# HG changeset patch # User fubar # Date 1370681168 14400 # Node ID 431f07da87b62c5fd6b1e5d519e91b869fe6ed1b # Parent 9cbae8e9e3da8eea650c3ceba4c16939b5aca0b3 Uploaded diff -r 9cbae8e9e3da -r 431f07da87b6 fastqc/test-data/FastQC_1000gsample.fastq_html.html --- a/fastqc/test-data/FastQC_1000gsample.fastq_html.html Thu Jun 06 04:14:45 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1810 +0,0 @@ - - -1000gsample.fastq FastQC Report - - - - - -
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FastQCFastQC Report
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-Wed 5 Jun 2013
-1000gsample.fastq -
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Summary

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[OK] Basic Statistics

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MeasureValue
Filename1000gsample.fastq
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences5000
Filtered Sequences0
Sequence length54
%GC43
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[WARN] Per base sequence quality

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Per base quality graph

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[WARN] Per sequence quality scores

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Per Sequence quality graph

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[WARN] Per base sequence content

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Per base sequence content

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[OK] Per base GC content

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Per base GC content graph

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[WARN] Per sequence GC content

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Per sequence GC content graph

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[OK] Per base N content

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N content graph

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[OK] Sequence Length Distribution

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Sequence length distribution

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[OK] Sequence Duplication Levels

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Duplication level graph

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[WARN] Overrepresented sequences

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SequenceCountPercentagePossible Source
CGGAAGAGCGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGTTCAGCAGGAAT70.13999999999999999Illumina Paired End PCR Primer 2 (96% over 33bp)
CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGAC70.13999999999999999Illumina Paired End PCR Primer 2 (100% over 35bp)
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[FAIL] Kmer Content

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Kmer graph

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SequenceCountObs/Exp OverallObs/Exp MaxMax Obs/Exp Position
CCCCC11809.95745929.63803150
AAAAA21754.1332177.12965947
CTCCC5553.66894211.5627211
CCTCC5253.470620611.5627214
CTGGG4653.09459428.33113939
GGGGG3502.986570812.81857241
TGGAA8002.92615966.39764617
CCCAG4552.8559999.42934340
GAATG7752.834717510.05344520
GTGTG5302.7631727.824055733
GGGAG4352.74877296.322054443
TGTGT6702.73036386.10957627
ATGGA7352.6884096.39764620
GGAAT7302.67012077.311595419
GCTGG4002.66201668.32279931
GGAGG4202.65398747.910485740
GCAGG4052.553506414.1787716
CCTGG3752.49008666.63677747
CAGCC3902.44799926.27993738
GGCTG3652.42908989.9773724
TGGGA4902.42024477.4050620
CCAGC3852.41661456.28622941
AATGG6602.41408185.483696518
GCCTG3602.39048278.2959715
GCCTC3602.38516266.628634531
CCCTC3602.3798548.26735234
CTGTG4502.34086789.0986444
GGAAG5002.339722914.0310372
CAGCA5002.3293210.4764914
CAGGA4952.311170613.9998117
TCCCA4702.3059947.37046939
CTGCC3452.2857818.27750810
GGTGG3402.26776085.00983242
CCAGG3602.2647326.30025141
TTCCT5552.25166277.09614561
TCCCC3352.21458658.26735329
CAGGC3502.20182286.30025142
CTCCT4252.20098976.470133315
GGCAG3402.14368446.30167616
CCCCA3402.1294036.2659631
CTCTG4102.12804415.192845348
TGGTG4052.11148056.52004633
TTCCA5452.0947786.729583733
CCCCT3152.08237226.60726812
CTCAG4202.06527196.14959646
AGGGA4402.05895617.022541531
CAGAG4402.0543745.839093738
AGCAG4402.054373510.49985715
CCCTG3102.053896.62200624
CTTCC3902.01973186.470133317
AGGAA5802.009866710.39045518
AGAGC4302.007683510.4998585
TCTCC3851.99383785.18128829
TCCTC3851.99383785.18128848
TCAGC4051.991512212.28689444
TGCTG3801.97673276.505534647
CACCC3151.97282956.2596949
TCCTG3801.97233366.48456538
CAGGG3101.9545366.301676321
GATGG3951.95101346.17088271
TGGCT3751.95072339.09864145
AAGAG5601.94056079.5245844
TGTGG3701.9290076.520046730
CTGAG3901.92203026.16331335
CCTGT3701.92043016.48456536
CAGAA5551.91895436.04761036
TCCCT3701.91615586.476609733
CCCAC3051.91019996.2596944
CACCA4051.88254996.975756633
AAAGA7301.87329825.139934542
CAGTG3801.87274746.16331330
GAAGA5401.87125527.79284226
TCTCT4601.86624325.0686768
TTTCC4601.86624295.07374938
GAGGC2951.85996156.30167622
TCTGT4551.85007555.085067349
CCTGC2751.82199929.933016
CCTCT3501.81257997.76415972
TGCCT3451.79067135.18765212
TTCCC3451.78668576.47013318
GAGGG2801.7693256.328388741
CACAC3801.76634325.81313133
TCTGC3401.76471955.198048642
CTGGC2651.75966086.643420743
TTCAG4551.75275249.625512
AGCCA3751.746995.831935439
CTCTC3351.73489795.17610653
GGGTG2601.73417038.33302228
TGGGG2601.73417038.34972139
GTGGG2551.70082086.673090531
GGCCA2701.6985496.29394543
GCCCC2001.69146946.346058432
CTTTG4151.68743135.07998132
ACACA4851.67319155.172128714
GTGGT3201.66833025.21603731
CTCAC3401.66816597.36309231
TGCTT4101.66710085.09016240
GGGGC1951.66024348.52669440
AGTGG3351.6546576.17088273
TTCTG4051.64677045.085066349
AGAAG4751.64601155.195227622
ACTCC3351.64363416.129773610
GGCTC2451.62685628.30427546
TGGCA3301.62633318.63728440
TCCTT4001.62282016.094640
TCTGG3101.6125985.20442843
GGGGA2551.61134976.31573257
CTGCT3101.6090096.48456533
CCCAA3451.60365365.807317710
TGGCC2401.59365516.643420749
GTGCT3051.58658835.22010450
GCTTT3901.58577886.108194441
CCACA3351.55717095.81313130
CCTTC3001.55363996.470133317
CCACT3151.54550656.13590932
TCTTC3801.54167915.073749549
GTTCA4001.54088147.70040111
AGGCA3301.54078035.83325436
AAAAG6001.53969725.78242741
GCACA3301.53735115.820271518
ATGCC3051.499780812.28689322
GAAGG3201.49742265.84626538
GAGAG3201.49742265.85798141
TGTGC2851.48254995.204428729
TTGGC2851.48254955.19922315
GGGAT3001.48178267.4050621
AGCTG3001.47848466.163312430
AACAG4251.46946935.183665310
GAGTG2951.45708626.177060633
GGGAC2301.45013956.314304440
GTGTT3551.44668516.13411250
TTTGG3551.44668516.10957533
TCTTT4551.44611575.55909161
GAGAT3951.44479136.39764627
CAAAA5601.43385235.12336231
GGTTC2751.430530310.39844610
CCCTT2751.42416985.18647939
CTGTT3501.42313485.079981310
ATGGT3651.40919046.759639347
TGTTG3451.40593365.101516240
CTGTC2701.40139475.19804839
GAGAC3001.40070945.85668150
CTTCT3451.39968247.124644850
GGCCC1651.3985756.3538532
TGAGT3601.38988675.793977332
GGCAC2201.38400296.287650617
CCTTT3401.37939725.0686768
CCTTG2651.37544325.18765218
TTGAA4751.35804866.42951637
GAGCG2151.355565312.6033536
AAGGA3901.35146215.195227644
TTCTT4201.33487587.9415584
GGGGT2001.33397738.33302245
CAGAT3651.33208935.476969734
CTTGG2551.32649185.199223518
TGGTT3201.30405415.09131325
TTGGG2501.30338296.51352556
CTGGT2501.30048235.20442848
GCTCC1951.29196318.27750826
TGATG3301.27406285.793977346
TGTCC2451.27163615.18765221
GGCTT2401.24846285.1992234
GACAG2651.23729325.83325427
GGTGT2351.22517995.2108227
AATGC3351.222602210.03106821
TTTGC3001.21982995.07998139
GTCCT2301.19378095.192845347
GGGCC1401.18931666.374400643
ATCCC2401.17752876.13590943
GCTCT2251.16782927.78926847
AGCCC1851.16123036.279936331
GATCG2351.15814636.163312429
ACCCT2301.1284656.12977310
GTTGG2151.12090955.216037347
AGCTC2251.10639566.143446425
CCCAT2251.10393326.12977321
CGGAA2351.09722229.3332061
TCTTG2651.07751645.079981321
ATGCA2951.07661995.471491337
GCTTG2051.06639535.1992232
AGCGG1651.040317412.6033527
TTGCC2001.03807025.18765163
AACCT2851.03780945.459314313
AACCA3001.03496385.172128722
CCGAG1601.006547612.57530125
GTTCC1900.98616686.484565327
ACTCA2700.9831885.459315311
CTCAT2550.98012585.76244744
GAACC2100.97831445.82027225
GGCGG1100.9365474610.63705144
GCGGG1100.936547466.388619436
ATCGG1900.936373536.16331230
GTCTG1800.93634715.209642441
GCGGT1400.9317058313.3031628
CGGGG1050.89397716.388619446
GGGCG1050.89397718.51815943
TCGGA1700.837807957.39597531
CTTGT2050.833550455.085067338
TGCCG1250.8300288314.9327523
AGGCG1250.78811936.301676315
CGGTT1500.7802892310.3984469
GTGAC1500.73924246.16331332
GCCGA1150.72345612.57530124
CCCGC850.71887456.346058430
CCCCG850.718874510.57676429
CGAGA1350.63031929.33320626
CGGGA900.56744596.30167624
CACGG850.53472846.287650637
CGCCT800.53003616.628634530
CCGCA750.470769056.279936336
CGTTG400.208077135.204427746
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Files created by FastQC

