BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525185.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 = 762,341 number of mapped reads = 708,405 (92.92%) number of supplementary alignments = 1,966 (0.26%) number of secondary alignments = 0 number of mapped bases = 42,356,976 bp number of sequenced bases = 42,343,497 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,336 duplication rate = 1.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8958 >>>>>>> ACTG content number of A's = 10,734,764 bp (25.35%) number of C's = 7,871,515 bp (18.59%) number of T's = 12,889,966 bp (30.44%) number of G's = 10,846,175 bp (25.61%) number of N's = 1,077 bp (0%) GC percentage = 44.2% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 209,715 number of insertions = 3,000 mapped reads with insertion percentage = 0.42% number of deletions = 8,599 mapped reads with deletion percentage = 1.2% homopolymer indels = 42.21% >>>>>>> Coverage mean coverageData = 0.0137X std coverageData = 0.1626X There is a 1.29% of reference with a coverageData >= 1X There is a 0.05% 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 4720852 0.0189401814970804 0.30697135821705357 chr2 243199373 3589837 0.014760880983027863 0.17988730013521828 chr3 198022430 3372276 0.01702976778943678 0.13529205656658094 chr4 191154276 2373569 0.012417033244916791 0.11974545409031581 chr5 180915260 1939829 0.01072230722825703 0.1072380241726798 chr6 171115067 2147505 0.012550063753298826 0.1241519255309665 chr7 159138663 2552537 0.01603970368910288 0.2199353133999694 chr8 146364022 1991949 0.013609553582778697 0.14055853387018905 chr9 141213431 1444124 0.010226534330151641 0.12073953593572456 chr10 135534747 2216879 0.016356536231996656 0.1636325142556202 chr11 135006516 1978573 0.014655388929523965 0.14039008808262227 chr12 133851895 1956748 0.01461875455704232 0.12644867386148884 chr13 115169878 1322908 0.011486579850332046 0.11159258787380688 chr14 107349540 1604681 0.01494818701598535 0.1285370635395191 chr15 102531392 1203626 0.011739097426864156 0.11183678120394204 chr16 90354753 1227188 0.013581886500204367 0.12789591467546865 chr17 81195210 909530 0.011201769168402915 0.11251560934741915 chr18 78077248 912322 0.011684863687818505 0.2187246004899397 chr19 59128983 827748 0.013999023118662466 0.2062554769591767 chr20 63025520 834366 0.013238542101675639 0.12037935815066249 chr21 48129895 555081 0.011532977580773863 0.11822523788976541 chr22 51304566 360809 0.007032687889806923 0.08677069299732695 chrMT 16571 20797 1.2550238368233662 1.237984296303079 chrX 155270560 2158982 0.01390464489855643 0.12842272370989605 chrY 59373566 134260 0.0022612756660093485 0.08529904269114083