FastQCFastQC Report
Mon 6 Feb 2012
3.fastq

Summary

[OK] Basic Statistics

Measure Value
Filename 3.fastq
File type Conventional base calls
Encoding Sanger / Illumina 1.9
Total Sequences 8379883
Filtered Sequences 0
Sequence length 50
%GC 49

[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

[FAIL] Per base GC content

Per base GC content graph

[FAIL] Per sequence GC content

Per sequence GC content graph

[OK] Per base N content

N content graph

[OK] Sequence Length Distribution

Sequence length distribution

[FAIL] Sequence Duplication Levels

Duplication level graph

[FAIL] Overrepresented sequences

Sequence Count Percentage Possible Source
TAGCTTATCAGACTGATGTTGACAGATCGGAAGAGCACACGTCTGAACTC 1639302 19.56234949819705 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TAGCTTATCAGACTGATGTTGAAGATCGGAAGAGCACACGTCTGAACTCC 469918 5.607691658702156 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATG 454115 5.419109073479905 TruSeq Adapter, Index 4 (100% over 49bp)
TTCACAGTGGCTAAGTTCCGAGATCGGAAGAGCACACGTCTGAACTCCAG 135044 1.6115260797793955 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TAGCTTATCAGACTGATGTTGACAAGATCGGAAGAGCACACGTCTGAACT 111917 1.3355437062784767 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TTATCAGACTGATGTTGACAGATCGGAAGAGCACACGTCTGAACTCCAGT 67556 0.8061687734781022 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TAGCTTATCAGACTGATGTTGAGATCGGAAGAGCACACGTCTGAACTCCA 53641 0.6401163357531364 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAGCACCATTTGAAATCAGTGTTAGATCGGAAGAGCACACGTCTGAACTC 52275 0.6238153921719433 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
TAGCTTATCAGACTGATGTTGACAGATCGGAAGAGAACACGTCTGAACTC 50228 0.5993878434818243 Illumina Multiplexing PCR Primer 2.01 (96% over 27bp)
TGAGGTAGTAGATTGTATAGTAGATCGGAAGAGCACACGTCTGAACTCCA 49146 0.5864759686978923 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
CGCGACCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAA 48640 0.5804376982351662 TruSeq Adapter, Index 4 (100% over 40bp)
TGAGGTAGTAGATTGTATAGTTAGATCGGAAGAGCACACGTCTGAACTCC 42904 0.5119880552031574 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TGAGGTAGTAGTTTGTGCTGTTAGATCGGAAGAGCACACGTCTGAACTCC 39023 0.46567475942086545 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TAGCTTATCAGACTGATGTTGACTAGATCGGAAGAGCACACGTCTGAACT 31973 0.3815447065311055 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TAGCTTATCAGACTGATGTTGAAAGATCGGAAGAGCACACGTCTGAACTC 26733 0.31901400055346835 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
ATTCTACAGTCCGACGATCAGATCGGAAGAGCACACGTCTGAACTCCAGT 26729 0.3189662671901266 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
AAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTAT 25555 0.3049565250493354 TruSeq Adapter, Index 4 (100% over 48bp)
AAGCTGCCAGTTGAAGAACTGTAGATCGGAAGAGCACACGTCTGAACTCC 24936 0.29756978707220616 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TTCACAGTGGCTAAGTTCCGCAGATCGGAAGAGCACACGTCTGAACTCCA 22859 0.2727842381570244 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GTTCTACAGTCCGACGATCAGATCGGAAGAGCACACGTCTGAACTCCAGT 22615 0.2698725029931802 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
TTATCAGACTGATGTTGAAGATCGGAAGAGCACACGTCTGAACTCCAGTC 22264 0.2656839003599453 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TCAGTGCACTACAGAACTTTGTAGATCGGAAGAGCACACGTCTGAACTCC 21592 0.2576646953185385 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CAGAGTTCTACAGTCCGAAGATCGGAAGAGCACACGTCTGAACTCCAGTC 20815 0.24839248948941173 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
CTTATCAGACTGATGTTGACAGATCGGAAGAGCACACGTCTGAACTCCAG 20687 0.24686502186247708 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TCTACAGTCCGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGAC 20097 0.23982435076957517 TruSeq Adapter, Index 4 (100% over 37bp)
