FastQCFastQC Report
Wed 2 Apr 2014
mcf_T1D3_R1.fastq

Summary

[OK] Basic Statistics

Measure Value
Filename mcf_T1D3_R1.fastq
File type Conventional base calls
Encoding Sanger / Illumina 1.9
Total Sequences 5016400
Filtered Sequences 0
Sequence length 19-57
%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
CCCCC 35 464961.5 7015934.0 20
CACCC 75 8254.95 58251.2 27
CCCAC 70 7704.619 117678.75 49
CCTCC 70 6269.7603 23911.605 47
CCACC 55 6053.6294 116621.66 30
CCCCA 50 5503.2993 29557.861 53
CCCGC 20 5019.023 132608.73 22
CCCCG 20 5019.023 132567.02 21
ACCCC 45 4952.97 29510.424 52
CTCCC 50 4478.4004 70972.56 21
CCCTC 45 4030.5603 47217.934 15
TCCCC 45 4030.5603 47283.113 19
GCCCC 15 3764.267 67077.06 49
CCCCT 40 3582.7202 47915.453 50
CCGCC 10 2509.5115 66474.52 30
CGCGC 450 2133.2507 6285.9673 33
CGCCC 5 1254.7557 66632.91 36
CCGTC 430 727.5479 22975.246 42
CACAC 695 633.7854 13941.986 4
ACTCC 500 371.0455 10367.096 15
CTCCA 495 367.33502 10762.104 16
CGCGG 3540 317.00992 501.24182 44
CGGCG 3335 298.652 472.10526 6
TCGCG 9080 290.21454 423.0371 28
CGCGA 6535 256.67242 416.0414 29
GCGCG 2770 248.05579 406.64963 48
CCGGC 45 213.32507 3786.5835 42
CGTCG 6600 210.94888 320.15195 3
CGACG 5335 209.54051 341.6423 15
CGGCC 40 189.6223 1262.1945 42
CGCGT 5760 184.10088 278.02673 6
ACGCG 4480 175.95905 305.88025 53
GCACC 75 155.93896 2192.1797 8
CACCA 165 150.46704 966.5938 31
ACCAC 160 145.90742 975.6861 50
CGCCG 30 142.2167 1264.2157 45
CGGAC 3495 137.27162 228.50128 25
ACACC 140 127.669 723.70166 26
CGCCA 60 124.75118 1101.5126 30
CACGC 60 124.751175 1100.386 27
CAACC 130 118.54979 733.50146 52
CCACA 130 118.549774 723.45416 25
GGCCC 25 118.51393 1260.4053 39
GCCGC 25 118.51393 2511.455 30
CTCGC 65 109.97817 899.7128 39
CACCG 50 103.95932 1103.7092 35
ACCGC 50 103.95931 1668.4275 50
CACTC 140 103.892746 591.9148 39
TCCCG 60 101.5183 895.4571 27
AACCC 110 100.311356 722.1075 19
TCACC 130 96.47183 984.8236 35
CCCGG 20 94.811134 2509.7732 28
CGCAC 45 93.56338 1112.285 50
ACGCC 45 93.56338 556.749 51
CCGCT 55 93.05846 897.04144 32
CGCTC 55 93.05846 905.1402 50
GCTCC 55 93.05844 894.8607 25
CTCAC 125 92.76137 789.9336 41
CCATC 125 92.76137 983.5954 32
ACCCA 100 91.19215 482.79477 28
CCAAC 100 91.19213 483.47803 32
CTCTC 150 90.5833 484.58597 50
ACCTC 120 89.05092 595.48535 50
GTCCC 50 84.598595 892.7843 18
CCCGT 50 84.59859 1341.119 22
CCGCA 40 83.16746 1113.498 51
CGACC 40 83.16745 557.4625 52
CCGAC 40 83.16745 1653.4994 32
CCACG 40 83.16744 558.3586 53
CCCAG 40 83.16744 1098.9762 23
CACCT 110 81.63001 593.0674 43
CCACT 110 81.630005 793.9804 50
