FastQCFastQC Report
Mon 3 Feb 2014
filtered_BS_CgM3_GATCAG_L007_R1.fastq

Summary

[OK] Basic Statistics

Measure Value
Filename filtered_BS_CgM3_GATCAG_L007_R1.fastq
File type Conventional base calls
Encoding Sanger / Illumina 1.9
Total Sequences 5526741
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
GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGC 18276 0.3306831277239154 TruSeq Adapter, Index 9 (100% over 50bp)

[FAIL] Kmer Content

Kmer graph

Sequence Count Obs/Exp Overall Obs/Exp Max Max Obs/Exp Position
CCCCC 710 522327.3 1591820.0 66
CCGTC 45395 11440.157 684063.06 50
CACAC 52950 7047.422 354696.06 12
ACTCC 46095 5192.4478 295760.16 23
CTCCA 45950 5176.114 295169.8 24
CACGC 8005 2383.5884 135525.34 31
ACGCC 7745 2306.1702 134884.38 32
CGCCA 7710 2295.7483 135324.67 33
CCGCC 80 1771.0057 39884.5 50
ACCCC 155 1533.7551 10706.823 72
CGCCC 65 1438.9421 31907.6 50
CACCC 145 1434.8032 28524.53 50
CCCCA 145 1434.8031 10705.821 71
CCCGC 50 1106.8785 23950.22 66
CCCCG 45 996.1907 15965.872 70
GCCCC 45 996.1907 15967.4375 65
CCCAC 95 940.0435 10696.737 54
CCACC 75 742.1396 10692.036 55
CTCCC 85 711.86444 21086.305 24
CGCGC 845 562.90137 2636.5034 31
CACCA 3085 410.6005 19969.188 31
TGCCG 45905 348.12045 20833.967 48
GCCGT 45560 345.50415 20684.527 49
CCCCT 40 334.995 9060.596 67
TCACC 2955 332.8709 16981.127 30
TCCCC 35 293.12067 6040.6494 65
CCGGC 435 289.77765 15842.499 50
CGTCT 92710 265.9773 7792.6533 51
CCCTC 25 209.3719 9060.621 66
AGCAC 50315 201.51497 10883.619 10
GCACA 49975 200.15324 10873.539 11
ACACG 48640 194.80649 10768.418 13
ACGTC 50590 171.48596 9071.279 15
CACGT 48355 163.90993 9088.342 14
TCCAG 46535 157.74066 9032.382 25
GTCAC 46360 157.14745 9000.083 29
CAGTC 46330 157.04575 8978.677 27
CCAGT 46325 157.02881 8998.421 26
ATGCC 46040 156.06273 9308.357 47
TCTGC 45900 131.68329 7857.429 56
CTGCT 45835 131.49681 7854.659 57
CTCGT 45345 130.09105 7758.973 42
TCTCG 45265 129.86153 7753.189 41
CCTCC 15 125.62314 3020.207 66
TCACG 36600 124.06379 7034.3394 30
CGCAC 380 113.14973 2141.1968 12
CACGA 27865 111.60121 6474.5015 31
CGATC 31465 106.657555 5474.1973 33
CGGCG 5065 101.531456 180.18483 5
CGCTC 400 100.80544 5255.439 2
TCGCG 12935 98.092545 172.11263 43
CGCGG 4805 96.31957 165.888 32
CGCGA 9605 86.06229 142.03636 44
GCGCG 4270 85.59513 137.23944 53
CGTCG 10805 81.93969 147.2387 16
CGACG 8125 72.801254 128.90532 22
AACTC 47000 71.21249 4042.4106 22
CGCGT 8360 63.39804 101.08871 44
ATCTC 45175 57.930923 3462.784 40
ACGCG 6450 57.79299 93.426506 9
CGGAC 5795 51.924095 93.7192 72
TCTTC 45845 49.757477 2941.3462 53
CTTCT 45805 49.714066 2965.9954 54