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1000gsample_fastqc.zip (312.4 KB)
duplication_levels.png (14.5 KB)
fastqc_data.txt (15.0 KB)
fastqc_report.html (25.3 KB)
kmer_profiles.png (186.7 KB)
per_base_gc_content.png (12.1 KB)
per_base_n_content.png (7.4 KB)
per_base_quality.png (9.6 KB)
per_base_sequence_content.png (23.9 KB)
per_sequence_gc_content.png (29.6 KB)
per_sequence_quality.png (21.9 KB)
rgFastQCSBQEN1.log (1.2 KB)
sequence_length_distribution.png (18.9 KB)
summary.txt (509 B)
-FastQC documentation and full attribution is here
-FastQC was run by Galaxy using the rgenetics rgFastQC wrapper - see http://rgenetics.org for details and licensing -
Produced by FastQC (version 0.10.1)
diff -r 9cbae8e9e3da -r 431f07da87b6 fastqc/test-data/fastqc_data.txt --- a/fastqc/test-data/fastqc_data.txt Thu Jun 06 04:14:45 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,558 +0,0 @@ -##FastQC 0.9.1 ->>Basic Statistics pass -#Measure Value -Filename 1000gsample.fastq -File type Conventional base calls -Encoding Sanger / Illumina 1.9 -Total Sequences 5000 -Sequence length 54 -%GC 43 ->>END_MODULE ->>Per base sequence quality warn -#Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile -1 28.9946 31.0 27.0 33.0 22.0 34.0 -2 28.486 30.0 26.0 32.0 21.0 33.0 -3 28.5272 30.0 26.0 32.0 21.0 34.0 -4 28.6252 30.0 26.0 32.0 22.0 33.0 -5 28.4804 30.0 26.0 32.0 21.0 33.0 -6 28.5128 30.0 26.0 32.0 22.0 33.0 -7 28.4102 30.0 26.0 32.0 21.0 33.0 -8 28.4674 30.0 26.0 32.0 22.0 33.0 -9 28.182 30.0 26.0 32.0 21.0 33.0 -10 28.0908 30.0 26.0 32.0 21.0 33.0 -11 28.1876 30.0 26.0 32.0 21.0 33.0 -12 28.1742 30.0 26.0 32.0 21.0 33.0 -13 27.923 30.0 25.0 32.0 20.0 33.0 -14 27.8984 29.0 25.0 32.0 21.0 33.0 -15 27.6112 29.0 25.0 32.0 20.0 33.0 -16 27.6638 29.0 25.0 32.0 20.0 33.0 -17 27.5734 29.0 25.0 32.0 20.0 33.0 -18 27.6348 29.0 25.0 32.0 20.0 33.0 -19 27.6526 29.0 25.0 32.0 20.0 33.0 -20 27.2716 29.0 24.0 32.0 19.0 33.0 -21 27.2642 29.0 25.0 31.0 19.0 33.0 -22 26.881 28.0 24.0 31.0 19.0 33.0 -23 26.8124 28.0 24.0 31.0 19.0 33.0 -24 26.8204 28.0 24.0 31.0 19.0 33.0 -25 26.6606 28.0 24.0 31.0 18.0 33.0 -26 26.3806 28.0 23.0 31.0 18.0 33.0 -27 25.947 28.0 23.0 31.0 17.0 33.0 -28 25.7446 27.0 22.0 31.0 16.0 33.0 -29 25.6856 27.0 22.0 31.0 16.0 33.0 -30 25.5228 27.0 22.0 31.0 16.0 33.0 -31 25.354 27.0 22.0 30.0 16.0 32.0 -32 25.1656 27.0 22.0 30.0 16.0 32.0 -33 25.0164 26.0 21.0 30.0 15.0 32.0 -34 24.75 26.0 21.0 30.0 15.0 32.0 -35 24.3926 26.0 21.0 30.0 15.0 32.0 -36 24.1122 25.0 20.0 30.0 14.0 32.0 -37 23.8612 25.0 20.0 29.0 13.0 32.0 -38 23.7544 25.0 20.0 29.0 13.0 32.0 -39 23.485 25.0 19.0 29.0 13.0 32.0 -40 23.1984 24.0 19.0 29.0 13.0 32.0 -41 23.0976 24.0 19.0 29.0 13.0 32.0 -42 22.9212 24.0 19.0 28.0 13.0 31.0 -43 22.5172 24.0 18.0 28.0 12.0 31.0 -44 22.3234 23.0 18.0 28.0 12.0 31.0 -45 22.1372 23.0 18.0 28.0 11.0 31.0 -46 22.2166 23.0 18.0 28.0 11.0 31.0 -47 22.075 23.0 18.0 28.0 11.0 31.0 -48 21.4592 22.0 17.0 27.0 11.0 31.0 -49 21.0954 22.0 16.0 27.0 10.0 30.0 -50 20.9356 22.0 16.0 27.0 10.0 30.0 -51 20.6152 21.0 15.0 27.0 9.0 30.0 -52 20.6588 21.0 16.0 27.0 9.0 30.0 -53 19.5852 20.0 14.0 25.0 9.0 29.0 -54 19.9424 21.0 14.0 26.0 7.0 30.0 ->>END_MODULE ->>Per sequence quality scores warn -#Quality Count -8 4.0 -9 4.0 -10 2.0 -11 2.0 -12 4.0 -13 6.0 -14 4.0 -15 11.0 -16 20.0 -17 50.0 -18 98.0 -19 149.0 -20 210.0 -21 275.0 -22 367.0 -23 425.0 -24 518.0 -25 540.0 -26 539.0 -27 532.0 -28 468.0 -29 360.0 -30 234.0 -31 122.0 -32 51.0 -33 5.0 ->>END_MODULE ->>Per base sequence content pass -#Base G A T C -1 1075 1632 1296 997 -2 1202 1586 1327 885 -3 1079 1443 1471 1007 -4 1079 1414 1445 1062 -5 1058 1486 1416 1040 -6 1119 1462 1286 1133 -7 1067 1516 1412 1005 -8 1079 1453 1397 1071 -9 1015 1424 1429 1132 -10 1060 1542 1328 1070 -11 1057 1432 1364 1147 -12 1066 1444 1450 1040 -13 1018 1461 1447 1074 -14 1001 1460 1461 1078 -15 1010 1461 1419 1110 -16 1017 1469 1465 1049 -17 1030 1457 1425 1088 -18 1030 1396 1470 1104 -19 1083 1423 1429 1065 -20 1000 1462 1448 1090 -21 1086 1425 1409 1080 -22 1026 1544 1365 1065 -23 1036 1445 1486 1033 -24 1056 1431 1379 1134 -25 1055 1453 1458 1034 -26 1109 1419 1406 1064 -27 1067 1426 1438 1068 -28 967 1527 1373 1133 -29 1045 1456 1452 1046 -30 1055 1470 1372 1103 -31 1042 1402 1433 1123 -32 992 1418 1437 1151 -33 1104 1431 1363 1101 -34 1065 1464 1363 1107 -35 1054 1471 1411 1063 -36 1070 1433 1440 1056 -37 1044 1471 1426 1057 -38 1093 1451 1403 1052 -39 1096 1412 1352 1138 -40 1066 1425 1391 1118 -41 1083 1405 1380 1129 -42 1114 1401 1385 1097 -43 1062 1421 1391 1125 -44 