{ "summary": { "before_filtering": { "total_reads":28220296, "total_bases":1185252432, "q20_bases":1145221378, "q30_bases":1126481470, "q20_rate":0.966226, "q30_rate":0.950415, "read1_mean_length":42, "gc_content":0.421144 }, "after_filtering": { "total_reads":28074554, "total_bases":1179055901, "q20_bases":1141572933, "q30_bases":1123193171, "q20_rate":0.968209, "q30_rate":0.952621, "read1_mean_length":41, "gc_content":0.420815 } }, "filtering_result": { "passed_filter_reads": 28074554, "low_quality_reads": 120324, "too_many_N_reads": 738, "too_short_reads": 24680, "too_long_reads": 0 }, "duplication": { "rate": 0.732077, "histogram": [1097880,280378,177878,136372,113402,96352,82968,70859,60356,49448,39888,32150,24774,19045,14478,10698,7998,5997,4466,3398,2675,2227,1690,1391,1218,1025,807,719,597,552,3930], "mean_gc": 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"G":[29.244,31.2767,31.5159,31.6105,31.5939,35.2299,35.1928,35.1821,35.1672,35.2053,35.1961,35.1415,35.0994,35.0502,35.0183,34.973,34.9712,34.9246,34.9065,34.8507,34.7908,34.7166,34.6508,34.5623,34.5317,34.4773,34.4099,34.3418,34.2814,34.1587,34.0992,34.0446,33.9985,33.9573,33.9536,33.938,33.7683,33.6273,33.484,33.3639,33.2041,31.9788], "mean":[30.4336,31.4795,31.5864,31.6412,31.6703,35.2608,35.2526,35.2316,35.2686,35.2782,35.2947,35.293,35.2631,35.2326,35.2026,35.1808,35.1693,35.1573,35.1357,35.1193,35.0973,35.052,35.0053,34.955,34.9229,34.8594,34.826,34.7927,34.7637,34.7232,34.687,34.6393,34.5928,34.5522,34.4963,34.4349,34.3818,34.296,34.2321,34.1637,34.076,33.1235] }, "content_curves": { 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"C":[31.2125,31.567,31.5704,31.6766,31.7026,35.1794,35.1668,35.257,35.2518,35.2233,35.2087,35.2193,35.1699,35.1162,35.0675,35.0586,35.0164,34.964,34.8878,34.8599,34.8222,34.7713,34.7378,34.7212,34.679,34.6085,34.5114,34.4643,34.4091,34.3378,34.2841,34.2914,34.2205,34.1745,34.0546,33.9246,33.7759,33.6823,33.5355,33.4368,33.43,32.0369], "G":[29.2625,31.2938,31.5309,31.6243,31.609,35.2663,35.2309,35.2212,35.2195,35.2616,35.2522,35.2034,35.1625,35.1133,35.0805,35.0371,35.0337,34.9908,34.9727,34.9202,34.8631,34.7906,34.7251,34.6398,34.6087,34.5564,34.4909,34.425,34.3642,34.2472,34.1886,34.1344,34.0868,34.0455,34.0362,34.0194,33.8558,33.7167,33.5749,33.4553,33.2946,32.0401], 