GCCGC 70 46.630886 1440.1475 49
GCGCC 70 46.630886 1917.483 32
CTCCG 175 44.102383 2628.7305 24
CTTCC 455 43.37943 2056.746 6
CGCCG 65 43.300106 719.11865 33
CCCAG 135 40.19793 535.53265 26
GCACC 115 34.24268 429.18167 51
GCTCC 125 31.501701 1812.8108 23
GCCAA 7815 31.299604 1857.6763 34
ACACC 220 29.28107 287.73697 49
CCACG 95 28.287432 321.38477 30
AACCC 210 27.950113 191.47832 22
CGCCT 105 26.461428 454.05164 51
CAACC 195 25.953676 383.50327 55
CACCG 85 25.309807 428.53864 31
CCAAC 185 24.62272 335.71295 54
CCAGC 80 23.820995 749.7457 26
CCGAC 80 23.820995 1072.9366 50
GCGGC 1185 23.754152 65.0252 60
CCCGG 35 23.315443 240.23367 66
GGCCC 35 23.315443 240.26506 72
GCCAC 75 22.332182 535.6316 29
GCGTC 2910 22.067978 76.34564 15
CACTC 190 21.402864 445.52042 7
TCGGC 2705 20.513361 87.252235 3
CGTCC 80 20.161089 634.2794 16
CGGGC 1005 20.145926 50.603146 66
TTCGC 7020 20.139795 36.165142 42
CAGCC 65 19.354559 535.5913 27
CGGTC 2550 19.33792 81.84355 27
ACCCG 60 17.865746 321.88626 51
CCCGT 70 17.640953 181.76091 69
CCACA 130 17.302452 143.86328 46
ACCCA 130 17.302452 143.99342 67
ACCAC 130 17.302452 143.5629 13
CCGCG 25 16.653887 480.0318 46
GCCCG 25 16.653887 240.24306 65
CCCAA 125 16.636972 143.98923 68
GTCGC 2125 16.114931 81.84969 29
ACGGC 1795 16.083477 115.97773 15
CCAAT 10145 15.37129 701.21704 35
CGAGC 1690 15.14266 45.134586 32
TCGCC 60 15.120816 272.6327 70
CCCTA 130 14.644066 526.5242 15
TCGTC 5095 14.617132 25.787983 19
ACGAC 3610 14.458294 31.685535 21
ATCGG 141000 14.382308 292.22397 2
GGCGC 710 14.232445 43.244358 5
CGTTC 4940 14.17245 22.737528 43
ATCGC 4140 14.0334425 31.73562 40
TCCCG 55 13.860748 181.49542 41
AGCGC 1535 13.753837 70.87528 10
CGGAA 111575 13.446905 338.1225 4
ACCGC 45 13.399309 214.55135 45
GATCG 130845 13.346476 290.61975 1
TGCGC 1750 13.27112 32.71956 14
CGTAC 3855 13.067374 24.426336 46
TCGGA 125465 12.797705 287.16287 3
CCGCT 50 12.60068 272.64804 67
TCGAC 3665 12.423327 24.375355 3
ACCAG 3055 12.235482 618.2059 32
CGACC 40 11.910498 214.53716 43
GCCCA 40 11.910498 214.11966 11
CTCAC 100 11.264667 162.35233 49
CCTAC 100 11.264666 445.52246 16
AACGC 2775 11.114062 28.809464 22
TCCCT 110 10.487333 445.6279 14
TACGC 3025 10.253904 47.565117 31
CCATC 90 10.138199 202.78998 58
TTCCC 105 10.010635 445.62787 13
CGGCC 15 9.992332 240.24263 71
GCGAC 1100 9.856171 25.781252 23
CCAGA 2450 9.812416 612.49493 33
GACGC 1085 9.721767 41.89453 23
CGTGC 1265 9.593124 24.593267 53
GACCA 2395 9.592136 601.0341 35
CGGGG 14840 8.9516 14.538916 1
GACCC 30 8.932873 214.75555 68
CTCGC 35 8.820477 90.88292 66
GCCCT 35 8.820477 181.76535 67
