BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089604.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 9,050,157 number of mapped reads = 7,388,733 (81.64%) number of supplementary alignments = 296 (0%) number of secondary alignments = 0 number of mapped bases = 347,329,207 bp number of sequenced bases = 347,259,128 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,538,193 duplication rate = 25.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2459 >>>>>>> ACTG content number of A's = 110,975,830 bp (31.96%) number of C's = 67,246,273 bp (19.36%) number of T's = 91,989,221 bp (26.49%) number of G's = 76,983,558 bp (22.17%) number of N's = 64,246 bp (0.02%) GC percentage = 41.53% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,846,052 number of insertions = 15,218 mapped reads with insertion percentage = 0.21% number of deletions = 46,648 mapped reads with deletion percentage = 0.63% homopolymer indels = 45.4% >>>>>>> Coverage mean coverageData = 0.1122X std coverageData = 1.0001X There is a 3.83% of reference with a coverageData >= 1X There is a 1.88% of reference with a coverageData >= 2X There is a 1.24% of reference with a coverageData >= 3X There is a 0.88% of reference with a coverageData >= 4X There is a 0.66% of reference with a coverageData >= 5X There is a 0.5% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.3% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% 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 27041550 0.10849140472151522 1.0737795250796132 chr2 243199373 29120406 0.11973882021480377 1.1075064616283758 chr3 198022430 23380160 0.1180682410573388 0.9653380451037011 chr4 191154276 22934724 0.11998017768642538 1.0133197735334192 chr5 180915260 21694536 0.11991545655131579 0.9759727391271887 chr6 171115067 20558102 0.12014197440602936 1.0586587095408078 chr7 159138663 19313785 0.12136450461444433 1.0577913687388931 chr8 146364022 17576342 0.12008649229385074 1.1569002731397076 chr9 141213431 13982347 0.09901570198375818 0.8928625832198451 chr10 135534747 16160632 0.11923608047167418 1.0141740694806507 chr11 135006516 15237260 0.1128631450647908 1.046464147631471 chr12 133851895 16156007 0.12070062213164783 0.9735806127699371 chr13 115169878 11006900 0.09557099643710658 0.8606104544958476 chr14 107349540 10761920 0.10025119809549254 0.930275263912961 chr15 102531392 10140928 0.09890559176256965 0.8831745393274985 chr16 90354753 9804818 0.10851468986916493 0.9311555652107193 chr17 81195210 9129943 0.11244435478398294 0.919609632991721 chr18 78077248 9108253 0.116656942109435 1.0181604502761201 chr19 59128983 6565985 0.11104511978499614 1.0007732662840891 chr20 63025520 7297373 0.11578441558276711 0.9570517566584538 chr21 48129895 4523573 0.09398676228153001 0.894249728225435 chr22 51304566 3998082 0.07792838555539092 0.8267511239452097 chrMT 16571 152240 9.187134150021121 17.006768431517997 chrX 155270560 20774910 0.1337981263157678 1.0651809259725076 chrY 59373566 908431 0.015300260051754345 0.30397674213755466