GCGGC 900 80.59574 189.17604 20
CTTCC 125 75.486084 1273.4142 1
CCCAA 80 72.953705 482.00583 23
GCCAC 35 72.771515 558.3586 53
CCGCG 15 71.10835 1260.4052 39
CTCCT 115 69.4472 480.84976 35
TCGCC 40 67.67888 898.1615 35
GCCCT 40 67.67888 449.4466 37
TCCCA 90 66.788185 784.278 22
TCCAC 90 66.788185 393.76538 34
CCTCT 110 66.42775 639.2026 27
CAGCC 30 62.375587 558.3586 53
GACCC 30 62.375587 556.749 51
CGGGC 690 61.79007 142.37947 31
TTCCC 100 60.388863 483.65308 47
GCCTC 35 59.219017 895.167 26
CTGCC 35 59.219017 450.97406 44
CTCCG 35 59.21901 891.9949 5
TTCGC 4980 56.810215 102.50402 23
CTACC 75 55.656826 1189.3516 48
CCCTT 90 54.349976 320.95563 38
TCGGC 1675 53.536274 101.92313 38
ACCCG 25 51.97966 553.0736 40
AGCCC 25 51.979656 555.3864 48
ACCCT 70 51.946373 391.21115 14
GGCGC 575 51.491722 142.08661 25
CCTTC 85 51.330536 1116.5321 21
GCGTC 1540 49.22141 109.6226 18
CGGTC 1515 48.42236 101.096794 7
CCTAC 65 48.235912 396.45053 48
CGAGC 1160 45.560825 84.04585 50
GTCGC 1405 44.906548 76.095116 26
ATCCC 60 44.52546 394.0821 36
CCCAT 60 44.525455 591.6114 38
CGTTC 3790 43.23508 75.54455 30
TCCGC 25 42.299297 450.26337 41
CCTGC 25 42.299297 449.6259 38
TGCCC 25 42.299297 454.3735 53
CCCTG 25 42.299294 453.0636 51
ATCGC 2995 41.985004 70.481094 27
CCAGC 20 41.583725 555.07184 47
CCCGA 20 41.58372 556.14246 50
TGCGC 1275 40.75149 92.80026 19
TCTCC 65 39.252766 480.6496 34
TCGTC 3380 38.55794 60.138306 14
GCGAC 960 37.70551 83.065544 24
CATCC 50 37.10455 393.6043 33
CCTCA 50 37.104546 198.71158 51
ACGGC 940 36.91998 94.317 46
ACGAC 2115 36.434093 73.624 48
CGTAC 2580 36.167377 63.361725 39
TCGAC 2560 35.887012 55.425728 8
CGATC 2485 34.835636 71.41234 52
CGTCC 20 33.839436 448.5207 32
CCTCG 20 33.839436 450.49503 42
ACGTC 2405 33.71417 214.3128 7
TCCCT 55 33.213875 319.38846 25
AACGC 1855 31.955202 78.51793 52
GCCCA 15 31.187796 550.9599 31
TACGC 2180 30.560036 70.20858 3
TCCTC 50 30.194431 319.83783 29
TACCC 40 29.683641 393.034 29
CGTGC 910 29.085379 67.7121 29
GACGC 710 27.886368 72.47211 4
CCCTA 35 25.973183 198.11299 47
AGCGC 630 24.744242 51.77942 11
GCGCC 5 23.702787 1255.3717 29
CGAAC 1295 22.308344 46.18701 52
CGCCT 10 16.91972 445.99747 2
TGCCG 495 15.821167 467.6119 40
CGGGG 9315 15.757694 20.511946 6
GCCGT 490 15.661359 450.79877 41
GGCGG 7865 13.304806 20.065273 7
GCGGG 7385 12.492815 19.619379 8
GGGCG 7380 12.484355 20.065271 7
GCACA 670 11.54177 258.82828 3
ACACG 665 11.455637 254.28743 5
AGCAC 645 11.111106 258.82825 2
GACGG 14625 10.850998 14.641895 45
CGTCT 950 10.83729 158.02509 43
TCGGG 16100 9.720742 12.138584 26
