FastQCFastQC Report
Wed 10 Sep 2014
scahan_VGN_20140730_2014_RAD4_R1.fastq.gz

Summary

[OK] Basic Statistics

Measure Value
Filename scahan_VGN_20140730_2014_RAD4_R1.fastq.gz
File type Conventional base calls
Encoding Sanger / Illumina 1.9
Total Sequences 139150442
Filtered Sequences 0
Sequence length 140
%GC 49

[FAIL] 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

[FAIL] Per base GC content

Per base GC content graph

[OK] Per sequence GC content

Per sequence GC content graph

[FAIL] Per base N content

N content graph

[OK] Sequence Length Distribution

Sequence length distribution

[FAIL] Sequence Duplication Levels

Duplication level graph

[OK] Overrepresented sequences

No overrepresented sequences

[WARN] Kmer Content

Kmer graph

Sequence Count Obs/Exp Overall Obs/Exp Max Max Obs/Exp Position
AAAAA 75978740 4.2937193 9.47324 55-59
GCGCG 49813205 3.0009868 6.3267064 55-59
CGCGC 50605395 2.9771397 6.1482024 55-59
CGCGA 47468330 2.796669 15.287356 1
CCGGA 45613140 2.6873677 592.3065 6
CGGAA 45089960 2.6604292 187.34418 7
GAGAG 43998145 2.6584194 17.25436 1
CGCCG 38065250 2.239397 46.10949 4
CCGGT 38940675 2.210339 436.63806 6
CGGAT 38208305 2.1719406 145.01132 7
CGGAG 35724065 2.155337 140.14049 7
GTCGT 38787290 2.124212 10.382003 9
GAAAA 36462755 2.1070437 15.99086 9
CGGTG 33221420 1.9310383 111.312965 7
GACGA 32370485 1.9099458 21.606941 9
GCCGG 31118230 1.8747119 237.08344 5
CGGAC 31608185 1.8622445 121.012314 7
CTCGC 32939235 1.8257936 18.233976 2
CTCCG 32035315 1.7756903 51.403385 4
CGGTA 31079430 1.7667017 105.39527 7
TTCGC 32984000 1.7639835 24.624363 2
GAGAA 29757960 1.758368 14.824426 9
GATCG 30378260 1.7268438 11.154548 9
GTCGA 30352820 1.7253975 17.768368 9
GGAAA 29194820 1.7250925 52.64443 8
CGTAT 32010970 1.7144499 21.537918 1
GATTC 31927165 1.7099614 12.214139 9
CCCGG 29003365 1.7062819 283.45767 5
CGGTT 30610890 1.6764262 117.67301 7
CGGTC 29285640 1.6623029 100.17518 7
TCCGG 29216615 1.6583849 277.30466 5
GTCGC 29010380 1.6466786 9.964596 9
GAAAT 29493965 1.6420089 15.024429 9
ATTCC 30613395 1.6011065 18.85056 3
GCGAC 27142990 1.5991707 15.45383 2
ATTCG 29803555 1.5962248 24.86935 1
TGCCG 27978220 1.5880914 22.495197 4
GGAGA 26264680 1.5869427 44.693466 8
TCGAG 27619455 1.5700203 17.529572 1
TCGAC 28185570 1.5645871 17.050472 2
TCGCC 28097010 1.5573933 43.1399 3
CGAGC 26391585 1.5549004 18.36206 2
GAGCG 25336745 1.5286398 11.834173 9
CACTC 28103615 1.5234138 26.858854 2
GAAGA 25743705 1.5211695 12.652141 9
GATAA 26803230 1.4922085 9.559054 9
AACGC 25509430 1.4697901 21.034578 1
GGTCG 25244035 1.4673424 47.65733 8
GGAAG 24280495 1.4670558 53.999104 8
