BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525232.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 = 1,178,407 number of mapped reads = 638,007 (54.14%) number of supplementary alignments = 2,173 (0.18%) number of secondary alignments = 0 number of mapped bases = 38,571,631 bp number of sequenced bases = 38,558,517 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,105 duplication rate = 1.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4217 >>>>>>> ACTG content number of A's = 10,025,801 bp (26%) number of C's = 7,229,347 bp (18.75%) number of T's = 12,221,559 bp (31.7%) number of G's = 9,081,016 bp (23.55%) number of N's = 794 bp (0%) GC percentage = 42.3% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 192,867 number of insertions = 2,717 mapped reads with insertion percentage = 0.42% number of deletions = 8,154 mapped reads with deletion percentage = 1.27% homopolymer indels = 43.6% >>>>>>> Coverage mean coverageData = 0.0125X std coverageData = 0.1486X There is a 1.18% 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 3118426 0.012511206541788316 0.246216490520033 chr2 243199373 3180131 0.013076230258208766 0.16861741834086175 chr3 198022430 2560203 0.012928853564719915 0.11777247688772471 chr4 191154276 2399793 0.012554220863989461 0.12180404641326412 chr5 180915260 2370218 0.013101260778112361 0.11840163732581241 chr6 171115067 2197392 0.012841604415816872 0.12543889742269382 chr7 159138663 2158787 0.01356544638055681 0.19428882955356647 chr8 146364022 1979360 0.013523542008158262 0.14018245152880993 chr9 141213431 1604489 0.01136215577114616 0.1276254717448961 chr10 135534747 1811347 0.013364447420999723 0.15339146270759846 chr11 135006516 1793573 0.013285084699171112 0.13195555246543292 chr12 133851895 1781858 0.013312161176350921 0.12010459527114788 chr13 115169878 1214167 0.010542400678760814 0.10591988579248092 chr14 107349540 1162313 0.01082736824023652 0.11052376854342887 chr15 102531392 1121385 0.010936991862940865 0.10799696222999929 chr16 90354753 1162356 0.012864359221921619 0.1243424080209728 chr17 81195210 1056287 0.013009228007415708 0.12280045379141077 chr18 78077248 1022166 0.013091726798567491 0.20624690250580577 chr19 59128983 784626 0.013269736095410265 0.1902547864532612 chr20 63025520 840418 0.013334566696157367 0.12070959404256744 chr21 48129895 529289 0.010997094425408574 0.11551992362274079 chr22 51304566 461304 0.00899148040741637 0.09833914100470963 chrMT 16571 4918 0.2967835375052803 0.5586261706958682 chrX 155270560 2125628 0.013689832766752435 0.12680576583270445 chrY 59373566 131197 0.002209687051641803 0.08452334491341483