1070 1449 1377 1103 -45 1093 1464 1337 1106 -46 1063 1377 1387 1173 -47 1081 1413 1402 1102 -48 1064 1422 1320 1194 -49 1052 1452 1359 1136 -50 1091 1407 1340 1160 -51 1051 1386 1400 1161 -52 1091 1507 1297 1104 -53 1058 1416 1402 1123 -54 1072 1345 1339 1221 ->>END_MODULE ->>Per base GC content pass -#Base %GC -1 41.44 -2 41.74 -3 41.72 -4 42.82 -5 41.959999999999994 -6 45.04 -7 41.44 -8 43.0 -9 42.94 -10 42.6 -11 44.080000000000005 -12 42.120000000000005 -13 41.839999999999996 -14 41.58 -15 42.4 -16 41.32 -17 42.36 -18 42.68 -19 42.96 -20 41.8 -21 43.32 -22 41.82 -23 41.38 -24 43.8 -25 41.78 -26 43.47739095638256 -27 42.70854170834167 -28 42.0 -29 41.82836567313463 -30 43.16 -31 43.3 -32 42.87715086034414 -33 44.10882176435287 -34 43.44868973794759 -35 42.34846969393879 -36 42.528505701140226 -37 42.03681472589035 -38 42.90858171634327 -39 44.697879151660665 -40 43.68 -41 44.266559935961574 -42 44.24654792875725 -43 43.74874974994999 -44 43.468693738747746 -45 43.980000000000004 -46 44.72 -47 43.677470988395356 -48 45.16 -49 43.76875375075015 -50 45.038015206082434 -51 44.25770308123249 -52 43.908781756351274 -53 43.628725745149026 -54 46.071930882057465 ->>END_MODULE ->>Per sequence GC content warn -#GC Content Count -0 3.0 -1 5.0 -2 7.0 -3 7.0 -4 7.0 -5 5.0 -6 2.0 -7 1.0 -8 1.5 -9 2.0 -10 1.5 -11 1.0 -12 2.5 -13 4.0 -14 4.0 -15 4.0 -16 5.0 -17 6.0 -18 11.0 -19 19.5 -20 23.0 -21 37.5 -22 52.0 -23 61.0 -24 70.0 -25 79.0 -26 88.0 -27 117.5 -28 147.0 -29 159.5 -30 172.0 -31 203.0 -32 243.0 -33 252.0 -34 290.0 -35 328.0 -36 330.0 -37 332.0 -38 332.5 -39 333.0 -40 342.0 -41 351.0 -42 343.5 -43 336.0 -44 318.5 -45 279.5 -46 258.0 -47 254.5 -48 251.0 -49 234.5 -50 218.0 -51 209.5 -52 201.0 -53 198.5 -54 196.0 -55 177.0 -56 162.5 -57 167.0 -58 147.0 -59 127.0 -60 106.5 -61 86.0 -62 85.0 -63 84.0 -64 61.5 -65 39.0 -66 42.5 -67 46.0 -68 34.0 -69 17.0 -70 12.0 -71 14.0 -72 16.0 -73 12.5 -74 9.0 -75 6.5 -76 4.0 -77 4.5 -78 5.0 -79 5.0 -80 5.0 -81 3.0 -82 1.0 -83 1.0 -84 1.0 -85 1.0 -86 1.0 -87 1.0 -88 1.0 -89 1.0 -90 2.0 -91 3.0 -92 2.5 -93 2.0 -94 2.0 -95 3.0 -96 4.0 -97 5.0 -98 6.0 -99 3.5 -100 1.0 ->>END_MODULE ->>Per base N content pass -#Base N-Count -1 0.0 -2 0.0 -3 0.0 -4 0.0 -5 0.0 -6 0.0 -7 0.0 -8 0.0 -9 0.0 -10 0.0 -11 0.0 -12 0.0 -13 0.0 -14 0.0 -15 0.0 -16 0.0 -17 0.0 -18 0.0 -19 0.0 -20 0.0 -21 0.0 -22 0.0 -23 0.0 -24 0.0 -25 0.0 -26 0.04 -27 0.02 -28 0.0 -29 0.02 -30 0.0 -31 0.0 -32 0.04 -33 0.02 -34 0.02 -35 0.02 -36 0.02 -37 0.04 -38 0.02 -39 0.04 -40 0.0 -41 0.06 -42 0.06 -43 0.02 -44 0.02 -45 0.0 -46 0.0 -47 0.04 -48 0.0 -49 0.02 -50 0.04 -51 0.04 -52 0.02 -53 0.02 -54 0.45999999999999996 ->>END_MODULE ->>Sequence Length Distribution pass -#Length Count -54 5000.0 ->>END_MODULE ->>Sequence Duplication Levels pass -#Total Duplicate Percentage 0.66 -#Duplication Level Relative count -1 100.0 -2 0.08053150795248641 -3 0.040265753976243206 -4 0.0 -5 0.020132876988121603 -6 0.0 -7 0.040265753976243206 -8 0.0 -9 0.0 -10++ 0.0 ->>END_MODULE ->>Overrepresented sequences warn -#Sequence Count Percentage Possible Source -CGGAAGAGCGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGTTCAGCAGGAAT 7 0.13999999999999999 Illumina Paired End PCR Primer 2 (96% over 33bp) -CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGAC 7 0.13999999999999999 Illumina Paired End PCR Primer 2 (100% over 35bp) ->>END_MODULE ->>Kmer Content fail -#Sequence Count Obs/Exp Overall Obs/Exp Max Max Obs/Exp Position -CCCCC 1110 9.557241 23.193876 44 -AAAAA 2130 4.1300144 5.698024 7 -CTCCC 530 3.5749238 11.56272 11 -CCTCC 510 3.440021 11.56272 14 -CTGGG 465 3.1575248 8.314476 45 -TGGAA 785 2.929684 6.397646 17 -GGGGG 335 2.9167063 10.660779 6 -GAATG 775 2.8923633 10.053445 20 -CCCAG 450 2.8820548 7.8420706 22 -GTGTG 520 2.7661672 6.513526 23 -TGTGT 660 2.744307 6.109576 27 -GGGAG 425 2.7401958 6.315732 6 -ATGGA 730 2.7244196 6.397646 20 -GCTGG 395 2.6821985 6.651581 16 -GGAGG 410 2.643483 7.894665 7 -GGAAT 700 2.612457 7.3115954 19 -GCAGG 400 2.5732677 14.17877 16 -CCTGG 370 2.5068476 6.6367774 7 -CAGCC 380 2.4337354 6.273657 4 -TGGGA 480 2.419065 7.40506 20 -AATGG 645 2.4071925 5.4836965 18 -GCCTC 355 2.3998654 6.622006 2 -CCCTC 355 2.394524 8.259085 13 -CCAGC 370 2.3696895 6.2736564 14 -GGAAG 495 2.3634295 14.031037 2 -GGCTG 345 2.3426795 9.97737 24 -CAGGA 490 2.3343499 13.99981 17 -CCAGG 360 2.3107867 6.2876506 11 -CTGTG 435 2.3088553 9.09864 44 -GCCTG 340 2.3035896 8.295971 5 -TCCCA 460 2.3028264 6.1297736 9 -CTGCC 340 2.2984629 8.277508 10 -CAGCA 480 2.2816207 10.47649 14 -TTCCT 545 2.256056 7.0961456 1 -CTCCT 