FastQCFastQC Report
Mon 3 Feb 2014
filtered_BS_CgLarv_T1D5_ACAGTG_L007_R1.fastq

Summary

[OK] Basic Statistics

Measure Value
Filename filtered_BS_CgLarv_T1D5_ACAGTG_L007_R1.fastq
File type Conventional base calls
Encoding Sanger / Illumina 1.9
Total Sequences 2709822
Filtered Sequences 0
Sequence length 76
%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

[OK] Sequence Length Distribution

Sequence length distribution

[OK] Sequence Duplication Levels

Duplication level graph

[WARN] Overrepresented sequences

Sequence Count Percentage Possible Source
GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGC 5508 0.2032605831674553 TruSeq Adapter, Index 5 (100% over 50bp)
ATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCC 3772 0.13919733473268725 TruSeq Adapter, Index 5 (100% over 50bp)

[FAIL] Kmer Content

Kmer graph

Sequence Count Obs/Exp Overall Obs/Exp Max Max Obs/Exp Position
CCCCC 530 940922.06 1919126.9 50
CCGTC 20500 11649.718 553083.6 50
CACAC 35530 11235.176 305505.03 12
ACTCC 20300 5118.445 238315.8 23
CTCCA 20255 5107.0986 238236.98 24
CACCC 90 2132.4248 34096.938 30
CACGC 2500 1781.7395 101030.54 31
ACCCC 75 1777.0206 17089.834 65
CGCCA 2395 1706.9066 101551.266 33
ACGCC 2395 1706.9065 101287.9 32
CCACC 70 1658.5525 8544.917 65
CCCCA 70 1658.5525 8544.917 65
CCCAC 65 1540.0845 17089.36 66
CTCCC 80 1511.397 61152.83 23
CCCCG 20 1068.0234 19257.758 69
GCCCC 20 1068.0234 19258.72 65
CCGCC 15 801.0176 19242.55 53
CCCCT 30 566.77386 13593.506 1
CGCCC 10 534.0117 19258.186 66
CCCGC 10 534.0117 19257.436 70
CGCGC 315 505.98123 2315.2642 54
CCGGC 260 417.63522 14469.996 50
CACCA 1255 396.85184 24916.152 31
CCTCC 20 377.84924 13589.517 23
TGCCG 20815 355.80417 16938.633 48
GCCGT 20640 352.81277 16813.982 49
TCACC 1210 305.08954 19775.28 30
CCCTC 15 283.38693 6813.66 71
CGTCT 41065 248.33858 5890.1816 51
GCACA 22355 212.63382 9384.43 11
AGCAC 22345 212.53871 9408.369 10
ACACG 21050 200.22107 9237.37 13
ACGTC 21955 166.51312 7256.4795 15
CACGT 20980 159.11841 7330.107 14
ATGCC 20840 158.05664 7494.2207 47
CAGTC 20580 156.08472 7251.8975 27
TCCAG 20570 156.00888 7278.133 25
GTCAC 20555 155.89513 7211.4927 29
CCAGT 20480 155.32626 7264.667 26
CGCAC 195 138.9757 2306.2842 12
TCTGC 20715 125.272934 5957.9937 56
CTGCT 20650 124.87985 5948.569 57
TCTCG 20490 123.912254 5879.4146 41
CTCGT 20485 123.88202 5865.407 42
CACAG 12745 121.22647 4572.4614 33
TCGCG 6625 113.24536 166.29211 49
CGCGG 2290 110.64514 243.74513 48
CGGCG 2230 107.74614 209.09377 64
CGCGA 4765 102.15042 161.95438 28
GCGCG 1980 95.66698 226.51907 66
TCCCC 5 94.46231 6792.8906 3
CGTCG 5090 87.00664 147.8278 51
CGACG 3770 80.819954 154.16342 18
CGCGT 4400 75.21203 159.799 14
GCGCC 45 72.283035 1155.8729 32
CGCCG 45 72.28303 579.3581 72
CCCAG 100 71.269585 1281.7207 25