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"GC":[0.473128,0.48343,0.222993,0.421899,0.582507,0.411206,0.428644,0.535195,0.374306,0.374812,0.369636,0.375465,0.387899,0.410489,0.422876,0.432357,0.438039,0.424758,0.415023,0.411495,0.401248,0.405645,0.420837,0.435918,0.437441,0.450295,0.430123,0.428412,0.421308,0.404994,0.403304,0.421325,0.418275,0.427569,0.437898,0.442199,0.416548,0.415545,0.408132,0.406832,0.415191,0.429024] }, "kmer_count": { "AAAAA":5964543, "AAAAT":6393121, "AAAAC":3707925, "AAAAG":2016223, "AAATA":2524713, "AAATT":2053888, "AAATC":2889780, "AAATG":3991172, "AAACA":1725284, "AAACT":3047023, "AAACC":847933, "AAACG":598324, "AAAGA":1773765, "AAAGT":1271706, "AAAGC":956603, "AAAGG":1510364, "AATAA":1584203, "AATAT":2098816, "AATAC":1224787, "AATAG":658156, "AATTA":1237225, "AATTT":2159964, "AATTC":927290, "AATTG":925506, "AATCA":2649273, "AATCT":1005065, "AATCC":831148, "AATCG":138932, "AATGA":2680783, "AATGT":1610896, "AATGC":865756, "AATGG":1153647, "AACAA":1273156, "AACAT":1038531, "AACAC":743698, 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"AGTCC":558336, "AGTCG":208737, "AGTGA":981384, "AGTGT":1293262, "AGTGC":575791, "AGTGG":1209452, "AGCAA":866723, "AGCAT":851787, "AGCAC":809069, "AGCAG":1151890, "AGCTA":569840, "AGCTT":756245, "AGCTC":849269, "AGCTG":1171529, "AGCCA":832878, "AGCCT":893816, "AGCCC":847315, "AGCCG":248013, "AGCGA":209191, "AGCGT":195674, "AGCGC":142988, "AGCGG":307931, "AGGAA":1959894, "AGGAT":834667, "AGGAC":1097124, "AGGAG":1460157, "AGGTA":521530, "AGGTT":750090, "AGGTC":761299, "AGGTG":1311419, "AGGCA":1081854, "AGGCT":831853, "AGGCC":1060234, "AGGCG":307280, "AGGGA":1329067, "AGGGT":987809, "AGGGC":700741, "AGGGG":1155860, "TAAAA":2541909, "TAAAT":1545419, "TAAAC":759431, "TAAAG":1223777, "TAATA":1107100, "TAATT":1496021, "TAATC":810140, "TAATG":923479, "TAACA":793507, "TAACT":828335, "TAACC":501593, "TAACG":182793, "TAAGA":1157544, "TAAGT":754184, "TAAGC":493947, "TAAGG":699585, "TATAA":1079012, "TATAT":1400736, "TATAC":614097, "TATAG":734628, "TATTA":1113589, "TATTT":2860284, "TATTC":1167747, 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"TTTTA":3011688, "TTTTT":30919832, "TTTTC":3500273, "TTTTG":4321028, "TTTCA":2031688, "TTTCT":4790200, "TTTCC":2245006, "TTTCG":619262, "TTTGA":1797557, "TTTGT":4404292, "TTTGC":1583673, "TTTGG":2779331, "TTCAA":1271325, "TTCAT":1662212, "TTCAC":1009708, "TTCAG":1506213, "TTCTA":1457277, "TTCTT":3749460, "TTCTC":2167170, "TTCTG":3036747, "TTCCA":1645264, "TTCCT":2797187, "TTCCC":1392789, "TTCCG":562259, "TTCGA":314929, "TTCGT":454684, "TTCGC":240411, "TTCGG":392533, "TTGAA":1543251, "TTGAT":1150456, "TTGAC":792877, "TTGAG":1169610, "TTGTA":1603891, "TTGTT":3702281, "TTGTC":1258699, "TTGTG":2338360, "TTGCA":995658, "TTGCT":2118694, "TTGCC":1183575, "TTGCG":308689, "TTGGA":1428854, "TTGGT":2067323, "TTGGC":1168148, "TTGGG":1996770, "TCAAA":1187453, "TCAAT":742419, "TCAAC":659849, "TCAAG":972274, "TCATA":808924, "TCATT":1633486, "TCATC":908530, "TCATG":1438008, "TCACA":1089629, "TCACT":1255392, "TCACC":793996, "TCACG":1558823, "TCAGA":1084250, "TCAGT":1358102, "TCAGC":