FastQCFastQC Report
Mon 3 Feb 2014
filtered_BS_CgLarv_T1D3_TGACCA_L007_R1.fastq

Summary

[OK] Basic Statistics

Measure Value
Filename filtered_BS_CgLarv_T1D3_TGACCA_L007_R1.fastq
File type Conventional base calls
Encoding Sanger / Illumina 1.9
Total Sequences 3343987
Filtered Sequences 0
Sequence length 76
%GC 17

[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

[OK] Sequence Length Distribution

Sequence length distribution

[OK] Sequence Duplication Levels

Duplication level graph

[WARN] Overrepresented sequences

Sequence Count Percentage Possible Source
GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGC 11738 0.3510181110153837 TruSeq Adapter, Index 4 (100% over 50bp)

[FAIL] Kmer Content

Kmer graph

Sequence Count Obs/Exp Overall Obs/Exp Max Max Obs/Exp Position
CCCCC 190 198373.83 1128625.1 50
CCGTC 25755 9760.436 545397.8 50
CACAC 32045 6589.3726 297370.03 12
ACTCC 27335 4636.93 241970.75 23
CTCCA 27245 4621.6636 241617.33 24
CACCC 120 1758.282 15851.1045 63
CCCCA 115 1685.0201 15809.829 23
ACCCC 115 1685.0201 15809.781 22
CCCCG 40 1309.373 11804.106 67
GCCCC 40 1309.373 11804.425 65
CCCAC 80 1172.188 15837.401 59
CTCCC 95 1148.3086 26084.645 23
CACGC 2280 1047.4054 58677.285 31
CCTCC 85 1027.434 8717.581 66
ACGCC 2165 994.5757 57852.055 32
CGCCA 2155 989.9817 58353.773 33
CCACC 60 879.141 5283.2896 61
CCCCT 55 664.81024 4358.7905 66
CGCCC 20 654.6865 11794.132 46
CCCGC 20 654.6865 11773.369 22
TCCCC 50 604.373 4355.486 51
CGCGC 500 513.152 2215.8564 33
CCGCC 15 491.0149 11793.425 45
CCCTC 35 423.06107 8710.423 49
CCGGC 395 405.39008 14792.231 50
TGCCG 26205 311.36118 17374.26 48
GCCGT 25880 307.4996 17222.832 49
CGTCT 55275 242.51614 6316.5493 16
CACCA 1010 207.68501 11097.797 31
AGCAC 31105 200.53337 9476.297 10
GCACA 30930 199.40515 9460.07 11
ACACG 30175 194.53769 9392.848 13
TCACC 990 167.93712 9581.724 30
ACGTC 31510 167.58401 7674.0513 15
CACGT 30090 160.03183 7714.2095 14
TCCAG 27570 146.62936 7673.1294 25
CCAGT 27490 146.20389 7652.2573 26
GTCAC 27225 144.79451 7613.5293 29
CAGTC 27205 144.68814 7639.8145 27
ATGCC 26215 139.42287 7762.203 47
GACCA 19625 126.52202 6795.7227 35
CTGCT 26210 114.99499 6391.6187 57
TCTGC 26205 114.97305 6395.5156 56
TCTCG 25815 113.261955 6344.5215 41
CTCGT 25815 113.26195 6314.57 42
CTGAC 19745 105.01258 5649.563 33
CACTG 19705 104.79984 5639.311 31
TGACC 19660 104.5605 5613.192 34
CGCGG 3185 102.4845 173.59505 22
CGGCG 3155 101.51918 185.65147 67
TCGCG 7760 92.202354 123.991714 33
GCGCG 2755 88.648285 185.26031 34
GCGCC 80 82.10432 1846.3619 32
CGCGA 5540 79.79254 160.86148 44
CGCAC 170 78.096 1816.954 12