415 2.1929073 6.4701333 15 -TCCCC 325 2.1921701 6.6072683 28 -CAGGC 335 2.1503155 6.2876506 14 -CCCCA 335 2.1407545 6.259694 20 -TGGTG 400 2.127821 6.513526 9 -CCCCT 315 2.1247187 6.607268 12 -GGCAG 330 2.122946 6.301676 16 -CTCTG 400 2.1183603 5.187652 16 -TTCCA 540 2.1177678 6.7228537 28 -CAGAG 440 2.0961509 5.833255 28 -CCCTG 310 2.095657 6.622006 24 -AGGGA 435 2.0769534 5.846266 1 -CTCAG 410 2.0570977 6.143447 24 -CTTCC 385 2.034384 6.4701333 17 -AGCAG 425 2.0246909 10.499857 15 -AGGAA 570 2.015381 10.390455 18 -TCCTC 380 2.0079634 5.1761065 1 -TCAGC 400 2.0069244 12.286894 44 -AGAGC 420 2.0008712 10.499858 5 -TCCTG 375 1.9859626 6.4845653 8 -TCTCC 375 1.9815428 5.1761065 8 -CACCC 310 1.9809967 6.259694 9 -TGTGG 370 1.9682345 5.210821 4 -GATGG 390 1.9654902 6.1708827 1 -TGGCT 370 1.9638538 9.098641 45 -TCCCT 370 1.9551222 5.1761065 37 -CAGGG 300 1.9299511 6.3016763 21 -AAGAG 545 1.9269869 9.524584 4 -CAGAA 545 1.9226985 6.0476103 6 -CTGAG 380 1.9108309 6.15715 11 -TCTCT 460 1.9041945 5.068676 8 -GAGGC 295 1.897785 6.301676 22 -CCCAC 295 1.885142 6.259694 4 -CCTGC 275 1.8590509 9.93301 6 -CCTGT 350 1.8535651 6.4845653 6 -TTTCC 445 1.8421009 5.0686755 14 -TGCCT 345 1.8270856 5.187652 12 -CACAC 380 1.8022629 5.8073177 17 -CCTCT 340 1.7965988 7.7641597 2 -TTCCC 340 1.7965986 6.470133 18 -GAAGA 500 1.767878 7.792842 26 -CTGGC 260 1.7615684 6.636777 8 -TTCAG 440 1.7294377 9.6255 12 -CTCTC 325 1.717337 5.1761065 3 -GTGGT 320 1.7022567 5.2108207 24 -GGGTG 250 1.7013805 8.333022 28 -TGCTT 410 1.7010024 5.0799813 4 -CTTTG 405 1.6802584 5.0799813 2 -AGAAG 475 1.6794841 5.1952276 22 -ACTCC 330 1.6520276 6.1297736 10 -CTGCT 310 1.6417291 6.4845653 3 -GCCCC 190 1.6395733 6.339712 37 -AGTGG 325 1.6379085 6.1708827 3 -TGGCA 325 1.6342632 6.1571493 16 -GGCTC 240 1.626063 6.636776 25 -ACACA 460 1.6192161 5.1721287 14 -GCTTT 390 1.6180266 5.0799813 5 -TTCTG 390 1.6180266 5.0799813 3 -TCCTT 390 1.6144258 6.0824113 16 -CCCAA 335 1.588837 5.8073177 10 -GCACA 330 1.5686142 5.8202715 18 -GTTCA 395 1.5525635 7.700401 11 -TCTTC 375 1.5523325 5.068676 4 -AGGCA 325 1.5482932 5.8332543 6 -GGGGA 240 1.5474048 6.3157325 7 -CCTTC 290 1.5323931 6.4701333 17 -ATGCC 305 1.5302798 12.286893 22 -GAAGG 320 1.5278738 5.8462653 8 -GGGAT 295 1.4867171 7.40506 21 -TGTGC 280 1.4861598 5.199224 7 -AACAG 420 1.4817125 5.1836653 10 -TCTTT 455 1.4755235 5.5590916 1 -TTGGC 275 1.4596211 5.199223 15 -GAGAT 385 1.4368514 6.397646 27 -TTTGG 345 1.4345239 6.1095753 3 -GGTTC 270 1.4330826 10.398446 10 -CCTTG 265 1.4034137 5.187652 18 -CCCTT 265 1.4002901 5.176106 14 -CTGTT 335 1.3898433 5.0799813 10 -CCTTT 335 1.3867503 5.068676 8 -GGCAC 215 1.3800533 6.2876506 17 -TTGAA 465 1.3564935 6.4295163 7 -CTTGG 255 1.3534669 5.1992235 18 -GTGTT 325 1.3513632 5.091313 28 -GGCCC 155 1.3405302 6.353853 2 -TGGTT 320 1.330573 5.091313 25 -TTCTT 410 1.3295923 7.941558 4 -GGGGT 195 1.327077 8.333022 45 -AAGGA 375 1.3259085 5.1952276 44 -CAGAT 350 1.3033215 5.471493 10 -CTGGT 245 1.3003898 5.1992235 12 -TGTCC 245 1.2974956 5.187652 21 -GCTCC 190 1.2844352 8.277508 26 -GACAG 265 1.2624544 5.833254 27 -GAGCG 195 1.2544682 12.603353 6 -TTGGG 235 1.2500948 6.5135255 6 -AATGC 335 1.2474647 10.031068 21 -GGCTT 235 1.2473125 5.199223 4 -TTTGC 295 1.223892 5.0799813 9 -GGTGT 230 1.223497 5.21082 27 -GATCG 235 1.181698 6.1571493 45 -AGCTC 225 1.1288949 6.1434464 25 -ACCCT 225 1.1263824 6.129773 10 -CGGAA 235 1.119535 9.333206 1 -CCCAT 220 1.1013516 6.129773 21 -TCTTG 265 1.0994283 5.0799813 21 -ATGCA 295 1.0985136 5.4714913 37 -GCTTG 205 1.0880812 5.199223 2 -AGCGG 165 1.061473 12.603352 7 -AACCA 300 1.0560105 5.1721287 22 -AACCT 280 1.0403365 5.4593143 13 -CCGAG 160 1.0270164 12.575301 25 -TTGCC 190 1.0062209 5.1876516 3 -ACTCA 265 0.9846043 5.4593153 11 -CTCAT 250 0.98044825 5.7624474 4 -GTTCC 185 0.9797416 6.4845653 27 -GAACC 205 0.97444224 5.820272 25 -GGCGG 110 0.9555928 10.637051 44 -GCGGT 130 0.8827489 13.303162 8 -GCGGG 100 0.86872077 6.3822303 45 -TGCCG 125 0.846908 14.93275 23 -AGGCG 120 0.7719804 6.3016763 15 -CGGTT 140 0.74307984 10.398446 9 -GCCGA 115 0.738168 12.575301 24 -CGAGA 130 0.61931723 9.333206 26 -CGGGA 85 0.5468194 6.301676 24 -CACGG 85 0.54560244 6.2876506 37 ->>END_MODULE diff -r 9cbae8e9e3da -r 431f07da87b6 fastqc/test-data/fastqc_report.html --- a/fastqc/test-data/fastqc_report.html Thu Jun 06 04:14:45 2013 -0400 +++ b/fastqc/test-data/fastqc_report.html Sat Jun 08 04:46:08 2013 -0400 @@ -1,108 +1,213 @@ -dataset_100.dat FastQC Report +1000gsample.fastq FastQC Report -
FastQC Report
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-

