FastQC Report![[OK]](Icons/tick.png)
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]](Icons/error.png)
Per base sequence quality
Per sequence quality scores
Per base sequence content
Per base GC content
Per sequence GC content
Per base N content
Sequence Length Distribution
Sequence Duplication Levels
Overrepresented sequences
No overrepresented sequences
![[WARN]](Icons/warning.png)
Kmer Content
| 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 |