CACGT 665 9.322212 192.1498 6
GACCA 525 9.043924 241.59901 27
CGAGG 11565 8.580635 11.7416315 17
GCGAG 11270 8.361761 11.324388 51
CACTG 585 8.200744 185.23894 23
GTCAC 585 8.200744 188.83559 21
GGACG 10985 8.150306 12.160819 24
GGTCG 13445 8.117725 10.34765 13
CGGAG 10765 7.9870768 11.343342 5
GTCGG 13055 7.882254 11.016788 25
CGGGA 10485 7.779331 10.2060585 26
GGCGA 10265 7.616102 9.9743185 6
CCAGT 535 7.499825 207.11368 18
CGGTA 28320 7.4994736 9.981891 4
ATCGG 28295 7.4928536 9.4990425 17
AGCGG 10005 7.423196 9.224707 26
CGGGT 12280 7.41433 9.550978 52
TTCGG 34405 7.414107 8.917841 1
ACGGA 22730 7.396687 9.204896 24
TCGGT 34220 7.3742404 9.997449 2
GCGGA 9790 7.2636766 10.319767 50
ATGCC 510 7.149366 208.72101 39
TGACC 505 7.079275 196.54147 26
CTGAC 500 7.0091825 203.88835 25
TTTCG 89900 6.914499 8.369821 35
CAGTC 490 6.8689985 199.80864 19
ACGGG 9210 6.8333464 9.082494 41
GAGCG 9170 6.8036685 8.996444 2
GCGGT 11215 6.771312 8.593922 15
TCTCG 590 6.730528 166.39203 33
GGCCG 75 6.716312 47.641907 40
GCCGG 75 6.716312 95.32419 41
GGGGG 206615 6.602552 8.043761 21
TCCAG 470 6.588631 207.05644 17
CGGAA 20085 6.535964 9.521022 1
TCGGA 24005 6.35681 7.889864 9
CGAGA 19465 6.3342066 8.23471 4
CACGG 160 6.2842517 42.122665 52
TCGAG 23550 6.236321 7.661174 35
AGGCG 8375 6.2138195 8.705992 45
GTTCG 28460 6.132989 8.066124 3
CTCGT 530 6.0460668 154.35393 34
GGCGT 9930 5.995464 8.753374 3
CGGAT 22635 5.994018 7.516393 51
CGGTT 27450 5.915339 7.391014 18
TACGG 22205 5.880149 7.786013 49
TGGCG 9445 5.702635 8.190931 40
GCACG 145 5.695103 42.068752 51
AGACG 17390 5.6589704 7.9839435 45
TCGTT 73390 5.6446614 6.4787946 30
GACGA 17335 5.6410723 7.398598 50
TTCGT 72685 5.590438 6.762604 37
AGCGA 16990 5.528804 6.9960694 35
CGAAA 38630 5.5134892 6.6520796 29
CGTTT 71260 5.4808364 6.3660483 5
TATCG 57985 5.480459 6.3952956 43
GCGAA 16770 5.4572124 7.2072678 11
ACGGT 20575 5.4485054 6.9123588 10
GTCGA 20570 5.447181 6.541923 37
ACCAA 715 5.402163 106.00165 28
AACGG 16405 5.3384366 6.723548 30
GATCG 20095 5.3213964 7.0752187 26
AAGCG 16340 5.3172846 6.561481 34
CGGTG 8790 5.307163 7.6413417 13
CTGCT 465 5.3045683 164.6553 49
GACGT 19920 5.2750535 6.6334357 16
CGAAG 16210 5.27498 6.8669953 48
GTACG 19895 5.268434 6.9736853 40
CGTGG 8710 5.258861 7.544877 39
GCGAT 19755 5.2313595 6.653502 49
TCTGC 455 5.190492 164.54803 48
TTCGA 54865 5.1855717 6.1235 25
GTCGT 23990 5.1697264 6.3620133 3
GGCAC 130 5.1059546 31.517195 50
TAGCG 19120 5.063204 5.9348536 10
TGACG 18825 4.9850855 6.5606394 43
GCGTT 23025 4.9617734 6.1345844 14
AAACG 34600 4.938306 5.9295697 27
