BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524668.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 = 1,570,202 number of mapped reads = 1,457,874 (92.85%) number of supplementary alignments = 6,479 (0.41%) number of secondary alignments = 0 number of mapped bases = 86,593,057 bp number of sequenced bases = 86,567,993 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,829 duplication rate = 2.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8542 >>>>>>> ACTG content number of A's = 21,171,878 bp (24.46%) number of C's = 16,358,671 bp (18.9%) number of T's = 27,519,072 bp (31.79%) number of G's = 21,506,590 bp (24.84%) number of N's = 11,782 bp (0.01%) GC percentage = 43.74% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 432,048 number of insertions = 5,375 mapped reads with insertion percentage = 0.37% number of deletions = 15,767 mapped reads with deletion percentage = 1.07% homopolymer indels = 43.4% >>>>>>> Coverage mean coverageData = 0.028X std coverageData = 0.266X There is a 2.53% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6908362 0.027716528738357688 0.46055092877145976 chr2 243199373 7342502 0.03019128671849002 0.35776776494100965 chr3 198022430 5712294 0.028846701860996252 0.18329870314400581 chr4 191154276 5600154 0.029296514402848094 0.20772669385652004 chr5 180915260 5166121 0.028555473982681174 0.1828931403214484 chr6 171115067 4939211 0.02886485150954007 0.2022453401835797 chr7 159138663 4805993 0.030200033790657145 0.323227382131293 chr8 146364022 4485772 0.030648050926067063 0.2849256843682543 chr9 141213431 3620407 0.025637837522692865 0.22051861778223142 chr10 135534747 4255937 0.031401076802836395 0.2757604166897584 chr11 135006516 3977283 0.029459933622759362 0.24010436037319247 chr12 133851895 3866384 0.02888553800452358 0.18544686801771482 chr13 115169878 2651548 0.023022929658742888 0.16473923055639217 chr14 107349540 2586123 0.02409067612213336 0.1730067121427528 chr15 102531392 2433654 0.023735696478206402 0.1670532374681461 chr16 90354753 2514365 0.027827700442056433 0.19892374775009788 chr17 81195210 2394260 0.029487700074918213 0.19640755514072905 chr18 78077248 2298970 0.029444813423751822 0.39506226955893087 chr19 59128983 1837469 0.031075606357038137 0.3515819505784483 chr20 63025520 1862382 0.02954964909452552 0.18912443723826006 chr21 48129895 1144365 0.023776594567679818 0.18783281458104553 chr22 51304566 1023242 0.019944462642954627 0.15219430652672872 chrMT 16571 9186 0.5543419226359302 0.8454893005253817 chrX 155270560 4871755 0.03137590925156707 0.20823668017662378 chrY 59373566 285318 0.0048054718492064295 0.16531620962831248