BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084268.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,941,321 number of mapped reads = 1,592,892 (82.05%) number of supplementary alignments = 10,161 (0.52%) number of secondary alignments = 0 number of mapped bases = 101,520,072 bp number of sequenced bases = 101,484,427 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,115 duplication rate = 2.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6239 >>>>>>> ACTG content number of A's = 29,119,234 bp (28.69%) number of C's = 19,157,348 bp (18.88%) number of T's = 30,888,536 bp (30.44%) number of G's = 22,318,217 bp (21.99%) number of N's = 1,092 bp (0%) GC percentage = 40.87% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 867,961 number of insertions = 8,013 mapped reads with insertion percentage = 0.5% number of deletions = 22,371 mapped reads with deletion percentage = 1.39% homopolymer indels = 45.68% >>>>>>> Coverage mean coverageData = 0.0328X std coverageData = 0.2726X There is a 2.92% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7862080 0.03154287025828514 0.40599150384738286 chr2 243199373 8376859 0.03444441034804806 0.3513735959621484 chr3 198022430 7545705 0.03810530453545086 0.21418488584637937 chr4 191154276 6527234 0.03414641898986345 0.2091418159448544 chr5 180915260 6255497 0.034576945029402166 0.20430412963661562 chr6 171115067 6029980 0.035239328165064504 0.24459862750107964 chr7 159138663 5413830 0.03401957700247865 0.281267191421222 chr8 146364022 4998449 0.034150803808875925 0.2934206830350965 chr9 141213431 4473734 0.031680655078765135 0.2671564811593755 chr10 135534747 4603007 0.033961822350987235 0.2723733842510702 chr11 135006516 4602360 0.03408991014922569 0.24410340252420812 chr12 133851895 4723283 0.03528738237138891 0.2085213467960219 chr13 115169878 3096840 0.026889322570959048 0.18162801720190308 chr14 107349540 3193143 0.029745288149348383 0.20470273224759733 chr15 102531392 2951179 0.02878317501043973 0.18980434108443395 chr16 90354753 2578976 0.02854278180584479 0.21445680452900878 chr17 81195210 2266297 0.027911708092139918 0.19055605962749153 chr18 78077248 3213445 0.04115725236627193 0.5611589710154273 chr19 59128983 1991504 0.03368067399366568 0.31611107493523016 chr20 63025520 2102328 0.03335677357362542 0.20596380886404503 chr21 48129895 1426284 0.0296340559230391 0.196428529402199 chr22 51304566 1074684 0.020947141429868053 0.1571173913013864 chrMT 16571 5660 0.3415605576006276 0.5966316270628889 chrX 155270560 5958317 0.038373771563649926 0.2348423973483581 chrY 59373566 249397 0.0042004719743462945 0.09148009966342627