824572, "TCAGG":982588, "TCTAA":898516, "TCTAT":1224543, "TCTAC":785754, "TCTAG":715700, "TCTTA":1422236, "TCTTT":3266409, "TCTTC":2302808, "TCTTG":2105040, "TCTCA":1520957, "TCTCT":3556658, "TCTCC":1665348, "TCTCG":428171, "TCTGA":1643585, "TCTGT":2641104, "TCTGC":1726207, "TCTGG":1804363, "TCCAA":818223, "TCCAT":1141631, "TCCAC":1104079, "TCCAG":1269762, "TCCTA":1087203, "TCCTT":2105685, "TCCTC":1517856, "TCCTG":2177796, "TCCCA":1347597, "TCCCT":1598470, "TCCCC":1110133, "TCCCG":359175, "TCCGA":301490, "TCCGT":464809, "TCCGC":317646, "TCCGG":300893, "TCGAA":186949, "TCGAT":236836, "TCGAC":159150, "TCGAG":266327, "TCGTA":235065, "TCGTT":303200, "TCGTC":279487, "TCGTG":305572, "TCGCA":160231, "TCGCT":328138, "TCGCC":435757, "TCGCG":150164, "TCGGA":380656, "TCGGT":178327, "TCGGC":272855, "TCGGG":264565, "TGAAA":4458613, "TGAAT":1389590, "TGAAC":767450, "TGAAG":1757052, "TGATA":813702, "TGATT":1455334, "TGATC":556344, "TGATG":1319577, "TGACA":871729, "TGACT":1165147, "TGACC":730593, "TGACG":546646, "TGAGA":2788061, "TGAGT":1117612, "TGAGC":719271, "TGAGG":1486723, "TGTAA":1574520, "TGTAT":1865723, "TGTAC":1030961, "TGTAG":1210610, "TGTTA":1294464, "TGTTT":4008659, "TGTTC":1452390, "TGTTG":2026365, "TGTCA":1108568, "TGTCT":2156549, "TGTCC":1357614, "TGTCG":216945, "TGTGA":1535418, "TGTGT":4142602, "TGTGC":1597223, "TGTGG":2160640, "TGCAA":778857, "TGCAT":1199584, "TGCAC":964362, "TGCAG":1111415, "TGCTA":731463, "TGCTT":1916632, "TGCTC":1535825, "TGCTG":2141055, "TGCCA":1187400, "TGCCT":1700720, "TGCCC":1041962, "TGCCG":349754, "TGCGA":237588, "TGCGT":291681, "TGCGC":258570, "TGCGG":311953, "TGGAA":3161503, "TGGAT":1325118, "TGGAC":824471, "TGGAG":1617696, "TGGTA":1086181, "TGGTT":2036247, "TGGTC":869811, "TGGTG":2409388, "TGGCA":1263509, "TGGCT":1767091, "TGGCC":1154537, "TGGCG":1742377, "TGGGA":1757107, "TGGGT":1790641, "TGGGC":1011749, "TGGGG":1996957, "CAAAA":1412734, "CAAAT":1003045, "CAAAC":733499, "CAAAG":1020358, "CAATA":612027, "CAATT":648393, "CAATC":459262, "CAATG":694048, "CAACA":768758, "CAACT":750941, "CAACC":724666, "CAACG":152725, "CAAGA":1157127, "CAAGT":740974, "CAAGC":566563, "CAAGG":919067, "CATAA":726080, "CATAT":1044888, "CATAC":584356, "CATAG":533634, "CATTA":746029, "CATTT":1965453, "CATTC":887979, "CATTG":901792, "CATCA":876096, "CATCT":1198443, "CATCC":970690, "CATCG":277334, "CATGA":1132920, "CATGT":1240245, "CATGC":720803, "CATGG":1572354, "CACAA":815126, "CACAT":1064544, "CACAC":1504580, "CACAG":919171, "CACTA":678258, "CACTT":965945, "CACTC":781237, "CACTG":1476832, "CACCA":884217, "CACCT":1018293, "CACCC":826912, "CACCG":258421, "CACGA":220945, "CACGT":441895, "CACGC":245686, "CACGG":1387496, "CAGAA":1287467, "CAGAT":806685, "CAGAC":794347, "CAGAG":1226772, "CAGTA":714135, "CAGTT":985317, "CAGTC":590282, "CAGTG":1377346, "CAGCA":1209620, "CAGCT":1113809, "CAGCC":1033344, "CAGCG":270381, "CAGGA":1188090, "CAGGT":960404, "CAGGC":813550, "CAGGG":1098435, "CTAAA":1198765, "CTAAT":660993, "CTAAC":539319, "CTAAG":561585, "CTATA":716615, "CTATT":875083, "CTATC":691930, "CTATG":860831, "CTACA":823713, "CTACT":987544, "CTACC":706339, "CTACG":162007, "CTAGA":648932, "CTAGT":554591, "CTAGC":478639, "CTAGG":535666, "CTTAA":1020831, "CTTAT":1174348, "CTTAC":677381, "CTTAG":809129, "CTTTA":1449145, "CTTTT":2603651, "CTTTC":2117757, "CTTTG":1948214, "CTTCA":1504451, "CTTCT":2587279, "CTTCC":2006667, "CTTCG":294550, "CTTGA":1190719, "CTTGT":1579530, "CTTGC":1241597, "CTTGG":1479727, "CTCAA":813731, "CTCAT":1232868, "CTCAC":985132, "CTCAG":1293907, "CTCTA":811598, "CTCTT":1989597, "CTCTC":2791802, "CTCTG":2001893, "CTCCA":1263166, "CTCCT":1797260, "CTCCC":1511852, "CTCCG":347070, "CTCGA":223710, "CTCGT":289371, "CTCGC":431377, "CTCGG":361956, "CTGAA":3935887, "CTGAT":934790, "CTGAC":865698, "CTGAG":1586811, "CTGTA":1612105, "CTGTT":1763647, "CTGTC":1543133, "CTGTG":2104349, "CTGCA":1298974, "CTGCT":1986684, "CTGCC":1489449, "CTGCG":379882, "CTGGA":2297728, "CTGGT":1407576, "CTGGC":1199106, "CTGGG":1749616, "CCAAA":890673, "CCAAT":526827, "CCAAC":638190, "CCAAG":941308, "CCATA":814620, "CCATT":920030, "CCATC":920400, "CCATG":1279573, "CCACA":970349, "CCACT":998966, "CCACC":866191, "CCACG":308626, "CCAGA":951071, "CCAGT":777470, "CCAGC":1268598, "CCAGG":1265535, "CCTAA":784497, "CCTAT":684717, "CCTAC":726397, "CCTAG":635572, "CCTTA":785712, "CCTTT":1778563, "CCTTC":1611383, "CCTTG":1144041, "CCTCA":1084296, "CCTCT":1646057, "CCTCC":1435466, "CCTCG":372374, "CCTGA":1306345, "CCTGT":1540629, "CCTGC":1172135, "CCTGG":2322735, "CCCAA":790981, "CCCAT":824916, "CCCAC":722917, "CCCAG":1453387, "CCCTA":665793, "CCCTT":1058166, "CCCTC":1247704, "CCCTG":1381121, "CCCCA":994806, "CCCCT":1007391, "CCCCC":828788, "CCCCG":398024, "CCCGA":325313, "CCCGT":360164, "CCCGC":479738, "CCCGG":321766, "CCGAA":224880, "CCGAT":228428, "CCGAC":302662, "CCGAG":336779, "CCGTA":191568, "CCGTT":304609, "CCGTC":253049, "CCGTG":534450, "CCGCA":212452, "CCGCT":345901, "CCGCC":512874, "CCGCG":265433, "CCGGA":188993, "CCGGT":199170, "CCGGC":288138, "CCGGG":469795, "CGAAA":479768, "CGAAT":181815, "CGAAC":98149, "CGAAG":349246, "CGATA":131302, "CGATT":198468, "CGATC":151895, "CGATG":318998, "CGACA":198919, "CGACT":361972, "CGACC":212578, "CGACG":99236, "CGAGA":1606604, "CGAGT":210293, "CGAGC":179044, "CGAGG":510529, "CGTAA":163517, "CGTAT":222331, "CGTAC":122099, "CGTAG":227992, "CGTTA":189327, "CGTTT":436171, "CGTTC":273850, "CGTTG":212308, "CGTCA":317265, "CGTCT":282