TAGCTTATCAGACTGATGTTAGATCGGAAGAGCACACGTCTGAACTCCAG 18945 0.22607714212716334 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
TTCACAGTGGCTAAGTTCCGTAGATCGGAAGAGCACACGTCTGAACTCCA 18151 0.21660206950383434 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGC 17154 0.2047045286909137 TruSeq Adapter, Index 4 (100% over 50bp)
TGAGGTAGTAGGTTGTATAGTAGATCGGAAGAGCACACGTCTGAACTCCA 16548 0.19747292414464498 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
TAGCCTATCAGACTGATGTTGACAGATCGGAAGAGCACACGTCTGAACTC 15595 0.1861004503284831 Illumina Multiplexing PCR Primer 2.01 (100% over 27bp)
AGAGTTCTACAGTCCGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCA 15391 0.183666048798056 Illumina Multiplexing PCR Primer 2.01 (100% over 33bp)
TTCAAGTAATCCAGGATAGGCTAGATCGGAAGAGCACACGTCTGAACTCC 13974 0.16675650483425605 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CATTGCACTTGTCTCGGTCTGAAGATCGGAAGAGCACACGTCTGAACTCC 12859 0.153450829802755 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
CAAGGGTTTGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACC 12770 0.152388762468402 TruSeq Adapter, Index 4 (100% over 38bp)
TAGCNTATCAGACTGATGTTGACAGATCGGAAGAGAACACGTCTGAACTC 12703 0.1515892286324284 Illumina Multiplexing PCR Primer 2.01 (96% over 27bp)
TGAGGTAGTAGGTTGTATAGTTAGATCGGAAGAGCACACGTCTGAACTCC 12226 0.14589702505392976 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
TTCACAGTGGCTAAGTTCCGAAGATCGGAAGAGCACACGTCTGAACTCCA 12130 0.14475142433372876 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)
GGGGATGTAGCTCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGA 11698 0.13959622109282432 TruSeq Adapter, Index 2 (97% over 36bp)
TGAGAACTGAATTCCATAGGTTAGATCGGAAGAGCACACGTCTGAACTCC 11414 0.13620715229556307 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
AGTTCTACAGTCCGACGATCAGATCGGAAGAGCACACGTCTGAACTCCAG 11018 0.13148154932473402 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
ACTGGACTTGGAGTCAGAAGGCAGATCGGAAGAGCACACGTCTGAACTCC 10932 0.13045528201288728 Illumina Multiplexing PCR Primer 2.01 (100% over 28bp)
GTTCTACAGTCCGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTG 10533 0.12569387901955195 TruSeq Adapter, Index 2 (97% over 35bp)
AGTTCTACAGTCCGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACT 10380 0.12386807787173161 Illumina Multiplexing PCR Primer 2.01 (100% over 34bp)
TGGCTCAGTTCAGCAGGAACAGATCGGAAGAGCACACGTCTGAACTCCAG 10231 0.12209001008725302 Illumina Multiplexing PCR Primer 2.01 (100% over 30bp)
CTACAGTCCGAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACC 9687 0.11559827267278075 TruSeq Adapter, Index 4 (100% over 38bp)
TAGCCTATCAGACTGATGTTGACAGATCGGAAGAGAACACGTCTGAACTC 9661 0.11528800581105966 Illumina Multiplexing PCR Primer 2.01 (96% over 27bp)
TAGCTTATCAGACTGATGTTGACGAGATCGGAAGAGCACACGTCTGAACT 9472 0.11303260439316397 Illumina Multiplexing PCR Primer 2.01 (100% over 26bp)
TATCAGACTGATGTTGACAGATCGGAAGAGCACACGTCTGAACTCCAGTC 9379 0.11192280369546927 Illumina Multiplexing PCR Primer 2.01 (100% over 32bp)
TAGCTTATCAGACTGATGTAGATCGGAAGAGCACACGTCTGAACTCCAGT 9271 0.11063400288524314 Illumina Multiplexing PCR Primer 2.01 (100% over 31bp)
GGGGATGTAGCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACC 9236 0.1102163359560032 TruSeq Adapter, Index 4 (100% over 38bp)
TAGCGTATCAGACTGATGTTGACAGATCGGAAGAGAACACGTCTGAACTC 9113 0.10874853503324569 Illumina Multiplexing PCR Primer 2.01 (96% over 27bp)
AGGGTTTGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAA 8614 0.10279379795636766 TruSeq Adapter, Index 4 (100% over 40bp)
AAGTTCTACAGTCCGACGATCAGATCGGAAGAGCACACGTCTGAACTCCA 8509 0.1015407971686478 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp)