CGACA 25346325 1.4603925 19.496828 1
GATTT 28069545 1.4504888 10.487333 9
GGAGG 23368110 1.4437608 39.30786 8
ACCGG 24471220 1.4417592 246.10684 5
GGACG 23865050 1.4398482 55.3446 8
GAGGA 23733035 1.4339777 12.004773 9
GAAAG 24175375 1.4284985 8.96698 9
GAACG 24034955 1.4181271 10.263431 9
CCTCG 25519135 1.4145039 18.096733 1
AAACA 25005375 1.4110429 22.619608 1
GTTTC 27271625 1.4071983 16.003576 9
GATAT 26104735 1.4001673 11.957526 9
CTCGG 24667335 1.4001601 27.463724 1
ATCCG 25218020 1.3998576 103.73411 4
TCGGC 24541285 1.3930053 27.757486 2
CACAC 24621980 1.3853526 29.686049 2
GAATT 25604090 1.3733145 12.007204 9
AATGA 24651520 1.372417 41.325726 1
GAGAT 24052225 1.3692418 10.67163 9
GGATA 23860475 1.358326 35.798473 8
GGAAT 23265145 1.324435 46.21726 8
CACCG 22874125 1.3160256 74.53053 4
GAAAC 22583475 1.303107 11.254696 9
TTCCG 24256005 1.2972107 19.692755 4
GCATT 24135900 1.2926754 19.321619 1
GTGTG 22961045 1.2877079 6.456342 9
GACCG 21813545 1.2851781 95.503006 4
GACGC 21804275 1.2846321 16.023167 9
GTCCG 22597285 1.2826604 98.42665 4
GTGCG 21979655 1.2775959 8.860763 9
CACGT 22761880 1.2635168 13.154111 1
GTATG 22990455 1.2609295 6.1091585 9
GTAAT 23342235 1.2519965 8.540968 9
GACGG 20718870 1.2500299 8.181145 9
GATGA 21859115 1.2443928 11.698995 9
GAATG 21649615 1.2324663 20.861303 1
GAATC 22157540 1.2317687 10.645805 9
GATAC 22118745 1.2296121 21.06291 2
GCGTC 21616820 1.2270076 21.618876 2
CTTCC 23383670 1.2211996 16.293863 2
GGATT 22263680 1.2210689 39.7157 8
AGCCG 20639370 1.2159998 94.75117 4
GTTTT 24350150 1.212269 9.130349 9
TGCGT 22106745 1.2106907 20.92298 1
GGCCG 19968820 1.2030177 70.535774 4
ACGCC 20684855 1.1900697 22.4159 2
TTCCC 22777795 1.189558 22.036898 2
GAATA 21366730 1.1895438 13.896105 9
GGATG 20342585 1.1841686 37.702045 8
CGTCC 21130835 1.1712642 35.32613 3
AATGC 21062845 1.1709131 21.664564 2
GGAGC 19390535 1.1698877 29.86183 8
GTGAT 21268440 1.1664841 26.761528 1
ATGCC 20987640 1.1650285 21.749847 3
CATCC 21469490 1.1637975 22.076748 3
GACGT 20410580 1.1602337 8.319852 9
TACAT 22138010 1.1595303 19.78524 1
GTTCG 21129275 1.1571591 11.9057865 9
GTATC 21508840 1.1519748 21.592434 2
CGACC 19972420 1.1490808 32.665695 3
ACGTC 20604005 1.1437328 14.27457 2
GTATA 21129645 1.133321 6.6139216 9
GCCCG 19069165 1.1218481 86.573395 4
GTCTT 21665195 1.1179099 5.3574586 9
GGAAC 18868855 1.1133133 34.44854 8
GATTA 20731765 1.1119801 9.1041975 9
GTCGG 19120435 1.1114 8.396038 9
GATGC 19515710 1.1093652 9.341896 9
TCCCG 19904960 1.103315 17.805576 4
GTACG 19235430 1.0934328 8.568272 9
GGATC 19121160 1.0869371 31.652126 8