Sun 29 May 2011

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dataset_100.dat

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Summary

+
+
FastQCFastQC Report
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+Sat 8 Jun 2013
+1000gsample.fastq +
+
+
+

Summary

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[FAIL] Basic Statistics

+
+
+

[OK] Basic Statistics

@@ -119,7 +226,7 @@ - + @@ -134,6 +241,10 @@ + + + + @@ -142,32 +253,32 @@
Measure
Filenamedataset_100.dat1000gsample.fastq
File type5000
Filtered Sequences0
Sequence length 54
43
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[FAIL] Per base sequence quality

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[FAIL] Per sequence quality scores

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[FAIL] Per base sequence content

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[FAIL] Per base GC content

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[FAIL] Per sequence GC content

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[FAIL] Per base N content

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[FAIL] Sequence Length Distribution

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[FAIL] Sequence Duplication Levels

-

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-

[FAIL] Overrepresented sequences

+
+

[WARN] Per base sequence quality

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Per base quality graph

+
+

[WARN] Per sequence quality scores

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Per Sequence quality graph

+
+

[WARN] Per base sequence content

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Per base sequence content

+
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[OK] Per base GC content

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Per base GC content graph

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[WARN] Per sequence GC content

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Per sequence GC content graph

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+

[OK] Per base N content

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N content graph

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[OK] Sequence Length Distribution

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Sequence length distribution

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+

[OK] Sequence Duplication Levels

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Duplication level graph

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+

[WARN] Overrepresented sequences

@@ -188,9 +299,9 @@
SequenceIllumina Paired End PCR Primer 2 (100% over 35bp)
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+