[FAIL] Kmer Content

Kmer graph

Sequence Count Obs/Exp Overall Obs/Exp Max Max Obs/Exp Position
GTCTG 8034115 32.166683 422.5921 41
CGTCT 7962415 32.13423 425.15698 40
TCTGA 8133000 26.682295 345.23114 42
GATCG 8142155 22.738329 297.9306 25
ATCGG 8129450 22.702848 298.12616 26
TCGGA 8096325 22.610344 289.3002 27
CACGT 7960025 22.407246 295.00955 38
ACGTC 7959255 22.405077 295.68176 39
AGATC 8106665 18.55092 243.30579 24
CTGAA 8042590 18.404295 240.6601 43
GAACT 7920820 18.12564 239.67212 45
TGAAC 7902335 18.08334 240.18643 44
AACTC 7520090 17.346073 241.3583 46
GGAAG 8181000 15.809627 200.50742 29
CGGAA 8048715 15.678215 201.67036 28
ACACG 7947435 15.604575 206.13411 37
AGCAC 7906600 15.524397 191.49529 34
GAGCA 7904590 15.397472 190.79446 33
AGAGC 7903575 15.3954935 191.15962 32
CACAC 7773255 15.384478 191.8779 36
GCACA 7795180 15.305626 191.08784 35
TGTTG 3241160 15.124014 635.54767 17
ACTCC 5231890 14.845252 142.40918 46
GAAGA 9194440 14.559437 164.04391 30
AAGAG 8076305 12.788866 163.75119 31
ACTGA 5532835 12.661087 314.73465 12
ATGTT 3265250 12.484959 523.76917 16
CTCCA 4113035 11.670549 82.41818 25
TTATC 3021160 11.643921 506.42615 5
CTTAT 2892740 11.148975 505.06152 4
CTGAT 3375350 11.07366 451.9569 13
TGATG 3330490 10.839909 447.87555 14
GATGT 3328800 10.834409 448.26587 15
GTTGA 3271325 10.647342 440.34103 18
TCCAG 3718555 10.4676285 81.69221 26
CAGTC 3467395 9.760619 75.06871 28
GACTG 3438470 9.602502 385.31918 11
GCTTA 2893645 9.493308 428.829 3
TAGCT 2885695 9.467227 427.34073 1
AGCTT 2841275 9.321497 428.13446 2
CCAGT 3263680 9.187167 75.31129 27
TCAGA 3806275 8.710106 325.51318 8
TATCA 3201785 8.607334 370.13382 6
TTGAC 2502190 8.209045 339.85016 19
TCACT 2482155 8.208356 87.4634 31
ATCAG 3571395 8.172617 316.14154 7
AGACT 3323355 7.605013 315.04807 10
CAGAT 3272555 7.4887652 217.3381 23
GTCAC 2606740 7.337899 74.94534 30
CACTG 2329405 6.55721 73.6582 32
CAGAC 3313065 6.505114 270.2218 9
AGTCA 2779685 6.360904 60.867424 29
CTGAC 2064510 5.8115377 71.080315 34
TGACA 2427700 5.5554376 228.11673 20
TGACC 1820145 5.1236567 69.771324 35
GACAG 2326640 4.532098 181.44287 21
TAGAT 1694125 4.5182166 38.202534 22
ACAGA 2454020 3.9169888 148.59496 22
TCTCG 917845 3.7041833 114.4571 42
AAGAT 1767000 3.287071 54.467335 22
CTCGT 814490 3.2870696 114.36352 43
ATCTC 968495 3.2027614 93.826355 41
GACCA 1607300 3.1558902 48.47183 36
CCAAT 1240700 2.8618371 62.186005 38
AATCT 1020275 2.7427974 74.66969 40
CGTAT 797420 2.616131 93.22125 45
CAATC 1109255 2.5586424 62.469967 39
TCGTA 758150 2.4872963 93.381996 44
GAGAT 1081415 2.4550524 23.89427 20
ACCAA 1455150 2.3411908 42.521214 37