638, "CGTCC":428739, "CGTCG":67202, "CGTGA":646565, "CGTGT":425497, "CGTGC":263256, "CGTGG":589176, "CGCAA":146166, "CGCAT":194469, "CGCAC":192517, "CGCAG":236870, "CGCTA":135343, "CGCTT":273840, "CGCTC":282796, "CGCTG":446206, "CGCCA":393652, "CGCCT":414705, "CGCCC":456314, "CGCCG":232735, "CGCGA":171439, "CGCGT":71901, "CGCGC":112955, "CGCGG":209417, "CGGAA":1600272, "CGGAT":171585, "CGGAC":133784, "CGGAG":259245, "CGGTA":140862, "CGGTT":202629, "CGGTC":185695, "CGGTG":285045, "CGGCA":182989, "CGGCT":297595, "CGGCC":396618, "CGGCG":284412, "CGGGA":336529, "CGGGT":312611, "CGGGC":407657, "CGGGG":450474, "GAAAA":8594077, "GAAAT":3145631, "GAAAC":1137007, "GAAAG":1398220, "GAATA":1627187, "GAATT":1065144, "GAATC":580454, "GAATG":1098446, "GAACA":833213, "GAACT":963236, "GAACC":529501, "GAACG":240050, "GAAGA":1794073, "GAAGT":922662, "GAAGC":825277, "GAAGG":1492357, "GATAA":780474, "GATAT":724859, "GATAC":400767, "GATAG":537279, "GATTA":869820, "GATTT":1430201, "GATTC":688292, "GATTG":687665, "GATCA":608478, "GATCT":719147, "GATCC":504119, "GATCG":155575, "GATGA":1057670, "GATGT":949143, "GATGC":750023, "GATGG":1165645, "GACAA":739145, "GACAT":715243, "GACAC":533761, "GACAG":880825, "GACTA":517846, "GACTT":959809, "GACTC":530279, "GACTG":915832, "GACCA":620360, "GACCT":1021328, "GACCC":552635, "GACCG":187503, "GACGA":440395, "GACGT":449064, "GACGC":175308, "GACGG":372338, "GAGAA":4256991, "GAGAT":881828, "GAGAC":655700, "GAGAG":1523208, "GAGTA":529531, "GAGTT":996921, "GAGTC":505407, "GAGTG":848113, "GAGCA":909816, "GAGCT":680990, "GAGCC":644660, "GAGCG":304245, "GAGGA":1768850, "GAGGT":794038, "GAGGC":1343166, "GAGGG":1324819, "GTAAA":1213223, "GTAAT":945949, "GTAAC":494582, "GTAAG":703954, "GTATA":807170, "GTATT":1315170, "GTATC":653283, "GTATG":1045600, "GTACA":695027, "GTACT":755053, "GTACC":519418, "GTACG":245897, "GTAGA":723468, "GTAGT":666006, "GTAGC":551768, "GTAGG":840159, "GTTAA":903575, "GTTAT":980587, "GTTAC":589147, "GTTAG":652996, "GTTTA":1229077, "GTTTT":4138155, "GTTTC":1686789, "GTTTG":2250556, "GTTCA":1019678, "GTTCT":1752529, "GTTCC":1072298, "GTTCG":298747, "GTTGA":810262, "GTTGT":1358166, "GTTGC":854076, "GTTGG":1391369, "GTCAA":582014, "GTCAT":761377, "GTCAC":605371, "GTCAG":712642, "GTCTA":520701, "GTCTT":1210113, "GTCTC":991339, "GTCTG":1392637, "GTCCA":732385, "GTCCT":1418628, "GTCCC":719747, "GTCCG":252045, "GTCGA":155033, "GTCGT":167165, "GTCGC":140485, "GTCGG":198655, "GTGAA":1458058, "GTGAT":956650, "GTGAC":789339, "GTGAG":1284057, "GTGTA":1274954, "GTGTT":1602431, "GTGTC":994539, "GTGTG":3371739, "GTGCA":925373, "GTGCT":1227615, "GTGCC":899032, "GTGCG":258987, "GTGGA":1835239, "GTGGT":1477938, "GTGGC":1307351, "GTGGG":1693185, "GCAAA":790924, "