[FAIL] Kmer Content

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+

Kmer graph

@@ -201,1149 +312,1499 @@ - - - - + + + + - - - - + + + + - - + + - - + + - - - + + + + + + + + + + - - + + - - - - - + + + + + - + - - - - - + + + + + - - - - - + + + + + - - + + - - - - - - - - - + + - - - - - - - - - - - - - - - - + + - + - + + + + + + + + + + + + + + + - - + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + - - + + - + - - - + + + - - - - - + + + + + - - - - - + + + + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - + + + + - - + + - - - - - + + + + + + + + + + + + - - + + + + + + + + + + + + + + + + - - + + - - - - - - - - - - - - + + + + + - - - - + + + + + + + + + + + - - - - + + + + + + + + + + + - + - - - - - + + + + + - - - - - - - - - - - - + + + + + - - - + + + + + + + + + + - + - - - - - - - - - - - - - - - - + + - - - - - - - - - + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - - - - - - - + - - - - - - - - - - + + + - - + + - - + + - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + - - + + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - + + + + + + + + + + - + + + + + + + + - + - - - - - + + + + + - + - + - - - - - - - - - - + + + - + - - - - - - - - - - - - - - - - + + - - - - - + + + + + + + + + + + + + + + + + + + - - - - + + + + - - + + + + + + + + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - + + + - - - - - + + + + + - - - + + + + + + + + + + - + + + + + + + + - - - + + + - + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - - - - - - - - - + + + + + - - - - - + + + + + - - - - - - - - - - - - + + + + + - - - + + + + + + + + + + - - - - - + + + + + + + + + + + + - - - - - + + + + + - - - - - + + + + + + + + + + + + + + + + + + + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - + + + + + + + + + + + + + + + + + + + + + + - - + + - - - - - + + + + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - - - - - - + + - - - - - + + + + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - - - - + + + + + - - - - - - - - - - - - - - - - - - - + + + + + - - + + - - + + - - - - - + + + + + - - - - - + + + + + + + + + + + + + + + + + + + - - - - + + + + + + + + + + + + + + + + + + - + - - - - - + + + + + - + - - - - - - - - + - - - + + + - + - - - - - - - - - + + - + - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - + + + + + + + + + + + + + + + + + - + - + - + - + - + - - - - - - - - + - + - + - + + + + + + + + + + + + + + + - + - - - - - - - - + - + - - - + + + - - + + - - + + - - - - - - - - - + + - + + + + + + + + + + + + + + + + + + + + + + - - + + - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - + + - - + + + + + + + + + - + + + + + + + + + + + + + + + - - + + - - + + - + + + + + + + + + + + + + + + + + + + + + +
Sequence
CCCCC11109.55724123.1938764411809.95745929.63803150
AAAAA21304.13001445.698024721754.1332177.12965947
CTCCC5303.57492385553.668942 11.56272 11
CCTCC5103.4400215253.4706206 11.56272 14
CTGGG 4653.15752488.314476453.09459428.33113939
GGGGG3502.986570812.81857241
TGGAA7852.9296848002.9261596 6.397646 17
GGGGG3352.916706310.6607796CCCAG4552.8559999.42934340
GAATG 7752.89236332.8347175 10.053445 20
CCCAG4502.88205487.842070622GTGTG5302.7631727.824055733
GTGTG5202.76616726.51352623GGGAG4352.74877296.322054443
TGTGT6602.7443076702.7303638 6.109576 27
GGGAG4252.74019586.3157326
ATGGA7302.72441967352.688409 6.397646 20
GCTGG3952.68219856.65158116
GGAGG4102.6434837.8946657
GGAAT7002.6124577302.6701207 7.3115954 19
GCAGGGCTGG 4002.57326772.66201668.32279931
GGAGG4202.65398747.910485740
GCAGG4052.5535064 14.17877 16
CCTGG3702.50684763752.4900866 6.6367774 7
CAGCC3802.43373546.2736574
TGGGA4802.4190657.4050620
AATGG6452.40719255.483696518
GCCTC3552.39986546.6220062
CCCTC3552.3945248.25908513
CCAGC3702.36968956.273656414
GGAAG4952.363429514.03103723902.44799926.27993738
GGCTG3452.34267953652.4290898 9.97737 24
CAGGATGGGA 4902.334349913.99981172.42024477.4050620
CCAGG3602.31078676.287650611CCAGC3852.41661456.28622941
CTGTG4352.30885539.0986444AATGG6602.41408185.483696518
GCCTG3402.30358963602.3904827 8.295971 5
GCCTC3602.38516266.628634531
CCCTC3602.3798548.26735234
CTGTG4502.34086789.0986444
GGAAG5002.339722914.0310372
CAGCA5002.3293210.4764914
CAGGA4952.311170613.9998117
TCCCA4602.30282646.129773694702.3059947.37046939
CTGCC3402.29846293452.285781 8.277508 10
CAGCA4802.281620710.4764914GGTGG3402.26776085.00983242
CCAGG3602.2647326.30025141
TTCCT5452.2560565552.2516627 7.0961456 1
TCCCC3352.21458658.26735329
CAGGC3502.20182286.30025142
CTCCT4152.19290734252.2009897 6.4701333 15
TCCCC3252.19217016.607268328
CAGGC3352.15031556.287650614GGCAG3402.14368446.30167616
CCCCA3352.14075456.259694203402.1294036.2659631
CTCTG4102.12804415.192845348
TGGTG4002.1278216.51352694052.11148056.52004633
TTCCA5452.0947786.729583733
CCCCT 3152.12471872.0823722 6.607268 12
GGCAG3302.1229466.30167616CTCAG4202.06527196.14959646
CTCTG4002.11836035.18765216
TTCCA5402.11776786.722853728AGGGA4402.05895617.022541531
CAGAG 4402.09615095.833255282.0543745.839093738
AGCAG4402.054373510.49985715
CCCTG 3102.0956572.05389 6.622006 24
AGGGA4352.07695345.8462661
CTCAG4102.05709776.14344724
CTTCC3852.0343843902.0197318 6.4701333 17
AGCAG4252.024690910.49985715
AGGAA5702.0153815802.0098667 10.390455 18
TCCTC3802.00796345.17610651
TCAGC4002.006924412.28689444
AGAGC4202.00087124302.0076835 10.499858 5
TCTCC3851.99383785.18128829
TCCTC3851.99383785.18128848
TCAGC4051.991512212.28689444
TGCTG3801.97673276.505534647
CACCC3151.97282956.2596949
TCCTG3751.98596263801.9723336 6.4845653 8
TCTCC3751.98154285.17610658
CACCCCAGGG 3101.98099676.2596949
TGTGG3701.96823455.21082141.9545366.301676321
GATGG3901.96549023951.9510134 6.1708827 1
TGGCT3701.96385383751.9507233 9.098641 45
TCCCT3701.95512225.176106537
CAGGG3001.92995116.301676321
AAGAG5451.92698695601.9405607 9.524584 4
TGTGG3701.9290076.520046730
CTGAG3901.92203026.16331335
CCTGT3701.92043016.48456536
CAGAA5451.92269855551.9189543 6.0476103 6
CTGAGTCCCT3701.91615586.476609733
CCCAC3051.91019996.2596944
