1125 34
GGCTG 25 76.96585 589.52045 25
CGTGG 25 76.96584 902.70337 2
GAGGC 30 76.669586 749.35724 2
AGGCG 30 76.669586 805.39154 33
CGCGG 10 72.82774 1069.9464 8
GGTGT 55 71.57838 346.37372 32
TGTGG 50 65.07125 445.5511 22
GATCG 2905 64.808105 295.28247 33
GGGAC 25 63.891323 575.7683 29
CGGGA 25 63.89131 603.46765 30
GCAGG 25 63.89131 423.3472 21
GCGGA 25 63.89131 680.1858 32
GCCGT 995 63.25595 559.3121 4
TGGCG 20 61.572674 509.97974 21
GCTGG 20 61.572674 773.1368 31
GTGAG 55 59.41904 475.31412 13
GCCGC 395 59.4038 154.46028 22
GGAGA 65 58.29349 583.40826 34
GTCGC 855 54.355614 568.5007 1
AGGAG 60 53.809383 291.70416 34
GCCCG 340 51.13239 161.45091 18
GGCGA 20 51.113052 509.72742 26
GCGTC 780 49.587578 103.391335 34
GAAGG 55 49.325268 450.43808 31
AGAGG 55 49.325268 307.03305 22
GAGGT 45 48.61558 383.39377 23
GGGTC 15 46.17951 526.99493 22
GTGGC 15 46.179504 639.9782 27
TGCGG 15 46.179504 452.42303 9
GCCGA 850 44.858116 93.94468 16
TGGGA 40 43.213844 369.86337 22
GTCGT 1595 42.864735 92.98407 32
GCGAA 2205 40.835285 62.475384 12
GCTCG 635 40.369373 114.58142 29
GCGAC 745 39.316814 76.40352 20
GGACG 15 38.33479 437.47192 22
GACGG 15 38.33479 680.18585 32
GGTGA 35 37.812115 430.95224 26
GCGCC 245 36.845398 110.24127 2
GGGCC 5 36.413876 1067.6276 1
CCGGG 5 36.41387 1141.5072 19
GACCG 645 34.039394 70.229225 32
GCGAT 1515 33.798374 62.217987 10
GGTTG 25 32.535625 572.39716 2
GTTGG 25 32.535625 382.50388 9
TGGTG 25 32.535625 307.30624 30
AGGGT 30 32.41039 191.69688 23
TGAGG 30 32.410385 316.7494 1
GGATG 30 32.410385 317.1554 10
GAGGA 35 31.388805 238.68907 32
AAGGG 35 31.388805 202.04712 29
GACGA 1675 31.02 53.892 22
GACGC 585 30.872938 66.17499 19
GAACG 1665 30.834806 46.26607 9
CGGGT 10 30.78634 1001.3684 34
GGGCT 10 30.78634 526.99493 22
TGGGC 10 30.786337 463.8089 17
GTCGA 1360 30.340456 55.286842 29
GTACG 1250 27.88645 62.170765 11
ATCGG 1215 27.105629 149.40392 28
GGGAT 25 27.008657 317.22604 5
AGGTG 25 27.008657 224.57953 27
TGGAG 25 27.008656 271.30716 31
GGAGT 25 27.008656 224.57951 27
GCGTA 1165 25.990171 47.410873 30
GCGCA 490 25.859385 73.68114 26
GCGCT 405 25.747396 57.465954 17
GGCAG 10 25.556526 1662.523 34
CGAGG 10 25.556524 375.21277 5
CAGGG 10 25.556524 437.4719 22
GCGTT 925 24.858858 51.228 4
TCGGA 1100 24.540077 134.45992 31
GATGG 20 21.606924 340.4616 33
GTGGA 20 21.606922 178.96075 21
GCACG 405 21.373573 52.629383 26
GACGT 940 20.97061 57.28262 22
TTGGG 15 19.521376 215.5828 21
GTTCG 715 19.215225 50.27929 27
CGGAA 970 17.963821 93.37963 33
GGTAG 15 16.205193 206.873 25
AGTGG 15 16.205193 224.57951 27
AGAGC 755 13.98215 46.177464 12
AGCGT 595 13.27395 35.152676 33
TCGTG 485 13.034105 59.284714 33