GTATG 713480 2.3221984 92.829765 46
TTGAA 847880 2.2612884 75.307724 19
GTAGA 939885 2.133748 19.842354 20
TCCGA 752330 2.1177878 26.865759 17
ACAGT 836885 1.9150895 32.750908 4
TGAAG 814585 1.8492892 61.71444 20
AGTTC 563440 1.8485025 42.579052 14
GTCCG 526070 1.8072301 15.003442 9
TGGCT 373145 1.4939837 52.4919 8
AGTCC 530185 1.4924557 12.06533 8
GTTCT 316760 1.4898818 12.670959 5
TTGTA 384035 1.4683902 38.172394 13
TTAGA 529720 1.4127586 22.446922 21
GTAGT 432155 1.406556 42.02477 5
TTTGT 250120 1.371097 26.391283 12
TGTAG 417600 1.3591832 10.910873 20
GGTAG 488900 1.3545165 35.84168 4
TCTAC 403535 1.3344688 14.202519 3
TTCTA 343220 1.322812 15.884169 2
TACAG 568790 1.3015931 9.8654175 5
AGTAG 539325 1.2243878 31.309778 7
TAGTA 453220 1.2087337 36.64927 6
TTCCG 299230 1.2076143 49.598072 16
GTTCC 299175 1.2073925 51.7686 15
CTACA 505575 1.166175 9.803233 4
CAGTG 416050 1.1618892 33.968216 5
GTGGC 337625 1.150667 46.030636 7
GTTAG 344415 1.1209844 24.908375 20
GTTTG 231145 1.0785768 22.609715 11
GGCTA 368515 1.0291396 36.67781 9
CGATC 335180 0.9435222 9.069971 15
TGAGA 415140 0.9424601 8.731783 20
AGTGG 334700 0.92729944 36.587177 6
TGAGG 334035 0.925457 33.136253 1
TTCAC 263525 0.8714632 37.894794 1
CGAGA 443040 0.8630044 16.972496 19
AAGTT 323130 0.86178493 34.307125 13
GAGGT 307470 0.8518577 33.664604 2
TAGTT 221690 0.8476504 17.209414 9
TAAGT 310275 0.82750076 34.433 12
TGTAT 215660 0.82459426 33.547543 14
GACGA 416500 0.8113067 6.653523 13
TGCTG 199600 0.7991508 14.169627 16
ATTGT 203520 0.7781759 26.284132 12
GATTG 236515 0.76979697 22.749147 11
CCGAC 316575 0.7646318 8.246223 11
CTAAG 327780 0.75007683 29.749979 11
TCACA 323110 0.7452956 28.184055 2
GTGCT 183675 0.73539096 14.271744 15
GCTAA 317855 0.72736484 30.037527 10
GATCA 316630 0.72456163 7.152901 16
GCTGT 179655 0.71929586 14.154869 17
AGAGA 452370 0.7163299 10.959717 32
AGGTA 313170 0.7109656 27.445053 3
TGTTA 185200 0.7081278 12.141398 20
ACGAT 304965 0.697868 7.44994 14
CCGAG 289745 0.6942834 20.34164 18
CGACG 288140 0.69043756 8.047684 12
CACAG 349985 0.6871861 23.500603 3
CTCAG 241680 0.6803224 12.343973 7
TCAGT 202165 0.66325164 10.84354 16
AGAAC 411835 0.6573512 10.821349 34
CTAGA 272685 0.6239999 5.3843904 23
TATAG 231505 0.6174218 22.657759 16
GAGTT 186090 0.60567623 8.806371 2
ATAGT 224950 0.5999397 21.719648 17
GTATA 219000 0.58407104 22.854464 15
AGATT 216075 0.5762701 17.599386 10
TTGTG 121600 0.56741416 17.241007 13
CTGTA 172130 0.5647145 6.1208124 19
GAACA 350050 0.55873287 10.847012 35
TTGAG 166650 0.54240394 11.313151 19
TTTGA 141410 0.54069304 12.733789 9
AGTTT 139870 0.53480476 17.102818 10