CACCA4051.88254996.975756633
AAAGA7301.87329825.139934542
CAGTG 3801.91083096.15715111.87274746.16331330
GAAGA5401.87125527.79284226
TCTCT 4601.90419451.8662432 5.068676 8
TTTCC4601.86624295.07374938
GAGGC 2951.8977851.8599615 6.301676 22
CCCAC2951.8851426.2596944TCTGT4551.85007555.085067349
CCTGC 2751.85905091.8219992 9.93301 6
CCTGTCCTCT 3501.85356516.48456536
TTTCC4451.84210095.0686755141.81257997.76415972
TGCCT 3451.82708561.7906713 5.187652 12
CACAC3801.80226295.807317717
CCTCT3401.79659887.76415972
TTCCC3401.79659863451.7866857 6.470133 18
GAAGA5001.7678787.79284226GAGGG2801.7693256.328388741
CACAC3801.76634325.81313133
TCTGC3401.76471955.198048642
CTGGC2601.76156846.63677782651.75966086.643420743
TTCAG4401.72943774551.7527524 9.6255 12
AGCCA3751.746995.831935439
CTCTC3251.7173373351.7348979 5.1761065 3
GGGTG2601.73417038.33302228
TGGGG2601.73417038.34972139
GTGGG2551.70082086.673090531
GGCCA2701.6985496.29394543
GCCCC2001.69146946.346058432
CTTTG4151.68743135.07998132
ACACA4851.67319155.172128714
GTGGT 3201.70225675.2108207241.66833025.21603731
GGGTG2501.70138058.33302228CTCAC3401.66816597.36309231
TGCTT 4101.70100245.079981341.66710085.09016240
GGGGC1951.66024348.52669440
CTTTGAGTGG3351.6546576.17088273
TTCTG 4051.68025845.079981321.64677045.085066349
AGAAG 4751.67948411.6460115 5.1952276 22
ACTCC3301.65202763351.6436341 6.1297736 10
GGCTC2451.62685628.30427546
TGGCA3301.62633318.63728440
TCCTT4001.62282016.094640
TCTGG3101.6125985.20442843
GGGGA2551.61134976.31573257
CTGCT 3101.64172911.609009 6.4845653 3
GCCCC1901.63957336.33971237
AGTGG3251.63790856.17088273CCCAA3451.60365365.807317710
TGGCA3251.63426326.157149316TGGCC2401.59365516.643420749
GGCTC2401.6260636.63677625
ACACA4601.61921615.172128714GTGCT3051.58658835.22010450
GCTTT 3901.61802665.079981351.58577886.108194441
CCACA3351.55717095.81313130
TTCTG3901.61802665.07998133CCTTC3001.55363996.470133317
CCACT3151.54550656.13590932
TCCTT3901.61442586.082411316TCTTC3801.54167915.073749549
CCCAA3351.5888375.807317710GTTCA4001.54088147.70040111
AGGCA3301.54078035.83325436
AAAAG6001.53969725.78242741
GCACA 3301.56861421.5373511 5.8202715 18
GTTCA3951.55256357.70040111
TCTTC3751.55233255.0686764
AGGCA3251.54829325.83325436
GGGGA2401.54740486.31573257
CCTTC2901.53239316.470133317
ATGCC 3051.53027981.4997808 12.286893 22
GAAGG 3201.52787381.4974226 5.8462653 8
GAGAG3201.49742265.85798141
TGTGC2851.48254995.204428729
TTGGC2851.48254955.19922315
GGGAT2951.48671713001.4817826 7.40506 21
TGTGC2801.48615985.1992247AGCTG3001.47848466.163312430
AACAG4201.48171254251.4694693 5.1836653 10
GAGTG2951.45708626.177060633
GGGAC2301.45013956.314304440
GTGTT3551.44668516.13411250
TTTGG3551.44668516.10957533
TCTTT 4551.47552351.4461157 5.5590916 1
TTGGC2751.45962115.19922315
GAGAT3851.43685143951.4447913 6.397646 27
TTTGG3451.43452396.10957533CAAAA5601.43385235.12336231
GGTTC2701.43308262751.4305303 10.398446 10
CCCTT2751.42416985.18647939
CTGTT3501.42313485.079981310
ATGGT3651.40919046.759639347
TGTTG3451.40593365.101516240
CTGTC2701.40139475.19804839
GAGAC3001.40070945.85668150
CTTCT3451.39968247.124644850
GGCCC1651.3985756.3538532
TGAGT3601.38988675.793977332
GGCAC2201.38400296.287650617
CCTTT3401.37939725.0686768
CCTTG 2651.40341371.3754432 5.187652 18
CCCTT2651.40029015.17610614
CTGTT3351.38984335.079981310
CCTTT3351.38675035.0686768
GGCAC2151.38005336.287650617
TTGAA4651.35649354751.3580486 6.4295163 7
CTTGG2551.35346695.199223518GAGCG2151.355565312.6033536
GTGTT3251.35136325.09131328
GGCCC1551.34053026.3538532
TGGTT3201.3305735.09131325AAGGA3901.35146215.195227644
TTCTT4101.32959234201.3348758 7.941558 4
GGGGT1951.3270772001.3339773 8.333022 45
AAGGA3751.32590855.195227644CAGAT3651.33208935.476969734
CAGAT3501.30332155.47149310CTTGG2551.32649185.199223518
TGGTT3201.30405415.09131325
TTGGG2501.30338296.51352556
CTGGT2451.30038985.1992235122501.30048235.20442848
GCTCC1951.29196318.27750826
TGATG3301.27406285.793977346
TGTCC 2451.29749561.2716361 5.187652 21
GCTCC1901.28443528.27750826GGCTT2401.24846285.1992234
GACAG 2651.26245441.2372932 5.833254 27
GAGCG1951.254468212.6033536
TTGGGGGTGT 2351.25009486.513525561.22517995.2108227
AATGC 3351.24746471.2226022 10.031068 21
GGCTT2351.24731255.1992234
TTTGC2951.2238923001.2198299 5.0799813 9
GGTGTGTCCT 2301.2234975.21082271.19378095.192845347
GGGCC1401.18931666.374400643
ATCCC2401.17752876.13590943
GCTCT2251.16782927.78926847
AGCCC1851.16123036.279936331
GATCG 2351.1816986.1571493451.15814636.163312429
ACCCT2301.1284656.12977310
GTTGG2151.12090955.216037347
AGCTC 2251.12889491.1063956 6.1434464 25
ACCCTCCCAT 2251.12638241.1039332 6.1297731021
CGGAA 2351.1195351.0972222 9.333206 1
CCCAT2201.10135166.12977321
TCTTG 2651.09942831.0775164 5.0799813 21
ATGCA 2951.09851361.0766199 5.4714913 37
GCTTG 2051.08808121.0663953 5.199223 2
AGCGG 1651.0614731.0403174 12.603352 7
TTGCC2001.03807025.18765163
AACCT2851.03780945.459314313
AACCA 3001.05601051.0349638 5.1721287 22
AACCT2801.04033655.459314313
CCGAG 1601.02701641.0065476 12.575301 25
TTGCCGTTCC 1901.00622095.187651630.98616686.484565327
ACTCA2650.98460432700.983188 5.4593153 11
CTCAT2500.980448252550.9801258 5.7624474 4
GTTCC1850.97974166.484565327
GAACC2050.974442242100.9783144 5.820272 25
GGCGG 1100.95559280.93654746 10.637051 44
GCGGG1100.936547466.388619436
ATCGG1900.936373536.16331230
GTCTG1800.93634715.209642441
GCGGT1300.88274891400.93170583 13.303162 8
GCGGG1000.868720776.382230345CGGGG1050.89397716.388619446
GGGCG1050.89397718.51815943
TCGGA1700.837807957.39597531
CTTGT2050.833550455.085067338
TGCCG 1250.8469080.83002883 14.93275 23
AGGCG1200.77198041250.7881193 6.3016763 15
CGGTT1400.743079841500.78028923 10.398446 9
GTGAC1500.73924246.16331332
GCCGA 1150.7381680.723456 12.575301 24
CCCGC850.71887456.346058430
CCCCG850.718874510.57676429
CGAGA1300.619317231350.6303192 9.333206 26
CGGGA850.5468194900.5674459 6.301676 24
CACGG 850.545602440.5347284 6.2876506 37
CGCCT800.53003616.628634530
CCGCA750.470769056.279936336
CGTTG400.208077135.204427746
-

