BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716463.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 = 574,663 number of mapped reads = 521,514 (90.75%) number of supplementary alignments = 1,630 (0.28%) number of secondary alignments = 0 number of mapped bases = 30,051,761 bp number of sequenced bases = 30,042,100 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,704 duplication rate = 1.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2425 >>>>>>> ACTG content number of A's = 7,341,848 bp (24.44%) number of C's = 5,818,418 bp (19.37%) number of T's = 9,493,415 bp (31.6%) number of G's = 7,388,090 bp (24.59%) number of N's = 329 bp (0%) GC percentage = 43.96% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 146,834 number of insertions = 2,372 mapped reads with insertion percentage = 0.45% number of deletions = 5,995 mapped reads with deletion percentage = 1.14% homopolymer indels = 42.48% >>>>>>> Coverage mean coverageData = 0.0097X std coverageData = 0.115X There is a 0.92% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% 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 2421475 0.009715020930680048 0.13411095457383357 chr2 243199373 2488827 0.010233690035047911 0.14414583203786047 chr3 198022430 1919933 0.009695532975734113 0.10280374505023798 chr4 191154276 1955451 0.010229700537800158 0.1088299122353596 chr5 180915260 1793535 0.009913674501531822 0.10364825897300912 chr6 171115067 1708932 0.009987034046510936 0.11120031979969788 chr7 159138663 1693795 0.010643516591565181 0.13869497769435338 chr8 146364022 1499396 0.010244293505408043 0.11878655531357307 chr9 141213431 1238963 0.00877369093878896 0.10341611379971152 chr10 135534747 1449467 0.010694431000782404 0.12489692303542826 chr11 135006516 1325862 0.009820725986292396 0.11027186878197329 chr12 133851895 1358071 0.010146072268905867 0.10498481534553275 chr13 115169878 943961 0.008196249022682824 0.09419812284834289 chr14 107349540 922941 0.008597531018763564 0.09716131812546144 chr15 102531392 846828 0.008259207092399565 0.09461751342444008 chr16 90354753 958446 0.010607588070104071 0.11149108752528121 chr17 81195210 865975 0.01066534589909922 0.10987592856678312 chr18 78077248 797619 0.010215767338520948 0.13504610290423263 chr19 59128983 651172 0.011012738034070364 0.12613857178803697 chr20 63025520 647669 0.010276297601352595 0.10633367756339464 chr21 48129895 380137 0.007898147294940079 0.0946151085112156 chr22 51304566 349222 0.00680684054514758 0.08549887776354341 chrMT 16571 1733 0.10458029086959146 0.3674790823754807 chrX 155270560 1745751 0.0112432839812003 0.11385475102063346 chrY 59373566 86600 0.0014585615423537135 0.04970827256734667