ACGCG 3260 69.88674 138.7445 12
AACTC 20720 69.72446 3237.4502 22
ACACA 13095 55.264168 2027.1022 32
ATCTC 20375 54.670162 2602.8257 40
CGGAC 2415 51.771935 108.12768 44
TCACA 15140 50.94731 2010.894 30
GCCGC 30 48.188686 1155.101 4
CCCGG 30 48.18868 1155.1007 4
CTTCT 20620 44.116264 2089.277 54
TCTTC 20495 43.848827 2074.6062 53
CCGAC 60 42.76175 513.6164 50
ACCCA 120 37.94599 341.77216 45
CGCTC 65 36.938137 1430.2954 2
CCAGC 50 35.634792 769.0324 25
CTTCC 175 35.183365 578.6317 1
CCCAA 110 34.783825 228.08214 65
CTCCG 60 34.096733 1226.3656 24
CCGCG 20 32.125786 579.31616 71
CACCG 45 32.071312 768.76135 14
CAACC 95 30.040579 228.0733 63
CCACA 95 30.040577 228.07538 67
CGGGC 600 28.989988 87.12175 63
GCACC 40 28.507835 257.02017 64
ACACC 90 28.459496 342.10046 70
CCAAC 90 28.459494 341.09232 10
GCGGC 580 28.023657 87.12175 63
ACCAC 85 26.87841 227.54688 32
TCACG 3385 25.672823 1541.6564 30
CGTCC 45 25.572556 408.6611 16
GACCC 35 24.944357 257.02017 64
GCCAA 2475 23.541431 1420.3458 34
GCGTC 1360 23.247355 79.8995 15
TCCCA 90 22.692614 453.43927 24
AACCC 70 22.135164 454.86203 21
TTCGC 3580 21.649872 41.3135 6
AGCCC 30 21.380877 257.02066 67
CGATC 2690 20.401745 455.74033 33
TCGGC 1175 20.085028 67.707825 56
GCTCC 35 19.889765 817.5364 23
TCCCG 35 19.889763 1021.9713 24
CACTC 75 18.91051 271.9752 13
CGGTC 1075 18.375666 43.112774 49
GTCGC 1050 17.948324 61.496098 29
GCCAC 25 17.817398 512.5076 11
CTCAC 70 17.64981 181.696 49
CGTTC 2860 17.295708 30.50784 48
GTCCC 30 17.04837 408.8723 28
CCCGT 30 17.048367 817.5996 25
CCGCT 30 17.048367 818.5273 56
ATCGC 2240 16.988813 32.73257 22
GGCGC 340 16.42766 69.7001 65
ACGGC 745 15.97105 131.03648 15
ACGAC 1665 15.836962 37.633053 25
CGAGC 735 15.756674 61.66423 11
AGCGC 725 15.542297 69.37225 10
TCGTC 2545 15.390761 39.224434 53
CCATC 60 15.1284075 90.92986 66
ATCGG 65835 15.019132 234.10358 2
CGTAC 1940 14.713527 38.22137 39
CGGAA 50900 14.56292 286.49823 4
GCCCA 20 14.253918 256.76453 45
CCGCA 20 14.253917 512.50757 5
CAGCC 20 14.253917 257.02112 66
ACCGC 20 14.253917 256.8139 52
TCCGC 25 14.206973 614.0419 55
CTCGC 25 14.206973 408.65576 4
TGCGC 800 13.674914 30.82345 65
TCGGA 57475 13.11194 231.15062 3
GCGAC 610 13.076969 61.664234 7
GATCG 57015 13.006999 231.52826 1
TACGC 1665 12.627845 46.389122 31
GCCGG 260 12.56233 435.22134 49
TCGAC 1590 12.059024 30.062284 52
CCAAT 3540 11.912384 497.70416 35
CCAGA 1245 11.842052 742.6827 33
ACCAG 1245 11.842052 752.89874 32
AACGC 1230 11.699378 30.788185 22
GACGC 540 11.576332 46.389572 71
CGCCT 20 11.365579 409.5399 50
CGTGC 630 10.768995 30.821398 70
CGACC 15 10.690438 256.74554 43
CCACG 15 10.690437 512.8454 31
ACCCG 15 10.690437 256.76453 45
GACCA 1085 10.320184 626.38715 35
TCCAC 40 10.085606 181.4246 30
CATCC 40 10.085606 181.4199 1
