BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173857.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 4,428,122 number of mapped reads = 4,311,550 (97.37%) number of supplementary alignments = 428,709 (9.68%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,161,509 number of mapped paired reads (second in pair) = 2,150,041 number of mapped paired reads (both in pair) = 4,235,372 number of mapped paired reads (singletons) = 76,178 number of mapped bases = 504,931,435 bp number of sequenced bases = 504,625,338 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,153,908 duplication rate = 62.02% >>>>>>> Insert size mean insert size = 828,318.1314 std insert size = 8,411,656.9654 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 52.8087 >>>>>>> ACTG content number of A's = 152,210,585 bp (30.16%) number of C's = 98,571,654 bp (19.53%) number of T's = 151,745,352 bp (30.07%) number of G's = 102,091,597 bp (20.23%) number of N's = 6,150 bp (0%) GC percentage = 39.76% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 5,262,998 number of insertions = 66,413 mapped reads with insertion percentage = 1.47% number of deletions = 119,200 mapped reads with deletion percentage = 2.68% homopolymer indels = 42.34% >>>>>>> Coverage mean coverageData = 0.1631X std coverageData = 2.5279X There is a 3.96% of reference with a coverageData >= 1X There is a 2.96% of reference with a coverageData >= 2X There is a 2.14% of reference with a coverageData >= 3X There is a 1.69% of reference with a coverageData >= 4X There is a 1.21% of reference with a coverageData >= 5X There is a 0.95% of reference with a coverageData >= 6X There is a 0.67% of reference with a coverageData >= 7X There is a 0.54% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.19% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% 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 0.02% of reference with a coverageData >= 21X There is a 0.02% 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 0.01% of reference with a coverageData >= 25X There is a 0.01% 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% 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 37481461 0.1503766002653209 1.5945783728794443 chr2 243199373 42708647 0.1756116657422468 7.2242901614175805 chr3 198022430 38739755 0.19563316640443207 1.1950370462143804 chr4 191154276 29019451 0.15181167592609857 2.715220960419688 chr5 180915260 31510122 0.1741706144633681 1.1184307110555816 chr6 171115067 30005467 0.1753525713781826 1.2803590550713662 chr7 159138663 26045015 0.16366239673636065 1.5220401969541273 chr8 146364022 27736246 0.18950180256730031 1.7603786615566221 chr9 141213431 21113615 0.1495156292888316 1.4080513476881356 chr10 135534747 23480766 0.17324535973051988 2.499983860058939 chr11 135006516 18743706 0.13883556553670343 1.029267088053449 chr12 133851895 23663392 0.17678787438907756 1.1320204726680838 chr13 115169878 14473113 0.12566752046051485 0.9510196113399546 chr14 107349540 15166651 0.1412828690276642 1.0001566720306798 chr15 102531392 16896918 0.1647975090399631 1.0716463052674352 chr16 90354753 16673003 0.1845282339491316 1.44401116678379 chr17 81195210 19798189 0.24383444540632385 1.44113505173183 chr18 78077248 11813871 0.1513100333659301 2.1314852309473276 chr19 59128983 8516686 0.144035726100684 1.2673572214830495 chr20 63025520 20283983 0.32183761435050434 1.8568650249940333 chr21 48129895 7105454 0.1476307812431338 1.6928351739584002 chr22 51304566 4487674 0.08747123988925275 0.76942757653686 chrMT 16571 993439 59.95045561523143 42.56943507940319 chrX 155270560 15787895 0.10167989991148355 0.8492472667562597 chrY 59373566 2686916 0.04525441507084146 2.1122905670516015