CGTCG 6405 76.102585 137.00357 51
CGCCG 70 71.841286 740.1218 61
CGACG 4910 70.718666 119.47773 72
AACTC 27820 66.22853 3439.4355 22
CGCGT 5435 64.57729 98.55268 71
ACGCG 4110 59.196278 108.96302 43
ACCAA 19810 57.166912 3038.4216 36
CCAAT 21765 51.813946 2498.022 37
GCTCC 135 51.161278 1635.6393 23
ATCTC 25830 50.72711 2836.3066 40
CGGAC 3345 48.177994 119.35368 59
CAATC 19570 46.588512 2504.8892 38
GCCGC 45 46.18368 1107.6763 1
CACCG 95 43.641888 826.4406 31
CCCAG 95 43.641884 495.83093 30
CTTCT 26140 42.349575 2350.835 54
ACACC 205 42.153893 443.6152 13
TCTTC 25865 41.904053 2330.3894 53
CAGCC 90 41.344948 331.31488 63
CCGAC 90 41.344944 662.12134 50
CCGCG 40 41.052162 369.7759 46
TCACT 20775 40.79968 2092.12 30
CTCCG 105 39.79211 1226.7937 24
CCCAA 180 37.013165 295.8456 24
CCCGG 35 35.920643 370.07703 68
GCACC 75 34.454124 331.04285 49
CCAAC 155 31.872454 370.4681 54
AACCC 150 30.844309 221.84274 21
GCCCG 30 30.789122 370.15414 72
CGGCC 30 30.78912 369.80914 51
GGCCC 30 30.78912 370.11472 71
TGCCC 80 30.317795 409.70828 47
GCGGC 935 30.085716 92.82602 66
CCAGC 65 29.86024 330.48773 26
CCACG 65 29.86024 495.53296 12
CCCTG 75 28.422935 136.65872 67
CGTCC 75 28.422934 545.0566 16
CTGCC 75 28.422934 273.13885 47
ACCCA 135 27.759878 222.05827 36
CCCGA 60 27.5633 496.2334 40
ACCAC 130 26.731735 222.17833 55
CAACC 125 25.703592 222.27956 53
GCCCA 55 25.266354 330.61578 34
CGCTC 65 24.63321 273.32114 64
CTCCT 175 24.489353 302.00345 24
GACCC 50 22.969416 495.92374 34
GCCCT 60 22.738346 409.6782 48
TCCCG 55 20.843487 681.55206 24
CCCGT 55 20.843487 545.25964 25
AGCCC 45 20.672474 165.66862 71
ACCCG 45 20.672474 330.74103 39
CCGCA 45 20.672472 330.35526 2
GCCAC 45 20.672472 825.8882 11
CCACT 120 20.356016 183.1026 31
CGGGC 615 19.789 92.7548 50
TCCCA 115 19.507849 183.51117 67
TCGGC 1615 19.189022 85.44402 3
GCGTC 1615 19.18902 55.538605 15
CTCGC 50 18.948622 136.53505 45
GCCTC 50 18.948622 273.30103 62
CCTGC 50 18.94862 136.66833 71
CGGTC 1580 18.773159 51.293324 27
TTCGC 4235 18.580837 31.615295 59
CCACA 90 18.506586 148.29613 68
GGCGC 535 17.21482 46.371006 44
GTCCC 45 17.05376 136.55428 50
CGATC 3200 17.019005 287.0713 33
CACCT 100 16.963346 182.98022 13
CCATC 100 16.963345 366.38058 37
CGAGC 1160 16.707466 41.429905 11
ATCGG 97760 16.30114 256.54904 2
TCACG 3055 16.247831 981.59875 30
CTCAC 95 16.115177 183.08833 29
CTTCC 115 16.093002 402.5322 4
ACCGC 35 16.07859 331.33725 71
CGGAA 76645 15.492193 305.39117 4
GATCG 92170 15.369027 254.17384 1
ACGGC 1040 14.979107 139.82593 15
GCCAA 2295 14.795821 856.04474 34
TCTCC 105 14.693611 100.842476 49