GCCGG 430 8.61965 476.7001 49
TCCCA 75 8.4485 202.59361 25
GGGGG 458700 8.32609 9.725883 54
CACTG 2420 8.203124 507.36127 31
CGAAC 2025 8.110262 15.850269 30
CTGAC 2375 8.050588 508.63202 33
AGAGC 66560 8.021744 334.7856 8
TGACC 2330 7.898049 507.41638 34
TCCAC 70 7.885267 121.583244 30
CCTTC 80 7.6271515 206.12363 53
CCCTG 30 7.5604076 90.88209 63
TGCCC 30 7.5604076 181.76617 64
GAGAG 2060360 7.472125 8.404004 42
CCCGA 25 7.444061 214.58987 52
TCTCC 75 7.150455 205.74162 23
TCACA 4700 7.1212482 407.2049 30
GGCGG 11520 6.948951 10.433194 52
ACCCT 60 6.7587996 121.77295 51
GGGCG 11105 6.6986194 12.1454 6
GAGCA 55085 6.6387873 333.35562 9
GCGGG 10825 6.5297213 10.214779 46
GCACG 725 6.496112 87.038895 30
GACGG 23385 6.305194 8.647102 48
GTCCC 25 6.3003397 90.88045 69
CCACT 55 6.195566 81.039055 26
ATCCC 55 6.195566 162.25125 40
ACACT 4025 6.098516 343.99612 32
CGGCT 795 6.0288806 172.1557 51
CCGCA 20 5.955249 214.58734 50
AGCCC 20 5.955249 214.11966 10
CCCTT 60 5.7203636 137.52348 68
TCGGG 24440 5.5772023 14.686735 3
CACTT 4095 5.251292 292.55347 33
CTCTC 55 5.243667 34.38646 72
CTCCT 55 5.2436666 171.46143 24
CCCAT 45 5.0690994 81.244286 68
AGATC 109480 4.9915867 75.20397 38
GGCAC 545 4.8832846 125.72057 29
GGACG 17920 4.831691 6.699184 41
ACCAA 2675 4.788814 269.36862 36
GTCGG 20625 4.7066193 6.3177557 2
GGTCG 20415 4.658697 6.2546635 65
GCGAG 17235 4.646997 6.8063817 67
CGAGG 16985 4.5795903 6.217944 54
TACCC 40 4.5058665 121.87052 64
TCGTA 114840 4.4315033 108.222885 43
CGGAG 16435 4.431297 6.125593 69
TCGGT 51075 4.409323 5.199231 64
TTCGG 50380 4.3493233 5.1853547 23
ACGGA 35875 4.3236184 5.6017704 49
CGGTA 42005 4.284602 5.173913 1
CGGGA 15845 4.2722173 13.765958 4
TTTCG 129605 4.232858 4.8368764 51
GTCTG 48620 4.197382 234.5389 17
GGCGA 15515 4.183241 5.719653 14
CGTAT 106345 4.103694 107.395905 44
GAGCG 15110 4.074042 6.495205 4
GCTTG 46230 3.9910524 236.32922 59
CGGGT 17440 3.9798036 5.4152203 5
CTACC 35 3.9426334 202.90416 43
CCTCA 35 3.9426332 121.869965 67
CACCT 35 3.9426332 81.18064 50
AGAGA 2401855 3.8935177 4.314444 43
CACAG 965 3.8648903 171.49858 33
AGCGG 14275 3.848905 5.913545 5
CACGG 425 3.808066 115.97774 14
CTGCC 15 3.780204 90.83265 60
CCTGC 15 3.7802038 90.80991 52
GCGGA 14020 3.7801504 5.0568433 72
GCGCA 415 3.7184641 67.65368 11
CAATC 2435 3.6894126 221.99057 38
ACGGG 13665 3.6844335 4.958431 61
GCGGT 15805 3.6066968 4.9334025 49
ACGAT 79040 3.6037178 77.036736 32
CGAGA 29900 3.6035175 5.128401 68
AGGCG 13195 3.5577092 5.1412773 30
TCGAG 34785 3.5481462 4.6210117 3
GGCGT 15505 3.538237 5.2668896 64
GTTCG 40870 3.5283217 4.4387083 4