TGGGT 10 13.01425 230.92516 23
CCCCG 4160 12.919057 20.202417 34
AGGGC 5 12.778264 375.4588 6
ACGGG 5 12.778262 374.69128 3
CGTGT 475 12.76536 69.93028 34
CCGCC 3525 10.947036 17.48454 20
GGGTA 10 10.803462 173.78479 20
CCCGC 3335 10.356984 17.33749 8
CGCCC 3135 9.735875 14.880143 24
CCGTC 7350 9.649081 13.019673 30
CCCGA 7730 8.4240675 11.311828 32
CGTCC 5800 7.6142406 10.655886 21
CCCCC 112390 7.2075124 8.508754 15
CCGAG 135 7.124524 56.18338 32
CGAGC 135 7.124523 31.021923 9
CCTCG 5335 7.0037885 9.560816 31
AAGAG 1065 6.921202 23.829851 11
TGTAG 725 6.8372645 40.617447 21
TCCGT 12125 6.7288594 8.350504 19
CTCGC 5120 6.7215366 10.200798 15
CCGAC 6140 6.6913037 9.757788 10
CGACC 6120 6.669508 9.910222 11
TCGCC 5065 6.6493325 15.974739 2
CCGAA 17095 6.53757 8.747133 14
GGGTT 5 6.5071254 410.1327 33
ACCCG 5970 6.5060396 8.165216 7
ACCGA 16665 6.373127 8.076185 13
CGTGC 100 6.357382 27.973944 12
GAAGA 975 6.336312 36.710835 22
TCCCG 4825 6.33426 9.239839 4
CTCCG 4815 6.321132 8.488637 9
CCGAT 13645 6.286039 8.375001 15
GTGTA 665 6.2714214 20.804035 33
TCCGC 4725 6.2029805 8.281377 29
CCGCT 4665 6.124212 9.949892 26
TACCG 13280 6.117889 7.9733286 12
CGAAA 45160 6.060467 7.0269966 11
TGGTC 225 6.046749 47.281635 3
CGCTC 4465 5.8616524 7.9837856 24
CAGCG 110 5.8051677 23.779242 29
ACCGC 5225 5.6941466 7.8574557 19
TCTCG 10225 5.674441 7.078567 21
CCCGT 4300 5.6450405 7.7021637 12
CTCGA 12200 5.62035 6.7680554 6
TTCCG 10060 5.582873 6.9151487 1
CGCCT 4245 5.572836 8.087182 11
AGCGC 105 5.5412965 38.702717 11
CCGTG 85 5.4037747 41.356537 34
CGCTG 85 5.4037747 63.186523 21
ATGGG 5 5.401731 158.71696 6
CGAGA 290 5.370627 46.689816 33
TCCGA 11480 5.2886567 6.8237233 13
AGCCG 100 5.2774253 23.21135 2
GAGCC 100 5.2774253 23.779242 29
ATCCG 11410 5.256409 6.8234897 33
CCGTA 11355 5.2310715 9.13089 5
TCGTC 9280 5.150006 7.089968 23
ACGCC 4725 5.1492524 7.443848 34
TGTCG 190 5.106144 66.7768 21
GAGCA 270 5.0002394 18.071081 34
CGATA 30595 4.946054 6.3625264 34
CGTCT 8890 4.933572 6.238582 24
TCGAG 220 4.9080153 29.44931 11
CACCG 4460 4.8604584 7.988577 2
AACCG 12680 4.84916 5.7307653 8
TCGCT 8735 4.8475537 6.585952 16
GTGTC 180 4.8373995 23.64761 13
ACGAA 35895 4.817105 6.027715 10
AACGA 35845 4.810395 6.1530924 9
CGAAC 12520 4.7879715 5.831835 4
CGTAC 10355 4.7703867 6.097586 33
GCTGT 175 4.7030272 50.603493 22
TCGAC 10185 4.6920705 7.259032 33
CGTAG 210 4.6849236 29.497887 8
TTTCG 19960 4.68254 6.3732314 21
CTTCG 8435 4.6810665 6.5535374 18
ATCGC 10125 4.6644297 6.387948 33
CCGTT 8295 4.603372 5.777536 4
CGCCA 4215 4.59346 6.679423 21
ACGTC 9945 4.5815063 5.928465 20
CGATC 9825 4.526224 5.7730956 24
TTCGC 8150 4.522904 5.540443 5
