BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525212.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 = 569,746 number of mapped reads = 472,101 (82.86%) number of supplementary alignments = 1,514 (0.27%) number of secondary alignments = 0 number of mapped bases = 29,061,989 bp number of sequenced bases = 29,051,760 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,383 duplication rate = 1.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9717 >>>>>>> ACTG content number of A's = 7,864,245 bp (27.07%) number of C's = 5,542,996 bp (19.08%) number of T's = 8,656,125 bp (29.8%) number of G's = 6,987,664 bp (24.05%) number of N's = 730 bp (0%) GC percentage = 43.13% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 144,305 number of insertions = 1,991 mapped reads with insertion percentage = 0.42% number of deletions = 6,285 mapped reads with deletion percentage = 1.32% homopolymer indels = 42.82% >>>>>>> Coverage mean coverageData = 0.0094X std coverageData = 0.1254X There is a 0.9% of reference with a coverageData >= 1X There is a 0.03% 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 2872828 0.011525860952619251 0.20828846310012683 chr2 243199373 2414195 0.009926814243883761 0.12692491964610925 chr3 198022430 2269931 0.011462999418803214 0.11035539277919412 chr4 191154276 1619693 0.008473224004677772 0.09637606153051466 chr5 180915260 1229495 0.006795971771535469 0.0845998907060947 chr6 171115067 1862051 0.01088186465777441 0.11136788450802515 chr7 159138663 2175899 0.013672975246750691 0.20138219905730448 chr8 146364022 1664138 0.011369856999420254 0.12001835223180216 chr9 141213431 975235 0.0069061065444971734 0.09829881297354638 chr10 135534747 1601601 0.011816903306721782 0.14650931195239958 chr11 135006516 1327394 0.009832073586729695 0.11008568074737375 chr12 133851895 1324602 0.00989602724713012 0.10277111935088763 chr13 115169878 908553 0.007888807523092106 0.09097008573913844 chr14 107349540 1081579 0.01007530167339329 0.10414498105849665 chr15 102531392 801838 0.007820414649203241 0.09067908267613548 chr16 90354753 795781 0.008807295394853218 0.10232680988311116 chr17 81195210 547674 0.006745151592070517 0.08546624353532518 chr18 78077248 616086 0.007890723812396666 0.14835304305795252 chr19 59128983 534069 0.009032271026883719 0.153519910752738 chr20 63025520 564089 0.008950168122373287 0.09755732093048328 chr21 48129895 387291 0.008046786721641507 0.0944960141881893 chr22 51304566 236990 0.00461927696649846 0.0697280618115763 chrMT 16571 19901 1.200953472934645 1.3256687105056442 chrX 155270560 1148051 0.007393874279837723 0.09122135150364745 chrY 59373566 83025 0.0013983495618235225 0.05908338525537836