GGTTT 20496765 1.0830458 37.72856 8
GGTGG 18155725 1.080696 26.86256 8
GCACA 18714170 1.0782641 29.969423 1
GACTC 19418955 1.0779504 24.07078 2
GTAAA 19338490 1.0766262 7.670388 9
GCAGC 18272065 1.0765265 20.487997 2
CGGCC 18286065 1.075778 28.570326 3
GATCT 20045160 1.0735826 7.743685 9
GATGT 19528655 1.0710642 8.5419035 9
ACATC 19729430 1.0710382 21.853716 2
CATTC 20476000 1.0709121 18.844072 2
ATAAC 19649780 1.0682745 21.291813 1
GACAA 18499515 1.0674553 7.832619 9
TCCAC 19590905 1.061965 19.377153 1
GGTAT 19242675 1.0553795 30.868383 8
CGCCC 18331065 1.0531079 22.6674 3
GACAC 18266665 1.0524801 19.649687 2
GTGTC 19198195 1.0514022 22.639923 2
GTTGC 19053775 1.0434929 7.108731 9
ACCCG 17953310 1.0329145 127.913124 4
GCTTC 19190305 1.0262972 16.752003 1
AACAC 18165635 1.0235821 24.128609 2
GGGAA 16859240 1.018655 14.624421 1
GAGAC 17250850 1.0178467 6.507687 9
TATCC 19358980 1.0124911 51.047043 3
GTGCA 17399265 0.9890564 7.1761317 9
GAAGG 16369365 0.98905605 9.845023 9
GTTCC 18477240 0.98816234 22.638903 1
GAGCA 16681665 0.98426324 7.0327697 9
GTATT 19017945 0.982749 9.429994 9
GTCTC 18355515 0.98165244 6.152593 9
GGACA 16621315 0.98070246 28.753181 8
GATTG 17823800 0.9775602 6.90207 9
GAAGC 16539305 0.9758636 18.183088 9
CCACC 17334555 0.97390217 20.176188 2
GAGGG 15757260 0.97353673 7.7045903 9
CCAGC 16887315 0.9715843 28.106668 2
TACCG 17497375 0.971283 21.373894 4
GGTAC 17013740 0.9671414 25.8224 8
GTGGA 16517835 0.96152484 7.5929346 9
GTTAC 17765460 0.95148605 12.302267 9
TCCCC 17578150 0.95146793 45.538483 3
AGAGC 16077735 0.9486297 18.102083 2
GGTGA 16245390 0.94566554 29.965471 8
GTAAC 16901970 0.9396042 22.357594 2
GATCC 16922560 0.9393749 26.99544 3
CCCCG 16325875 0.937911 48.619286 4
AACCG 16087435 0.9269182 52.56755 4
ACACC 16438175 0.92489195 72.586105 3
GGCAG 15306275 0.9234723 20.934814 1
TGATC 17240375 0.92336345 26.033607 2
GACAT 16515070 0.91809595 6.475065 9
GTGAA 16123835 0.9178955 7.5580215 9
AGTAA 16429075 0.91465116 22.462019 1
GTTAT 17603845 0.90967566 6.798267 9
CAGCC 15591325 0.89702165 47.890663 3
TCACC 16489995 0.89387375 23.1687 2
GTTTA 17288775 0.8933945 6.1585407 9
GATCA 16033985 0.89135176 6.0602365 9
GGTGC 15273685 0.88780284 27.299587 8
GAACA 15326640 0.8843746 7.466619 9
ATGAC 15896640 0.8837165 43.868484 2
GGTGT 15752290 0.88342446 27.020927 8
GTTTG 16681560 0.8814511 5.450396 9
GAGCC 14858420 0.8754065 36.078556 3
GAGTG 14952070 0.8703796 6.0390472 9
CCACT 16045825 0.86979663 26.737965 1
GTGTA 15768855 0.8648551 6.233744 9
GATGG 14846630 0.86424184 7.217622 9
GTGTT 16334420 0.8631082 6.07677 9
GACAG 14596630 0.86124057 5.720122 9