ACGAG 15170 4.936548 6.56148 34
CGTAG 18245 4.8314934 5.871377 19
AGTCG 18080 4.7878003 5.816174 27
CGTTA 50240 4.7484393 5.409805 31
TGCGG 7860 4.745654 6.52696 11
GCGTA 17860 4.729541 5.8182282 28
CGAGT 17830 4.7215967 6.293419 20
GCGTG 7775 4.6943336 6.2194858 21
TTACG 49610 4.688895 5.7103167 18
CGATA 40245 4.6742673 5.5502234 47
TCGAT 48820 4.6142282 5.3714905 46
TCGTG 21290 4.5878897 6.418817 3
TTGCG 21225 4.5738826 5.5744343 45
ACGTT 48245 4.559882 5.2865596 32
ATTCG 48195 4.555156 5.3555446 53
ATCGT 47905 4.527747 4.9807796 29
CGCAG 115 4.516806 31.274195 35
AGCGT 17020 4.507099 6.142702 2
AATCG 38725 4.4977264 5.451286 16
TCGTA 47395 4.479544 5.418591 35
CCGGG 50 4.477541 47.428844 29
CGGCT 140 4.4746737 33.698933 8
TGTCG 20740 4.469367 5.6367064 22
TCGAA 38325 4.451268 5.4541273 34
ACGAA 31175 4.44947 5.580957 40
ATCGA 37880 4.3995833 5.639013 34
CGTAA 37650 4.3728695 5.454163 46
CGATT 46190 4.3656535 5.564511 33
AACGA 30280 4.321731 5.3369565 33
CGTGT 19865 4.280809 5.509958 4
GAACG 13025 4.238533 6.038447 32
CGTTG 19645 4.2334003 5.282743 3
TACGT 44745 4.2290792 5.214709 44
GTGCG 6965 4.205278 5.729481 6
GGGGC 2465 4.1699104 7.6867647 49
TACGA 35885 4.1678734 4.891756 30
TCACT 830 4.1527824 67.4193 22
TGCAC 295 4.1354175 26.24751 50
ATACG 35220 4.0906367 4.7758307 1
ACGAT 35140 4.081345 5.5864754 23
ACGTA 34975 4.0621815 5.32748 45
CGATG 15220 4.0304375 5.2504454 24
TAACG 34510 4.0081735 5.2458267 21
ACACA 530 4.0044007 14.068545 40
CGTAT 42035 3.9729428 4.9557505 29
AACTC 645 3.9657114 89.13498 14
TGCGA 14960 3.9615865 5.655566 10
AACGT 33675 3.9111924 4.733082 27
CCAAT 625 3.8427432 84.66572 29
TGCGT 17390 3.747459 4.6158814 25
CGGCA 95 3.7312748 20.874773 38
CGCTG 115 3.6756248 25.340754 23
GCTCG 115 3.6756244 17.117067 51
ACGTG 13595 3.6001182 5.3843694 20
CCGGA 90 3.5348918 31.159267 25
CGAAT 30295 3.5186212 4.6240664 35
CGTGA 13240 3.50611 4.7716994 31
CAATC 570 3.5045822 94.46163 30
ATGCG 13130 3.4769807 4.468609 13
ATCTC 675 3.3772628 71.621635 32
CACAA 445 3.3621852 14.180186 52
CTCGG 105 3.3560052 25.439291 34
AACAC 425 3.211076 14.061787 39
CACAG 185 3.1869066 18.33712 41
AAACC 420 3.1732988 13.959919 19
GCGCA 80 3.142126 31.059477 5
CAGGC 80 3.1421258 31.132057 22
GACAC 180 3.1007738 13.689416 30
TGGCC 95 3.036386 16.849518 15
GCGCT 95 3.036386 25.647636 50
CACAT 480 2.951227 14.648022 28
AACCA 390 2.9466343 15.974106 23
GCAGC 75 2.945743 20.766386 24
GCACT 210 2.9438567 11.248934 50
CAGAC 170 2.9285085 18.252554 30
TCACA 475 2.920485 16.434113 49
TACAC 475 2.920485 14.801188 50
TTCCG 255 2.9089568 30.0702 2