GCAAT":507050, "GCAAC":510766, "GCAAG":835542, "GCATA":518234, "GCATT":1051088, "GCATC":753162, "GCATG":923334, "GCACA":860030, "GCACT":752563, "GCACC":741731, "GCACG":234943, "GCAGA":1045533, "GCAGT":796681, "GCAGC":889239, "GCAGG":1051818, "GCTAA":493399, "GCTAT":653635, "GCTAC":613685, "GCTAG":505336, "GCTTA":760449, "GCTTT":1581570, "GCTTC":1459849, "GCTTG":986003, "GCTCA":1037455, "GCTCT":1578172, "GCTCC":1198353, "GCTCG":326440, "GCTGA":1132426, "GCTGT":1466393, "GCTGC":1455215, "GCTGG":1589756, "GCCAA":744373, "GCCAT":1257785, "GCCAC":560215, "GCCAG":864142, "GCCTA":589697, "GCCTT":1265166, "GCCTC":963340, "GCCTG":1238888, "GCCCA":847572, "GCCCT":1091817, "GCCCC":696937, "GCCCG":450533, "GCCGA":291159, "GCCGT":254601, "GCCGC":309833, "GCCGG":370579, "GCGAA":290232, "GCGAT":172429, "GCGAC":174149, "GCGAG":1607006, "GCGTA":111479, "GCGTT":214876, "GCGTC":169057, "GCGTG":337297, "GCGCA":267937, "GCGCT":240151, "GCGCC":312913, "GCGCG":100633, "GCGGA":234400, "GCGGT":239657, "GCGGC":325420, "GCGGG":530009, "GGAAA":3835485, "GGAAT":1837200, "GGAAC":892847, "GGAAG":1472993, "GGATA":717772, "GGATT":952110, "GGATC":601377, "GGATG":972396, "GGACA":849156, "GGACT":751217, "GGACC":916663, "GGACG":530596, "GGAGA":1435844, "GGAGT":786176, "GGAGC":858580, "GGAGG":1719437, "GGTAA":836771, "GGTAT":861360, "GGTAC":436172, "GGTAG":680706, "GGTTA":734394, "GGTTT":2141634, "GGTTC":1054915, "GGTTG":989213, "GGTCA":674132, "GGTCT":980798, "GGTCC":858933, "GGTCG":182391, "GGTGA":1341055, "GGTGT":1215907, "GGTGC":796311, "GGTGG":2256422, "GGCAA":842397, "GGCAT":785918, "GGCAC":465601, "GGCAG":1249373, "GGCTA":634492, "GGCTT":884625, "GGCTC":1030061, "GGCTG":1358929, "GGCCA":1069177, "GGCCT":1050262, "GGCCC":772564, "GGCCG":410747, "GGCGA":1617473, "GGCGT":241754, "GGCGC":327288, "GGCGG":506079, "GGGAA":1454920, "GGGAT":883169, "GGGAC":976607, "GGGAG":1589034, "GGGTA":952307, "GGGTT":1275989, "GGGTC":705944, "GGGTG":1478179, "GGGCA":890763, "GGGCT":1057786, "GGGCC":784191, "GGGCG":402671, "GGGGA":1534462, "GGGGT":1144117, "GGGGC":920282, "GGGGG":1369783 }, "overrepresented_sequences": { } }, "command": "fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Klaas_kalisto/fastq/LW35-Friedllab-WeischnerS-Pilotexp-Celseq2-96w-Z33_S19_R1_001.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Klaas_kalisto/results/fastq_trimmed/LW35-Friedllab-WeischnerS-Pilotexp-Celseq2-96w-Z33_S19_R1_001_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Klaas_kalisto/results/qc/trimming/LW35-Friedllab-WeischnerS-Pilotexp-Celseq2-96w-Z33_S19_R1_001.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Klaas_kalisto/results/qc/trimming/LW35-Friedllab-WeischnerS-Pilotexp-Celseq2-96w-Z33_S19_R1_001.fastp.json " }