GTGTT 109445 0.51069605 14.692799 19
CAAGA 315885 0.50420046 11.162137 23
TGACT 153225 0.50269204 6.7117147 20
CTGTT 103785 0.4881531 13.599921 18
GAGAA 302000 0.47821835 10.857828 33
GACCT 168130 0.4732812 10.656031 4
ACAAG 290190 0.46318734 11.2068405 22
TGTGC 115105 0.460853 14.454785 14
GATAG 198050 0.44961756 6.3869224 15
TTCAG 132525 0.43478057 5.8632035 9
TTGGA 133045 0.433028 5.254532 8
ACCTC 151515 0.42991698 10.792677 5
TGAAA 230880 0.4294957 6.887491 11
GTTGT 89370 0.4170214 11.119963 12
TAGGT 126970 0.41325548 8.489203 9
AACAC 253165 0.40731716 10.834216 36
AGAGT 178125 0.40438333 6.29116 2
AGGTT 122780 0.3996181 8.770948 10
GGTTG 99045 0.39341047 10.367194 11
CAGTT 119150 0.39090067 5.811419 6
AGTGT 118850 0.3868269 10.664869 18
GTAGG 136720 0.3787881 7.8533626 8
TAGCA 162945 0.3728759 12.756362 1
GCTCA 130625 0.36770567 5.0828624 3
ATTTG 95735 0.36605087 12.565356 8
ATAGG 159070 0.3611243 8.763624 16
GACAA 220910 0.35260588 11.450323 21
GGACT 123875 0.3459416 5.119179 4
TTGTC 72650 0.3417095 5.880562 9
GCACC 137640 0.33244544 8.196531 3
CATTT 86005 0.33147386 12.84625 7
CCTCA 115400 0.32744226 12.128694 6
AGTTA 121465 0.3239461 10.752907 19
ACTTG 98030 0.32161134 5.1322894 6
TCGGG 88030 0.30001694 5.9978294 27
AAATC 157480 0.29529274 6.8709545 13
CAAGT 127610 0.29201692 5.198702 3
CCATT 86120 0.2847943 10.961215 6
CGACC 112835 0.2725333 8.764535 3
CAGGA 139715 0.272153 5.2877746 12
ACTTT 69720 0.26870945 5.9509726 16
GGCTC 77480 0.26617026 5.6256485 2
CGCGA 111020 0.26602477 8.444119 1
GAAAT 142655 0.2653747 6.756305 12
CTTGT 55230 0.25977448 5.8720226 8
AGCGT 92410 0.25807035 5.6701665 2
CTGCC 74495 0.25795975 5.4431667 4
CTTTG 53825 0.25316608 6.7977996 17
GGATA 111180 0.25240332 6.1058064 14
CACCA 127100 0.2515506 6.6406693 4
CTATC 75995 0.25131145 9.261874 5
CCTAT 74310 0.24573925 9.187272 4
GCGAC 102445 0.24547745 8.533785 2
AGCCT 86110 0.24239722 7.8595657 2
CTTGG 60460 0.24206749 6.2824965 7
TAGCC 84235 0.23711914 8.732288 1
GTTCA 71050 0.23309688 5.7638154 8
AGGAT 101450 0.23031405 6.04009 13
AGTTG 70725 0.23019212 5.254438 9
GTAGC 79190 0.22115129 5.1635737 7
ATTCT 57150 0.22026312 5.947487 1
TCAAG 96250 0.22025412 5.2279296 2
GCCTA 75910 0.2136845 7.8791556 3
TCCGT 52775 0.21298616 5.4952226 17
ACCAT 86515 0.19955818 7.710646 5
GCGTA 71450 0.19953604 5.652652 3
GTAAT 71910 0.19178334 6.923974 6
TATGC 56115 0.18409896 5.8377404 46
TTCAA 68255 0.18348937 6.8050323 1
TCAGC 64850 0.18255094 5.030059 10
AATCA 96400 0.18076088 6.1593046 14
TAGCG 63545 0.17746003 5.880013 1
GCTGC 50290 0.17276332 5.6702986 3
TCCGC 48465 0.16782361 5.2830596 17
GTATC 51030 0.16741638 6.6605864 5