CGGGG 6735 9.788303 15.176297 41
CACGA 1000 9.511689 557.82434 31
CCCTT 45 9.047152 145.00462 68
TACCC 35 8.824905 90.92954 64
ACCTC 35 8.824904 181.6298 55
TGCCC 15 8.524185 204.78851 47
TCGCC 15 8.524183 408.88815 1
CCTCG 15 8.524183 409.26367 56
GCCCT 15 8.524183 204.93933 67
CTGAC 1120 8.494407 502.133 33
CACTG 1110 8.418562 499.36523 31
GGGGG 192295 8.406415 10.420987 66
AGAGC 29320 8.388699 287.73267 8
TGACC 1100 8.342721 499.40677 34
GGGCG 5580 8.109686 12.578986 66
TCTCC 40 8.041912 144.6155 23
TTCCC 40 8.041912 72.50405 64
CGGCC 5 8.031448 578.80853 48
CGGCT 450 7.692139 153.98729 51
CGAAC 800 7.6093516 20.537283 35
GGCGG 5235 7.6082807 11.531057 65
CCTCA 30 7.564204 90.94216 72
CCCTA 30 7.5642037 181.85468 68
CCACT 30 7.5642037 90.929695 67
GCGGG 5015 7.2885437 12.555797 39
ACACT 2155 7.251748 410.44165 32
GAGCA 24925 7.131253 285.98386 9
TCCCT 35 7.036673 145.00838 67
GGCAC 325 6.9672375 138.81804 28
GACGG 10055 6.48384 8.810488 10
CTACC 25 6.303503 272.4971 43
CCCAT 25 6.303503 90.846306 46
GCACG 290 6.2169194 100.204384 11
CACTT 2285 6.131107 329.22513 33
CTCTC 30 6.031434 217.33276 50
TCGGG 11570 5.9489584 12.941114 3
GCCTC 10 5.6827903 204.77261 51
CCCTG 10 5.6827893 204.77449 52
CTGCC 10 5.6827893 204.71997 43
GGACG 8285 5.342478 7.898779 45
GAGAG 619625 5.3325214 5.9215546 43
ACCAA 1240 5.233109 274.95636 36
GGCGA 7925 5.1103363 7.8830676 9
CGAGG 7860 5.068422 7.187503 7
CACCT 20 5.0428023 90.935585 71
ACCCT 20 5.0428023 181.43631 31
CCTCT 25 5.026195 144.65793 1
GCGAG 7700 4.965249 8.132585 51
GGTCG 9470 4.8691993 7.0291715 1
CGGGA 7485 4.826608 12.520166 4
GTCGG 9120 4.68924 7.59009 58
CGGTA 20255 4.620833 6.073411 29
CACGG 215 4.609095 146.45255 14
TCGGT 25195 4.5831037 5.821051 5
TTCGG 24485 4.4539514 5.827524 37
TCGTA 55140 4.450333 81.67256 43
ACGGA 15460 4.4232364 5.969731 28
CGGAG 6855 4.4203615 7.4412856 70
AGCGG 6785 4.3752217 7.191072 27
CTCGG 255 4.358878 153.8766 41
GGCCG 90 4.348499 191.52856 47
GCGGA 6650 4.288169 6.260083 15
GCTCG 250 4.273411 153.87547 40
CGGGT 8235 4.234198 6.2994227 52
TTTCG 65635 4.2239485 5.0444202 16
CGTAT 51630 4.1670423 81.18444 44
CAATC 1220 4.1053977 219.24432 38
GAGCG 6335 4.085045 7.2090244 66
CCAGG 190 4.073154 131.08267 25
ACGGG 6290 4.056027 6.959782 30
AGATC 39725 4.0209837 31.506668 72
TCCTC 20 4.020956 72.287865 2
CAGGC 185 3.9659655 138.79675 26
GCGGT 7575 3.8948455 6.662807 36
CGAGA 13600 3.891075 5.760826 6
GTCTG 21295 3.8736734 177.77426 17
GCTTG 21005 3.820921 179.11758 59
TCGAG 16640 3.796132 5.1826816 61
AGGCG 5725 3.6916943 5.5737944 42
CATCT 1365 3.6625655 232.7732 39
TCATC 1350 3.6223173 216.34912 38
GTTCG 19840 3.6090014 4.64376 15
CGGAT 15755 3.5942347 5.8238807 4
TGGCG 6985 3.5914845 6.1145644 47
GGCGT 6970 3.583772 5.9198375 31
TCGTT 54725 3.521834 4.3302507 34