CGGCC 30 4.511681 44.20118 9
CGCTT 8125 4.5090294 6.0233874 11
CGTCA 9785 4.507797 6.554274 11
TCGAA 27610 4.4634924 5.174999 20
CCACG 4095 4.462685 6.734911 34
AAACG 33190 4.454095 5.737337 8
CTCGG 70 4.450167 30.023445 30
TGCGC 70 4.450167 20.678267 34
CCGCA 4075 4.4408894 6.406031 9
ACCGT 9480 4.367288 5.752847 6
CGTTT 18585 4.359969 5.3421702 8
ACGAC 11290 4.3175874 5.5011373 10
TGTGT 380 4.317021 18.329363 12
GTCTG 160 4.2999105 27.63775 8
CGACT 9285 4.277455 5.4711976 14
ACGAG 230 4.259463 19.01404 11
CTCGT 7640 4.2398753 5.790349 9
CGCTA 9190 4.23369 5.394384 34
GCAGC 80 4.2219396 46.532883 9
CTACG 9160 4.219869 5.2932153 29
ACTCG 9125 4.2037454 6.593136 34
GCTGC 65 4.132298 43.5298 22
CGAAT 25540 4.128852 5.0946407 33
AACGC 10795 4.128287 5.2265716 9
ATCGA 25470 4.1175356 5.1631584 32
TATCG 21135 4.11592 5.5848465 33
TACGC 8795 4.051719 6.6783094 33
GTTGT 355 4.0330067 42.783043 22
GTAGA 515 4.031767 37.52274 22
TGCTG 150 4.031166 48.969654 21
CGTTG 150 4.031166 35.614292 21
ACGTG 180 4.015649 19.632874 11
CGAGT 180 4.0156484 22.922417 10
ACGAT 24800 4.0092216 4.8908553 33
CGTAA 24785 4.006797 5.034907 24
CACGC 3675 4.004974 7.2753744 22
TAACG 24765 4.0035634 4.751438 9
CGACA 10405 3.9791412 5.7219095 34
TTCGT 16875 3.9588103 4.849119 1
CGCAA 10345 3.9561956 5.1447763 24
TACGA 24435 3.950215 5.036525 9
CAACG 10300 3.9389865 5.4498453 8
TCGAT 20195 3.9328604 4.7438912 31
CGTGA 175 3.9041028 19.633087 12
CATCG 8440 3.8881764 5.008416 8
CACGA 10045 3.8414679 5.803331 27
GCCCC 1235 3.8353446 7.743556 12
CGATT 19605 3.8179607 4.838946 21
TCGGC 60 3.8144295 18.679855 8
ACACG 9935 3.799401 5.1127415 8
AATCG 23435 3.788553 4.5837502 7
AACGT 23415 3.7853196 4.645017 1
CGTAT 19400 3.7780383 5.121274 6
TGCGT 140 3.7624218 19.708954 12
TCGTA 19310 3.7605116 4.4595146 28
TTCGA 19300 3.7585642 4.767043 22
ACGCT 8145 3.7522745 5.0681243 23
CGTTC 6690 3.7126656 5.317261 32
ACGTA 22965 3.7125716 4.819142 23
TTACG 19025 3.7050095 4.463283 8
CGCAC 3390 3.694384 5.7767982 21
CGATG 165 3.6810112 44.3465 21
ATACG 22485 3.6349738 4.68707 33
TTGCG 135 3.62805 27.592236 11
GTGCT 135 3.6280496 19.728102 5
AAGCG 195 3.6112835 14.786794 32
TCGTT 15245 3.5764184 4.6142898 10
GAGCT 160 3.5694659 18.550278 27
TACGT 18300 3.56382 4.5607157 34
ATCGT 18190 3.542398 4.4346724 8
GAAAG 545 3.541836 48.617836 34
GCCTG 55 3.49656 21.764902 22
GTGCC 55 3.49656 21.062174 21
TGCCG 55 3.49656 21.062174 21
CTGTG 130 3.4936779 14.857889 24
TGTTG 305 3.4649777 47.04739 21
GAGTC 155 3.45792 19.630486 13
GATGT 365 3.442209 46.815617 22
TCGCA 7405 3.411368 4.904637 23
AGTGT 360 3.3950555 15.215674 12
ACGTT 16985 3.307731 4.1770787 7