CATCT 2725 3.4944496 211.89207 39
TCACT 2690 3.4495673 209.92194 30
CGGAT 33795 3.447164 5.6225367 44
TCGTT 105210 3.4361253 4.051241 3
TTCGT 105100 3.432532 4.08367 52
CGGTT 39630 3.421272 4.323969 53
GGCCG 170 3.4077685 166.13783 48
TCATC 2605 3.340566 196.65446 38
CGTTT 102120 3.3352067 5.272504 16
TATCG 86390 3.3336606 4.196397 41
TACGG 32485 3.313541 4.009119 61
ACACA 1845 3.3029392 77.295 32
AGACG 26810 3.231114 4.208174 36
GACGA 26805 3.2305114 4.2551303 44
TGGCG 13960 3.185668 4.348585 4
GTCGA 31175 3.1799178 3.7801301 31
CGAAA 58920 3.1740408 3.854424 9
GTCGT 36155 3.1212738 3.855577 42
ACGGT 30160 3.076386 3.6700294 31
AACGG 25330 3.0527458 3.908428 50
TTCGA 78720 3.0376866 3.5946457 23
AGCGA 25190 3.0358732 3.8681436 67
GACGT 29640 3.0233448 3.96403 33
GCGAA 25080 3.0226161 3.6070032 61
CGGTG 13235 3.0202239 4.279507 65
CCTCT 30 2.8601818 68.70788 53
CATCC 25 2.8161664 40.623062 63
CCAGG 310 2.777648 125.697365 26
CAGGC 310 2.7776477 122.48776 27
GCTCG 355 2.6921418 120.15282 41
ACGCT 780 2.643982 71.94595 1
TGAAC 56030 2.554609 124.45826 20
GCCTC 10 2.520136 90.819305 47
CTCGG 330 2.5025542 120.17841 42
TCCTC 25 2.383485 34.38331 65
ACCTC 20 2.2529333 81.18197 51
CTGAA 48855 2.2274752 123.75213 19
GAACT 48450 2.2090096 123.8702 21
AGTCA 47370 2.1597686 122.36331 28
TATGC 55320 2.1347158 105.81909 46
TCCGA 625 2.1185756 75.56353 8
CACAT 1385 2.0984955 75.72333 12
CTTGA 49965 1.9280745 105.00811 60
GACAC 480 1.9224324 25.920237 12
TCTGA 48655 1.8775235 104.613716 18
CCGAT 545 1.8473977 74.34476 9
TCCGG 240 1.8200395 76.377426 25
CGGCA 195 1.7472302 80.54018 4
AGGCC 190 1.7024293 74.26727 47
AGCTC 485 1.6440145 53.706432 40
TTCCG 565 1.6209378 62.92227 7
AACAC 880 1.5753856 13.5593405 72
CCGGT 205 1.554617 79.106766 26
TGCTT 46975 1.5341883 89.30954 58
TTCTG 46745 1.5266767 89.67113 55
GGAAG 418655 1.518299 11.40427 5
GTCTT 46340 1.5134494 88.79335 52
GCTCT 510 1.4631478 62.922337 3
TACAC 960 1.4545529 33.77587 12
CATAC 930 1.409098 70.275604 12
ACTTC 1095 1.4041917 61.803856 23
GATCA 30655 1.3976717 73.992485 34
CAGAT 30405 1.3862733 73.51218 37
GCCAG 145 1.2992225 51.567127 25
CTTCA 1010 1.2951907 61.8075 24
CCGTG 170 1.2891946 71.04722 50
TCAGA 28230 1.2871072 73.888336 36
ATCAG 28220 1.2866513 73.90188 35
TCCGC 5 1.260068 90.668846 30
CCTCG 5 1.2600679 90.61101 6
GAAGA 765615 1.2410972 5.651256 6
CGCTA 365 1.2372482 45.130417 33
GCTTC 425 1.2192898 64.093475 53
TTCCA 935 1.199013 62.26874 24
CTGCG 155 1.1754421 43.687458 57
ATTCC 915 1.1733658 60.881416 23
GCCGA 130 1.1648201 32.28462 49
ACTCT 895 1.1477183 56.269184 23
GATCT 29685 1.1454996 64.95642 39