Back to summary

-
Produced by FastQC (version 0.9.1)
- - - - - - - + +

Files created by FastQC

dataset_100.dat_fastqc.zip (294.3 KB)
duplication_levels.png (14.4 KB)
fastqc_data.txt (11.6 KB)
fastqc_report.html (19.8 KB)
kmer_profiles.png (172.2 KB)
per_base_gc_content.png (12.0 KB)
+ + + + + + - - - - + + + + + - -
1000gsample_fastqc.zip (312.3 KB)
duplication_levels.png (14.5 KB)
fastqc_data.txt (15.0 KB)
fastqc_report.html (25.3 KB)
kmer_profiles.png (186.7 KB)
per_base_gc_content.png (12.1 KB)
per_base_n_content.png (7.4 KB)
per_base_quality.png (9.4 KB)
per_base_sequence_content.png (23.8 KB)
per_sequence_gc_content.png (29.4 KB)
per_sequence_quality.png (21.7 KB)
per_base_quality.png (9.6 KB)
per_base_sequence_content.png (23.9 KB)
per_sequence_gc_content.png (29.6 KB)
per_sequence_quality.png (21.9 KB)
rgFastQCmsd1Ke.log (1.3 KB)
sequence_length_distribution.png (18.8 KB)
summary.txt (487 B)

+summary.txt (509 B) + FastQC documentation and full attribution is here

FastQC was run by Galaxy using the rgenetics rgFastQC wrapper - see http://rgenetics.org for details and licensing - \ No newline at end of file +
Produced by FastQC (version 0.10.1)
diff -r 9cbae8e9e3da -r 431f07da87b6 fastqc/test-data/gentestdata.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastqc/test-data/gentestdata.sh Sat Jun 08 04:46:08 2013 -0400 @@ -0,0 +1,3 @@ +#!/bin/bash +python ../rgFastQC.py -d /tmp/foo -i 1000gsample.fastq -j 1000gsample.fastq -f fastq -o /tmp/foo/fastqc_report.html -e /home/rlazarus/galaxy-central/tool_dependency_dir/fastqc_dist_0_10_1/0.10.1/fubar/fastqc/9cbae8e9e3da/fastqc_dist/fastqc +