CAAAC 375 2.8333025 20.069965 37
TCTTC 695 2.8297343 56.461967 45
CGACA 160 2.7562435 13.705396 33
GGACC 70 2.74936 20.711767 11
CCGTT 240 2.7378416 15.0351 4
TCACG 195 2.733581 18.734938 49
GGCCT 85 2.7167664 17.028994 43
ACACT 440 2.7052915 13.170959 51
TTCAC 540 2.7018104 9.232055 2
GGGCC 30 2.6865246 23.809504 39
ACAAC 355 2.682193 14.048975 37
CCGAT 190 2.6634893 29.561508 4
CGTCA 190 2.663489 14.870651 33
CTTCT 650 2.6465142 58.663574 46
CACGA 150 2.5839784 18.233889 27
ACGCA 150 2.5839784 9.203001 48
CACTT 515 2.5767264 12.0732975 52
GGCTC 80 2.5569563 25.33422 22
TCCGG 80 2.5569563 16.850103 3
GCTGC 80 2.5569563 16.939085 31
GACCG 65 2.5529773 20.807966 30
AGGCC 65 2.5529773 31.328213 39
CGCAA 145 2.4978456 9.209002 49
AACCG 145 2.4978456 13.657896 23
ATCAC 400 2.4593558 13.011647 26
CAACA 325 2.4555287 12.046782 38
CGCTT 215 2.4526498 12.079034 28
TCCGA 170 2.383122 29.561508 3
TCGCA 170 2.383122 18.644766 40
CATCG 170 2.383122 11.15299 33
CCGAG 60 2.3565943 20.807966 30
CAGCG 60 2.3565943 20.866447 37
CCAAA 305 2.3044188 13.973737 22
CAACG 130 2.2394478 13.705396 33
CCTGG 70 2.2373369 16.898987 24
CTTCG 195 2.2244966 12.05619 22
CCAGG 55 2.1602116 31.140083 23
GCCAG 55 2.1602116 10.491448 48
ACCGG 55 2.1602116 21.011463 50
CATGC 150 2.1027548 7.493975 49
CAGCT 150 2.1027548 11.157556 34
ACGCT 150 2.1027548 11.128594 27
CCGTG 65 2.077527 17.020025 42
GAACC 120 2.0671828 13.634596 18
ACCAG 120 2.0671828 13.675416 27
CACTA 335 2.0597105 9.89088 52
TTGCC 180 2.0533814 12.035399 17
TCGCT 180 2.0533812 9.131291 46
ACCGT 145 2.0326629 11.117725 24
GTACC 140 1.9625714 7.480684 46
CGACT 140 1.962571 11.085145 1
GACTC 140 1.962571 18.635803 39
GCCTG 60 1.9177172 17.038122 44
GGTCC 60 1.9177172 16.928024 29
ACCAT 310 1.9060007 8.12697 24
ACAGC 110 1.8949176 9.203002 48
GCAAC 110 1.8949172 9.215529 50
TGCTC 165 1.8822663 9.19048 53
TCTCA 365 1.8262239 9.368108 50
TCCGT 160 1.8252277 9.023461 13
CTCGA 130 1.8223875 11.089092 16
TTCTC 445 1.8118442 7.5777392 39
CAAGC 105 1.808785 22.770102 24
GCCAA 105 1.8087848 9.129651 31
ACCGA 105 1.8087848 18.27386 33
CCAAG 105 1.8087847 13.705395 33
GTCTC 155 1.7681895 12.091598 31
GCCGA 45 1.7674459 21.011465 50
AGCTC 125 1.7522956 14.961367 46
ACCTG 125 1.7522956 7.472842 44
TCAGC 125 1.7522956 11.139987 30
ACTCA 280 1.721549 13.08401 40
GCCTT 150 1.711151 6.094372 48
CGCAT 120 1.6822038 11.191598 41
CCGTA 120 1.6822038 7.4848514 47
AACCT 270 1.6600652 6.5275865 35
TCCAA 270 1.660065 8.124493 23
CTCTG 145 1.6541127 18.046923 13
AGACC 95 1.6365198 9.173277 42
CAGCA 95 1.6365197 9.173276 42