AAGGG 14220140 0.8591974 18.798414 1
GTTCT 16583655 0.8557059 5.257517 9
TTGAC 15895590 0.85133916 18.12133 1
GAAGT 14860695 0.8459876 11.99001 9
GGTAA 14816800 0.8434888 28.733482 8
GAGTC 14783120 0.8403424 5.984416 9
GGAGT 14402030 0.8383611 26.605667 8
CTCAC 15402315 0.8349139 23.15545 1
GCTAT 15466915 0.8283801 30.809277 1
GTGAC 14485110 0.82340205 7.310667 9
GTGGT 14609310 0.8193235 6.817069 9
GAGGC 13539820 0.816897 6.450475 9
GAGTA 14295375 0.81380516 6.761789 9
CTGGA 14314605 0.8137098 14.79279 1
ACTCC 14899875 0.8076781 50.128563 3
ATACC 14849430 0.80612093 20.658762 3
GTGGC 13846020 0.8048179 7.891906 9
CTATC 15344295 0.80251956 30.001326 2
GTTGT 15177135 0.8019574 5.573062 9
GGACC 13584760 0.8003669 21.381145 2
GTTAA 14914535 0.799964 5.388537 9
ATCCC 14694430 0.7965415 22.717184 2
AGGAC 13420975 0.79187375 21.138988 1
GAGGT 13601660 0.7917705 12.108964 9
CCAAG 13673780 0.78784937 9.400137 1
GGTCC 13796540 0.78311515 38.743813 3
CAAGC 13531455 0.77964896 9.420493 2
CACCC 13778380 0.7741066 43.996765 3
TGACT 14408855 0.7717123 23.208714 1
GAGTT 13968710 0.7661248 7.1853623 9
TGGAC 13434615 0.76368695 14.787313 2
AAGCC 13211575 0.76121825 9.466416 3
GTGCC 13384300 0.75971574 5.7268257 9
AGTGT 13770980 0.75528014 22.498686 1
GATAG 13176325 0.7501001 5.5355644 9
TGTCC 14018410 0.74970424 22.114538 3
ACCAG 12879150 0.7420648 28.23868 1
GTGAG 12646515 0.73617023 6.310945 9
CAGAC 12765210 0.73549986 19.390305 1
GGTTC 13392285 0.7334376 26.695356 8
GTTGA 13372580 0.73342955 5.4632387 9
GGTCA 12816200 0.7285334 17.585703 8
GAACT 12972260 0.7211461 10.668294 9
GGACT 12671755 0.72032243 20.965761 8
GAGCT 12597590 0.71610653 5.1072702 9
GGTTG 12530375 0.7027321 23.446531 8
TGACC 12376875 0.687043 44.217213 3
TAACC 12486875 0.6778665 36.21503 3
GAACC 11659610 0.6717979 13.993464 3
GGTTA 12079890 0.66253096 29.224081 8
GTAAG 11622400 0.66163844 5.2794714 9
GGTAG 11324845 0.6592341 19.493908 8
GGGGC 10569205 0.65204746 21.789946 2
GACCC 11129395 0.64031166 60.60291 3
GTAGA 11218440 0.63864183 5.075802 9
GTACT 11866340 0.6355398 7.116172 9
GGGGT 10340070 0.61547923 16.532244 1
TGGGG 10256035 0.61047715 20.949945 1
GGTCT 10902010 0.597056 19.329489 8
AGGGC 9852370 0.59442234 20.044794 2
GTAGC 10408690 0.59167916 6.334956 9
GGGCC 9715960 0.58533615 41.154114 3
AACCC 9970505 0.5609892 21.915096 3
AGCCC 9644415 0.5548758 45.799423 3
AGACC 9358035 0.5391868 21.511393 2
CCTAA 9732245 0.52832776 14.566304 1
CTAAC 9554195 0.5186621 14.621975 2
GGCCC 8681045 0.51071006 16.696693 3
AGGCC 8229900 0.4848771 16.616488 2
TAGGC 8187915 0.4654398 14.901367 1
GGGTC 7625665 0.44325173 16.234503 2