BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524579.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,219,362 number of mapped reads = 1,118,282 (91.71%) number of supplementary alignments = 4,481 (0.37%) number of secondary alignments = 0 number of mapped bases = 65,580,444 bp number of sequenced bases = 65,558,805 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,120 duplication rate = 2.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8297 >>>>>>> ACTG content number of A's = 16,850,291 bp (25.7%) number of C's = 12,394,035 bp (18.91%) number of T's = 19,866,707 bp (30.3%) number of G's = 16,446,828 bp (25.09%) number of N's = 944 bp (0%) GC percentage = 43.99% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 333,155 number of insertions = 4,613 mapped reads with insertion percentage = 0.41% number of deletions = 12,921 mapped reads with deletion percentage = 1.15% homopolymer indels = 41.41% >>>>>>> Coverage mean coverageData = 0.0212X std coverageData = 0.2089X There is a 1.95% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 5396395 0.021650477653173027 0.3565085495095873 chr2 243199373 5502957 0.022627348632185823 0.23428897132696183 chr3 198022430 4388322 0.022160731993845342 0.1594080949726948 chr4 191154276 4230625 0.022131992485483296 0.17441107947274537 chr5 180915260 4000187 0.02211083244166357 0.15861303067471494 chr6 171115067 3683305 0.021525310801532166 0.17582700087727982 chr7 159138663 3606029 0.022659666306232572 0.26232095234259606 chr8 146364022 3400124 0.02323059966198524 0.21563385016553757 chr9 141213431 2759509 0.01954140608622419 0.18113510765334737 chr10 135534747 3173941 0.023417913636567308 0.20804086231552335 chr11 135006516 2983849 0.022101518418562848 0.19288679274062787 chr12 133851895 2962170 0.022130205926483147 0.15958493822813805 chr13 115169878 1996184 0.01733251814332911 0.13969406105311377 chr14 107349540 1940734 0.01807864290801805 0.14547264355035727 chr15 102531392 1893111 0.01846372084756247 0.14659374177857948 chr16 90354753 1889784 0.0209151587188778 0.16367302917688 chr17 81195210 1786914 0.02200762828250583 0.1669407559760277 chr18 78077248 1756379 0.022495400964952044 0.31923731378767595 chr19 59128983 1332536 0.022536088604804855 0.2647921866279043 chr20 63025520 1404158 0.02227919737909342 0.16202501392968857 chr21 48129895 851130 0.0176840194644098 0.1509783565436561 chr22 51304566 760703 0.014827198811115565 0.12921651127612924 chrMT 16571 4984 0.300766399131012 0.6178886321076364 chrX 155270560 3668314 0.023625302826240854 0.17607348522366123 chrY 59373566 208100 0.0035049267547783806 0.10980838974354354