CGGTT 19315 3.513501 4.7798796 37
GACGA 12255 3.506259 5.572469 72
TCACT 1305 3.501573 198.85847 30
TACGG 15340 3.4995592 5.0061 27
TTCGT 54235 3.4903 4.290085 48
TATCG 43180 3.4850452 4.1789036 17
GCGAA 12010 3.4361625 4.937851 8
GCGCA 160 3.4300246 69.37227 11
CGTTT 52535 3.380896 4.8824434 16
AGACG 11775 3.3689265 5.2542706 56
CGAAA 26480 3.3614686 4.1656857 62
GTCGA 14655 3.3432884 4.3610106 72
CGGTG 6465 3.3241158 5.377353 64
GTCGT 18050 3.2833908 4.916102 52
GACGT 14370 3.2782702 4.842314 29
AGCGA 11345 3.2459004 4.539598 62
ACGGT 14190 3.2372062 4.430631 22
GCGAT 14160 3.2303627 4.186456 34
AACGG 11200 3.2044146 4.528068 26
CCGTG 185 3.1623235 153.98529 50
CGAAG 11015 3.1514845 4.5398164 69
AAGCG 11010 3.1500537 4.423491 5
TTCGA 38810 3.1323435 4.004782 18
CGTGG 6090 3.1313016 5.1871758 46
GTACG 13665 3.1174366 4.594729 22
TGACG 13425 3.0626848 4.360696 71
AAACG 23920 3.0364928 3.799978 71
TAGCG 13165 3.00337 4.265432 16
CAGTG 12725 2.9029915 109.92655 35
CCTGC 5 2.8413947 204.60536 58
CACAT 795 2.6752386 65.33641 12
ACGAT 25380 2.568976 8.4127245 32
TGAAC 24995 2.530006 99.68756 20
CCTAC 10 2.5214014 90.86278 47
ATCCC 10 2.5214014 90.6584 2
GAACT 21460 2.1721916 99.22687 21
CTGAA 21420 2.1681428 98.99458 19
AGTCA 21195 2.145368 98.062035 28
TATGC 25420 2.0516407 79.387794 46
CCTTC 10 2.010478 72.38603 58
CTCCT 10 2.010478 72.44426 50
AGCTC 265 2.0098374 65.52235 39
CTGCG 110 1.8803004 61.55257 56
CTTGA 23035 1.859148 78.80742 60
TCCGA 245 1.8581514 24.54277 2
GCTTC 305 1.8444724 50.12039 52
CATAC 545 1.8339686 41.137737 12
GCCGA 85 1.8222005 23.137236 1
GACAC 190 1.807221 20.582628 71
TCTGA 21300 1.7191167 78.70268 18
CGGCA 80 1.7150123 53.956207 4
AGGCC 80 1.7150122 77.24004 46
GGAAG 184055 1.5839859 9.824569 5
AACAC 370 1.5614923 12.17731 72
ACTTC 580 1.5562549 49.21624 23
CCGAT 205 1.5547795 24.542768 4
TACAC 460 1.5479369 31.479006 31
CCGGT 90 1.5384275 30.742142 26
CGCAG 70 1.5006357 30.852724 32
TGATC 18220 1.4705307 39.51109 38
CACAA 345 1.4559859 9.131494 68
TCCGG 85 1.4529594 30.741405 25
CTTCA 520 1.395263 46.323475 24
CCGGA 65 1.3934474 23.124086 3
TGCTT 21490 1.3829916 63.371777 58
TTCTG 21305 1.3710859 63.557343 55
TTCCG 225 1.3606763 17.395159 2
GTCTT 21095 1.3575712 62.774845 52
ACGCT 175 1.3272508 27.287971 32
ACAGT 12930 1.308781 48.877537 34
CCAAA 305 1.287176 7.587071 4
CATGC 165 1.2514081 49.117897 31
ACTCT 445 1.1940231 47.28619 23
TTCCA 445 1.1940231 42.463184 24
ACAAC 275 1.1605686 7.5954804 36
GATCT 14020 1.1315501 43.986034 39
CAACA 265 1.1183661 7.5955086 37
GCACT 145 1.0997223 13.643987 32
CAAAC 255 1.0761636 9.109663 1
CTCTA 400 1.0732793 47.288548 24
GCCAG 50 1.0718827 46.26448 25
GACCG 50 1.0718827 15.424824 1
AGCCG 50 1.0718827 15.446811 44
CAGCG 50 1.0718826 7.7308087 70