TCGGA 87100 14.523623 252.7719 3
CACTC 85 14.418843 183.10257 31
TCCAC 85 14.418843 244.12033 30
GTCGC 1190 14.139279 81.21979 29
GCCGG 435 13.997098 463.74896 49
TCGTC 3165 13.8862705 25.294853 52
CGTTC 3135 13.754647 26.833443 1
ACGAC 2125 13.699837 30.1354 18
TGCGC 1150 13.66401 34.225918 40
ATCGC 2505 13.322688 24.907763 43
TCCGC 35 13.264035 136.65442 68
CGCCT 35 13.264035 272.52667 15
TCGCC 35 13.264035 273.19003 60
CCGCT 35 13.264035 273.3658 72
AGCGC 900 12.962688 67.32359 10
CGTAC 2430 12.923807 21.049784 32
CGACC 25 11.484708 330.61633 33
CCCAT 65 11.026174 122.23738 46
ACCTC 65 11.026174 122.24801 52
TCGAC 2060 10.955984 26.803028 38
GCGAC 750 10.80224 36.358917 71
TACGC 1980 10.530508 40.18511 31
TTCCC 75 10.495436 100.842476 49
CCTTC 75 10.495435 201.5421 58
CCTCT 75 10.495435 100.8479 50
AACGC 1590 10.250701 20.904293 45
GACGC 705 10.154106 31.13854 53
TCCTC 70 9.79574 100.927765 65
CTACC 55 9.32984 61.168457 68
CCTCA 55 9.32984 122.0357 26
CGGGG 8915 8.993789 17.809591 45
GGGGG 278375 8.804896 10.299419 63
AGAGC 42835 8.658204 303.21082 8
CGTGC 715 8.49545 25.633207 15
ACCCT 50 8.481673 122.26083 47
CATCC 50 8.481672 61.170563 66
CCCTT 60 8.39635 100.63305 2
CTCTC 55 7.696653 100.92534 66
CGGCT 645 7.6637263 175.53583 51
CCCTA 45 7.633506 61.181213 72
GAGCA 35650 7.2059054 301.0305 9
CGAAC 1095 7.059445 23.181425 20
GGCGG 6840 6.9004507 11.614136 1
CCTAC 40 6.785338 61.12354 54
ATCCC 40 6.785338 61.12592 48
GGGCG 6660 6.7188597 11.607607 5
GAGAG 1042285 6.605233 7.495867 40
GCGGG 6460 6.517092 10.186158 66
CCAGA 970 6.2535725 361.90567 33
ACCAG 935 6.027928 364.18906 32
GACGG 12865 5.8094497 8.6241255 48
CCTCG 15 5.684586 136.37077 34
CACGA 870 5.6088743 331.70667 31
TCCCT 40 5.597566 50.46252 67
TCGGG 14975 5.5785303 10.983434 3
GCACG 380 5.473135 62.144855 11
TCACA 2245 5.3444667 304.05267 30
GGCAC 370 5.3291054 72.54517 29
TACCC 30 5.0890036 61.171204 64
AGATC 67795 5.060091 38.65642 72
CACGG 340 4.8970156 150.18341 14
GGACG 10675 4.8205113 7.975327 60
GGTCG 12585 4.6882 7.109711 56
CGAGG 10375 4.68504 7.306495 8
GCGAG 10075 4.549569 7.144129 6
GTCGG 12140 4.522428 6.4425344 46
GGCGA 9775 4.4140983 6.670304 45
ACACT 1845 4.3922234 255.25551 32
CGGGA 9530 4.3034635 10.716193 4
TTCGG 31015 4.2663484 5.4963856 37
CGGAG 9330 4.2131495 6.0195427 45
TCGGT 30605 4.20995 5.343252 22
TCGTA 68025 4.1884847 91.921135 43
CGGTA 25105 4.1861715 5.3381677 26
GGCCG 130 4.1830406 115.947845 48
CGGGT 11155 4.155493 6.0274944 9
ACGGA 20520 4.1476912 5.6809125 53
TTTCG 81200 4.124508 4.9705057 1
GAGCG 9015 4.0709047 6.5135264 63
AGCGG 8785 3.9670436 5.692328 55