AGAGT 420 3.2880428 19.7371 33
CACGT 7125 3.2823763 4.4949694 22
ACGCA 8565 3.2754776 4.2750373 23
CGTTA 16770 3.2658608 4.311351 3
AGTCG 145 3.234828 22.17325 21
TGCAG 145 3.234828 32.77543 8
TCGGT 120 3.2249334 16.93849 33
GTTGC 120 3.224933 36.80254 22
AGATG 410 3.209756 61.11323 34
CGCAG 60 3.1664553 26.226374 21
CCGGA 60 3.1664553 28.09169 32
GAGTT 335 3.1592877 20.745895 13
CGAAG 170 3.1482985 19.045406 8
GTGTT 275 3.12416 11.675472 5
CAGTG 140 3.1232822 19.632874 11
AGTGC 140 3.1232822 22.90527 12
TGACG 140 3.1232822 13.110171 8
ATGTG 330 3.1121342 13.832279 11
TCACG 6655 3.0658548 4.8077173 21
GAGAC 165 3.0557017 21.72769 13
CGCAT 6630 3.0543375 4.530618 10
CCGGC 20 3.0077875 37.76726 31
AGAAG 460 2.9894395 33.372482 21
AGCAG 155 2.8705075 33.7454 21
CGGTC 45 2.860822 18.64909 11
GGAAA 440 2.8594635 29.593462 34
GAGAT 365 2.8574657 28.010235 34
ATGAG 360 2.8183224 18.372046 11
TGAGC 125 2.788645 13.348752 26
GTGAT 295 2.7820594 11.065824 11
TGAGT 295 2.7820594 12.449188 12
TGAGA 355 2.7791789 25.261839 12
AGACG 150 2.7779105 24.542109 21
CAGAG 150 2.7779105 29.879206 11
GTAGT 290 2.7349057 20.78846 9
GTAGC 120 2.6770992 22.94922 9
CTGAG 120 2.6770992 16.360727 11
GTGAC 120 2.6770992 9.826081 5
TGATG 280 2.6405988 24.995352 21
TGTGA 275 2.5934448 6.921393 10
GCAGA 140 2.5927165 25.360939 22
GTGAA 330 2.5834622 10.333018 13
TGCGA 115 2.5655534 16.360907 12
GCAGT 115 2.565553 42.007248 22
TCCGG 40 2.5429528 41.356537 34
CTGCG 40 2.5429528 28.001122 5
GCTGA 110 2.4540076 26.73189 22
ATGCG 110 2.4540076 13.088582 11
TAGTG 260 2.4519846 9.682595 11
AGTAG 310 2.4268887 19.45245 21
GTTGA 255 2.4048307 22.600641 22
AGTGA 305 2.3877454 12.630919 12
TTGTG 210 2.3857224 14.99659 11
CGGAC 45 2.3748412 15.473013 1
AGCTG 105 2.3424618 18.477709 21
TTGAG 245 2.310524 12.449052 11
AGTTG 245 2.310524 26.324684 8
GCTTG 85 2.2843275 15.793 8
GATGA 290 2.2703152 24.121761 22
CCCGG 15 2.2558408 25.743382 22
GGCCC 15 2.2558405 22.074778 10
GATGC 100 2.230916 22.913048 22
GGCTC 35 2.2250838 11.280554 23
CGGCT 35 2.2250836 11.715874 24
GAGAA 340 2.2095857 16.202328 13
GAAGC 115 2.1297314 19.050735 9
CGGCA 40 2.1109703 16.631342 33
ACCGG 40 2.1109703 26.50638 31
AGCGA 110 2.0371344 8.162128 7
GAAGT 260 2.035455 18.761372 22
TGTGC 75 2.015583 15.767163 12
AAGTG 255 1.9963117 18.372046 11
AGATC 12315 1.9908696 66.62249 34
GACCC 1820 1.9834157 5.11501 12
GAGTA 250 1.9571682 10.333018 13
GTATG 205 1.9332955 12.469587 8
GTTTG 170 1.9312991 20.028435 8
CCTGG 30 1.9072148 18.66326 10
GTCAG 85 1.8962785 9.835381 9
GTGCA 85 1.8962785 26.173979 13
CCAGG 35 1.8470991 19.451294 24
GGACC 35 1.8470988 15.479203 13
CACGG 35 1.8470988 15.510963 9