ACCGG 50 1.0718826 7.730937 69
CGTCA 140 1.0618008 21.831871 33
GACTC 140 1.0618008 32.72889 21
ATTCC 390 1.0464474 42.461075 23
CGACA 110 1.0462859 10.265779 1
ACGCA 110 1.0462857 17.111177 31
GTGCC 60 1.0256184 36.959816 47
ACTCG 130 0.98595786 10.910898 23
CGCTT 160 0.9675922 6.523185 4
CCGAG 45 0.9646943 15.461874 69
CAGAC 100 0.9511689 13.688058 30
GCATC 125 0.9480365 46.41072 38
TGCCA 120 0.91011506 51.850693 33
CTCGA 120 0.910115 10.911442 24
GTCTC 150 0.90711755 37.00705 39
CAACG 95 0.9036105 6.854761 50
GGACC 40 0.8575061 15.427501 34
GCTGC 50 0.85468215 18.470175 55
TCGCA 110 0.8342721 13.642978 30
AACCA 195 0.82294863 6.0696573 6
CGCTG 45 0.7692139 18.438583 16
CGCTA 100 0.7584292 27.289839 33
CTTCG 125 0.7559313 17.433275 54
TCGCT 125 0.7559313 6.5231843 3
GCAGC 35 0.7503178 7.716571 36
GAGCC 35 0.7503178 15.416058 9
CCGGG 15 0.72474974 17.423864 70
CGCAT 95 0.7205077 8.1855755 1
CCGAA 75 0.71337664 27.35985 3
GTCCG 40 0.6837457 6.164907 71
GCGCT 40 0.6837457 12.309037 57
ATCCG 90 0.68258625 27.285252 1
TGCAC 90 0.68258625 10.932488 47
ATATC 18615 0.666606 6.0970774 38
GAATC 6575 0.66552466 13.007416 38
ACCGT 85 0.6446647 8.206529 72
CATCA 190 0.63936526 6.053655 31
GCTCT 95 0.57450783 15.220764 3
CTTGC 95 0.5745078 15.251889 59
CAAGC 60 0.57070136 10.271486 38
GAACC 60 0.57070136 10.260283 20
CAGCA 60 0.57070136 10.263807 26
AGTCC 75 0.56882185 13.642097 28
CGACT 70 0.5309004 5.4658194 51
GCAAC 55 0.52314293 6.8399634 3
CCGTT 85 0.51403326 10.895494 50
GGCTC 30 0.5128093 6.1639714 61
CTGCA 65 0.49297893 5.4540496 19
CGCAA 50 0.47558448 10.259945 3
CCAAG 50 0.47558445 10.2686405 35
AAGCC 50 0.47558445 6.844534 32
TACCA 140 0.4711112 6.053655 31
CTCTT 220 0.4706876 5.384857 4
ACTGC 60 0.4550575 5.4540496 18
CACTA 135 0.4542858 9.685847 31
TGCTC 75 0.45355877 6.542136 61
AGCCA 45 0.42802605 10.259945 10
TTGCC 70 0.42332152 8.697579 2
GCTCA 55 0.41713607 5.4539495 9
CATCG 55 0.41713604 5.4570503 1
TCAGC 55 0.41713604 5.4600844 38
ACAGC 40 0.3804676 6.8542666 49
GTCCA 50 0.3792146 5.457051 29
CCTGA 50 0.37921458 5.4540496 19
CAGCT 50 0.37921453 5.460195 39
TGGCC 20 0.34187278 12.302648 35
CCGTA 45 0.34129307 5.465748 50
GGCCA 15 0.32156482 15.433144 36
CAGAT 2685 0.271777 8.049132 34
CAGGG 420 0.27083167 12.297432 34
GATCA 2635 0.26671597 8.197814 36
CTCAG 35 0.2654502 8.183581 24
GCCTG 15 0.25640464 6.1645074 67
CTGGC 15 0.2564046 12.301353 34
GGTCC 15 0.2564046 6.1501656 31
GGGCC 5 0.24158324 17.408531 46
ACTTG 2550 0.20580974 10.164409 34
CAATA 4000 0.17964241 6.7734513 36
ATCAG 1540 0.15587954 5.97374 35
TCAGA 1540 0.15587954 6.01173 36
ACAGG 540 0.15449856 5.1473846 33
ACTGA 1480 0.14980632 6.9559755 32
AATCT 4055 0.14521016 6.844849 39
GGCCT 5 0.08546821 6.158968 49
CCTGG 5 0.085468195 6.1649065 71
Produced by FastQC (version 0.10.1)