GTCTG 28695 3.947215 200.86029 17
CGTAT 63835 3.930495 92.06071 44
ACGGG 8630 3.8970504 6.024769 70
GCGGA 8560 3.8654404 6.1699295 11
CACTT 1950 3.829573 211.30087 33
GCGGT 9845 3.6674879 5.6256614 4
CACAG 560 3.6103098 136.87457 33
GCTTG 26170 3.5998821 198.34308 59
TCGAG 21550 3.593388 4.67652 9
CGAGA 17700 3.5776868 5.5266027 1
AGAGA 1241805 3.5225646 3.9364038 37
AGGCG 7705 3.4793477 5.2061057 44
GTTCG 25160 3.4609487 5.0466833 24
CAGGC 240 3.456717 72.540405 27
GGCGT 9215 3.4327984 6.164905 1
CGGAT 20250 3.3766172 5.40676 44
TACGG 20060 3.3449354 4.5663657 52
TTCGT 65785 3.3415117 4.1882863 40
TCGTT 65690 3.3366864 3.8734453 26
GACGA 16380 3.3108764 4.4333854 17
CGGTT 23900 3.287626 4.4019575 12
CGTTT 63930 3.2472882 4.547675 16
TATCG 52305 3.2205615 3.8343909 36
TGGCG 8645 3.22046 4.9662538 49
CGAAA 34995 3.166204 4.068885 30
GTCGA 18855 3.144006 4.3167877 5
CTCGG 260 3.0892541 128.38313 42
AGACG 15250 3.0824704 4.0089192 64
GCGAA 15245 3.0814598 4.296785 46
GACGT 18470 3.0798082 4.499183 1
AGCGA 15080 3.0481083 4.4359984 30
GTCGT 22050 3.0331447 3.9568162 7
TTCGA 48980 3.0158322 3.807923 8
ACACA 1030 2.9723334 62.299187 32
GCGCA 205 2.9526122 67.323586 11
CCAGG 180 2.5925376 82.89302 26
GCTCG 215 2.5545754 68.45316 41
TGAAC 33345 2.488808 109.68545 20
CCGGG 75 2.4132926 23.14805 25
CGGCA 165 2.3764927 77.68106 4
ACGAT 31840 2.3764775 5.800764 32
CATCT 1185 2.3272018 124.42469 39
CTGAA 28800 2.1495779 108.878685 19
GAACT 28585 2.1335304 109.61919 21
AGTCA 27770 2.0727003 108.18611 28
TCATC 1015 1.9933418 112.40471 38
TATGC 31915 1.9650936 89.936226 46
GCTTC 445 1.952414 63.236282 53
AGGCC 135 1.9444032 51.90371 47
GACAC 295 1.9018596 16.226536 11
CACAT 770 1.8330686 51.358295 12
GCCGA 125 1.8003733 25.947578 49
GCCAG 125 1.8003733 31.084185 25
TCTGA 28760 1.7708316 89.57596 18
GGGCC 55 1.769748 11.604035 71
AACAC 610 1.7603139 12.489586 72
CTTGA 27535 1.695405 86.996475 60
GCTGC 135 1.604036 38.507557 56
GGAAG 251915 1.5964514 10.87816 5
ACTGA 20365 1.5200052 80.109634 32
TCCGG 125 1.4852183 29.916723 25
AGCTC 265 1.4093864 28.72501 40
TCCGA 260 1.3827941 24.85987 2
GGACC 95 1.3682837 36.279755 34
CCGGA 95 1.3682837 15.536212 3
TGCTT 26895 1.3661163 73.95949 58
TTCTG 26830 1.3628147 74.31093 55
CATAC 570 1.356947 46.222466 12
GTCTT 26340 1.3379254 73.30253 52
CCGAT 245 1.3030175 17.23044 37
GACCG 90 1.2962688 46.650352 35
CTTCA 660 1.2961633 46.62095 24
ACTTC 660 1.2961631 46.6185 23
GAAGA 446010 1.2651737 5.4230494 6
CCGTG 105 1.2475834 64.21984 50
CTGCG 105 1.2475834 42.781242 57
CACAA 425 1.2264482 8.318631 51
CCAAG 190 1.2249266 30.169596 37
CCGAA 190 1.2249264 32.45307 3