AAGAG 674215 1.0929337 5.459496 7
CTCTA 835 1.0707765 56.2725 24
CACAA 580 1.0383223 7.729395 31
CGTCA 300 1.0169163 34.15275 33
ACAAC 515 0.9219586 7.7330704 36
GCTGC 110 0.83418477 35.499245 56
ACTCG 240 0.8135329 12.206008 40
CAGAC 200 0.80101347 7.2000656 12
CCGGA 85 0.76161313 12.886428 3
AAACC 410 0.73398644 6.4568286 72
GCATC 215 0.7287899 37.827484 38
TGCCA 215 0.72878987 32.933002 33
ATATC 41615 0.7177978 8.848079 38
CCGGG 35 0.7015994 7.2289553 63
GGGCC 35 0.7015994 7.229965 72
CAACA 390 0.6981822 7.7332106 37
GCACT 205 0.6948927 8.531365 11
CGCTG 90 0.6825148 8.185607 31
CCGAA 170 0.68086153 12.960132 3
CGCAG 75 0.6720116 6.4621673 70
GCAGC 75 0.67201155 6.456543 59
GAGCC 75 0.67201155 19.329622 9
GACTC 195 0.6609955 20.72565 22
CATGC 195 0.6609955 32.9297 31
CTCTT 585 0.63492477 24.194416 4
ACCGG 70 0.62721086 9.693515 68
CAACG 155 0.6207855 7.2000656 14
GAATC 13515 0.6161974 10.766871 38
CGCAA 145 0.58073485 5.7773275 67
GCAAC 140 0.5607094 5.7600527 11
CGCTT 195 0.5594388 5.1730313 67
CTTCG 190 0.54509425 17.574081 54
GTGCC 70 0.5308448 16.3974 47
ATCCG 155 0.52540666 12.194229 1
CGACA 130 0.5206588 7.200073 4
CGACT 150 0.5084581 14.657382 51
GTCTC 175 0.5020604 12.393356 39
AGCCA 125 0.5006334 7.204243 28
GTCCG 65 0.4929273 5.4532943 17
CCAAG 120 0.48060814 10.089303 35
GAACC 120 0.4806081 5.7610064 21
GCGCT 60 0.45500988 5.469629 66
CAGCG 50 0.4480077 6.4627886 71
AGCCG 50 0.4480077 9.688459 60
GCCTG 55 0.41709238 13.633236 17
CTCAG 120 0.4067665 12.192366 24
GACCG 45 0.40320694 9.670016 1
CCTGA 110 0.37286922 7.3126454 18
CTACA 245 0.371214 8.716363 4
TACCA 245 0.37121397 7.086987 31
CCGTT 125 0.35861462 7.23636 50
GGACC 40 0.3584062 6.4484115 34
GGCCA 40 0.3584062 9.673642 35
CCGTA 105 0.3559207 7.3285723 50
CATCA 225 0.3409108 9.812751 31
TCGCA 100 0.3389721 6.0977283 30
AGTCC 100 0.33897206 7.3168426 28
TCAGC 95 0.32202348 6.1012077 38
GTCCA 95 0.32202342 7.3154182 24
CCGAG 35 0.31360543 6.4511223 39
ACTCA 190 0.2878802 5.994451 23
TTTCC 265 0.28761548 5.463249 12
GCCTT 100 0.2868917 5.16889 52
CTGTC 95 0.27254713 5.160379 27
CATCG 80 0.27117765 6.0971146 1
TTACC 210 0.26929706 5.99777 30
CTTTC 240 0.26048192 5.073017 11
TCCTG 90 0.25820255 5.1597114 25
CAGCT 75 0.25422904 6.101318 39
TCTAC 180 0.23082606 7.377162 3
CTGGC 30 0.22750494 8.18643 33
TGGCC 30 0.22750492 8.186496 34
CAAGC 55 0.22027871 5.767023 38
CCTGT 70 0.20082416 5.159813 26
CAATA 9775 0.19921176 9.573599 36
ACTTG 4425 0.1707541 8.956222 34
TATCT 10160 0.1483201 7.0420785 39
ACTGA 3165 0.14430372 6.988426 32
AATCT 7530 0.12988147 6.606685 39
Produced by FastQC (version 0.10.1)