GCCAG 35 1.8470988 15.506624 8
GTTAG 190 1.7918348 23.553665 8
TTCGG 65 1.7468389 10.292251 25
GGTCT 65 1.7468387 7.891241 5
GATTG 185 1.7446814 8.916016 33
AGAGA 260 1.6896832 10.485249 12
TAGAG 215 1.6831647 8.037769 11
GATAG 215 1.6831647 9.201176 8
GGATC 75 1.6731869 13.088725 12
ACGGA 90 1.6667463 10.87342 10
GGTCC 25 1.5893455 18.649296 12
ACGGC 30 1.5832274 15.492846 10
TGAAG 200 1.5657346 15.56196 21
CTAGG 70 1.5616411 14.06107 33
GCATG 70 1.5616411 9.835381 9
GACTG 70 1.5616411 13.110171 8
TAGCG 70 1.5616411 7.6376824 22
AACGG 80 1.4815522 10.886134 9
CGGTT 55 1.4780942 8.469244 33
AGGTC 65 1.4500955 6.5442915 11
GGTCA 65 1.4500954 16.360907 12
TCTGG 50 1.3437222 8.903574 21
GCTAG 60 1.3385496 7.256364 34
CGGAT 60 1.3385494 6.5569196 9
AGGCC 25 1.3193563 15.481087 11
CAGGC 25 1.3193562 15.492846 10
AGGAC 70 1.2963583 13.581458 11
CAGGA 70 1.2963582 8.145267 2
GGCCT 20 1.2714764 18.649296 12
CCGGT 20 1.2714764 18.640837 2
GAATG 155 1.2134444 13.801763 8
GGACA 65 1.2037612 5.4310226 4
GGCAA 65 1.2037612 8.344549 29
TTGGT 105 1.1928612 10.0053215 10
TGGTA 125 1.1788386 8.299367 11
GGTAA 145 1.1351576 6.889592 12
ATTGG 120 1.1316851 7.104998 31
ATGGT 120 1.1316851 6.921394 10
CGGTA 50 1.115458 5.2678747 30
ACGGT 50 1.1154579 6.5550137 6
GACAG 60 1.1111642 5.443067 9
CTGGT 40 1.0749778 7.889485 10
GGCCA 20 1.0554851 9.725645 24
AAGGC 55 1.0185672 8.155066 10
GGTAC 45 1.0039122 16.360907 12
CTGGC 15 0.9536074 16.920147 32
ACAGG 50 0.92597014 8.1646 9
TAGGT 95 0.8959174 5.537115 10
AGGCT 40 0.89236647 6.5424123 4
TACGG 40 0.89236635 6.5408783 1
GGTTT 75 0.8520436 6.6780124 9
AGGCA 45 0.8333732 8.148875 11
GCAAG 45 0.8333731 11.672454 33
CTTGG 30 0.80623335 7.8987103 9
GGTTC 30 0.8062332 7.152621 32
GGTAT 85 0.80161035 5.532912 11
TTGGA 85 0.80161035 7.529938 32
TTTGG 70 0.7952408 5.003774 5
TAGGA 100 0.7828673 7.639154 34
CTGGA 35 0.78082067 6.554936 7
GGACT 35 0.78082055 16.360907 12
TCAGG 35 0.78082055 6.5408783 1
AAGGA 120 0.77985376 5.723509 10
TGGAT 80 0.75445676 6.9161396 11
TAAGG 95 0.7437239 6.8962855 5
CAGAT 4565 0.7379878 12.146641 34
TAGAT 10030 0.6854417 11.909675 33
GGCAT 30 0.6692748 13.088725 12
AAGAT 11765 0.6674293 11.75408 34
ATAGG 85 0.6654372 5.7523437 9
TGGCC 10 0.6357382 10.226501 20
TGGAA 80 0.62629384 7.401412 33
AGGAT 75 0.58715045 5.0927696 34
AATGG 75 0.58715045 5.7523437 9
GGATA 75 0.58715045 5.7709126 24
TATGG 60 0.56584257 5.5435896 9
TGGCA 25 0.557729 7.030535 33
ACTGG 25 0.557729 6.55692 9
TTGGC 20 0.5374889 7.889485 10
GGCAC 10 0.52774256 9.0338 22
CCAGA 1375 0.52583563 5.182281 33
TCAGA 3210 0.51893556 5.705998 33
CAAGA 3650 0.4898296 5.1173215 33
Produced by FastQC (version 0.10.1)