CATAC 265 1.6293232 9.860468 49
CTCAA 265 1.629323 8.152748 33
CTCAG 115 1.6121118 11.191596 41
GCTCA 115 1.6121118 11.248932 50
TCTCT 395 1.6082662 7.5552406 32
GGCCA 40 1.571063 20.71183 13
GAGCC 40 1.5710629 20.832254 33
CCTTT 385 1.5675505 5.4033375 35
GCCAT 110 1.5420201 14.80064 19
ACTGC 110 1.5420201 14.998578 50
ACTCG 110 1.5420201 7.4579062 40
TGCCA 110 1.5420201 22.190752 18
GCTCT 135 1.540036 9.163986 51
CTCTT 365 1.4861194 8.733193 52
TGCCT 130 1.4829975 6.094372 48
CTCAT 295 1.4759889 12.057844 51
CTACG 105 1.4719284 11.117725 24
CTGCA 105 1.4719284 11.157556 34
AGCCA 85 1.4642544 9.093913 19
TCAAC 235 1.4448715 6.48277 4
CCGGT 45 1.4382881 16.932825 30
CTGCG 45 1.438288 16.96659 35
CCTGT 125 1.4259592 9.126623 45
TCTAC 285 1.4259554 8.014348 47
CATCA 230 1.4141296 8.152749 33
TACCG 100 1.4018365 11.114336 23
TACCA 225 1.3833877 6.499595 23
CCGAA 80 1.3781217 9.22558 51
AGCCG 35 1.37468 10.442738 39
GCATC 95 1.3317447 7.4294033 31
CCTGA 95 1.3317447 7.4806833 46
CGCTA 95 1.3317447 11.2612 51
ACTTC 265 1.3258884 5.3033185 31
ACTCT 265 1.3258884 9.378324 51
ACTAC 215 1.3219038 6.522199 33
GCTTC 115 1.3118825 9.126623 45
CTTTC 320 1.3028992 6.4786544 33
CATTC 260 1.3008716 5.3162575 37
TTACC 260 1.3008716 5.2877884 22
CTCTA 260 1.3008716 9.288206 33
ATCCA 210 1.2911618 6.497919 22
GTCCG 40 1.2784781 8.4762945 33
ATCCG 90 1.2616528 11.124988 26
GTTCC 110 1.2548442 6.0156236 12
CTACT 250 1.2508382 6.6316333 32
CAACT 200 1.2296779 6.5355105 38
ACATC 200 1.2296779 6.512749 29
ACCTT 245 1.2258214 5.284789 20
TCATC 245 1.2258214 5.3053064 32
CCAGA 70 1.2058566 9.10804 24
CTATC 240 1.2008046 7.9361463 24
ACCTA 195 1.198936 6.5693626 48
TCCTG 105 1.1978058 6.0457983 31
GATCC 85 1.1915612 7.529173 53
TAGCC 85 1.191561 7.4505014 38
GCTAC 85 1.191561 11.114336 23
GACCT 85 1.191561 7.4543214 39
CCATG 85 1.191561 7.454321 39
CTTCA 230 1.1507711 5.334326 44
TACTC 230 1.150771 6.651382 39
TTCCA 225 1.1257544 5.2877884 22
GTCCA 80 1.1214691 11.088517 13
GTGCC 35 1.1186684 8.569503 52
CTTGC 95 1.0837291 9.075929 33
TGTCC 95 1.0837291 9.131292 46
CCTAT 210 1.0507039 5.2978077 28
CCTTG 90 1.0266906 6.109324 51
CTAGC 70 0.9812855 7.4475307 37
AGCCT 70 0.9812855 7.4768586 45
CATCT 195 0.97565377 5.301358 30
CTTAC 190 0.950637 7.9520373 30
TATCC 190 0.950637 5.3053064 32
TCCAT 190 0.95063686 6.6371484 34
ATACC 150 0.92225844 6.6045194 53
CTGTC 80 0.912614 9.154004 50
CTGGC 25 0.79904884 8.569503 52
GTCCT 65 0.74149877 9.126623 45
GCCTA 50 0.70091826 7.3948736 17
CCTAG 45 0.63082635 7.4768577 45
GAGCA 930 0.30263612 5.060724 1
Produced by FastQC (version 0.10.1)