CGCAG 85 1.2242538 10.357474 9
GAGCC 85 1.2242538 25.893686 9
ACTCG 225 1.1966488 26.81001 40
GTCCG 100 1.1881746 12.816755 17
GTGCC 100 1.1881746 34.25438 47
CGTCA 220 1.1700566 21.051895 33
TACAC 490 1.1664982 25.679148 12
GCAGC 80 1.152239 15.571114 47
GGCCA 80 1.1522388 31.100233 35
CCGAG 80 1.1522388 10.3656435 34
CCGGT 95 1.128766 34.191307 26
AAGAG 390825 1.1086333 5.193562 7
CCAAA 380 1.096589 16.620426 36
AAACC 380 1.096589 8.325504 71
AGCCG 75 1.080224 15.536214 4
TGGCC 90 1.0693572 25.653418 34
CAAGC 165 1.063752 27.848986 38
ACCGA 165 1.063752 23.206964 36
GCATC 200 1.0636878 32.546535 38
ATCCG 190 1.0105033 28.700602 1
GCACT 180 0.957319 13.3941345 30
CTGGC 80 0.9505398 25.65346 33
CAAAC 325 0.93787223 14.543136 37
AACCA 325 0.9378721 6.2447934 72
TGCCA 175 0.9307268 30.62094 33
CAACA 320 0.92344344 5.193977 37
TTCCA 470 0.92302525 36.73165 24
ATTCC 465 0.9132058 36.023388 23
ACGCT 170 0.90413463 26.790634 32
ACTCT 460 0.9033864 36.023388 23
ACAAC 310 0.8945858 6.244794 72
CCGTT 200 0.87748945 15.809189 50
ACCGG 60 0.86417925 10.36462 32
CTCTA 440 0.86410874 36.025272 24
CATGC 160 0.85095024 26.790075 31
CAGAC 130 0.83810765 9.272306 11
CGCTG 70 0.83172226 25.650349 31
CAGCA 125 0.80587274 6.96934 48
CATCG 150 0.79776585 9.566867 1
AGCCA 120 0.77363783 11.590383 10
GGCCT 65 0.77231354 8.561953 46
GACTC 145 0.77117366 17.215673 22
GCAAC 115 0.7414029 9.272306 10
AAAGC 7740 0.70028347 9.103271 71
CTCGA 130 0.6913971 11.477751 24
GCTCT 155 0.6800543 14.205941 1
AACCG 105 0.6769331 9.298862 70
CTGCA 125 0.6648049 5.7535396 67
GTCCA 125 0.6648049 13.39071 24
GGTCC 55 0.653496 8.544401 5
GCGCT 55 0.653496 12.853829 63
CAGCG 45 0.6481344 10.38714 70
TGCAC 120 0.6382127 5.753195 62
AATCT 22425 0.6180515 32.333652 39
CTTCG 140 0.6142427 14.228249 54
CTGTC 140 0.6142426 15.809189 50
TTCCG 140 0.61424255 12.620402 5
CGCAA 95 0.6124632 6.9542294 3
ACTGC 115 0.6116205 5.753557 66
AGTCC 110 0.58502823 13.390007 23
GAACC 90 0.5802284 6.9553323 21
TCCTG 130 0.57036805 7.8907366 25
CGCTA 105 0.5584361 19.138086 33
GAATC 7180 0.53590167 8.22155 38
CCGTA 100 0.5318439 9.581905 50
ACCGT 100 0.5318439 9.561489 15
GATCC 100 0.53184384 5.7401204 1
TCGCT 120 0.52649367 9.470995 30
CTCAG 95 0.5052517 5.7401204 1
CAGCT 95 0.5052517 5.7390647 25
CCTGA 95 0.5052516 5.7407293 31
CCTGT 115 0.50455636 7.890913 26
CACTA 210 0.49992785 5.150802 64
CTTGC 110 0.4826192 6.3255615 60
GTCTC 105 0.46068195 7.8989015 40
CTCTT 245 0.396926 5.825253 2
CGACT 50 0.26592195 7.665593 51
AAGCA 2125 0.19226128 8.582132 72
ACTTG 2270 0.13977009 6.7355905 34
Produced by FastQC (version 0.10.1)