BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716587.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 = 1,020,164 number of mapped reads = 659,598 (64.66%) number of supplementary alignments = 3,080 (0.3%) number of secondary alignments = 0 number of mapped bases = 37,557,235 bp number of sequenced bases = 37,547,442 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,963 duplication rate = 1.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7577 >>>>>>> ACTG content number of A's = 9,580,759 bp (25.52%) number of C's = 7,110,784 bp (18.94%) number of T's = 11,952,352 bp (31.83%) number of G's = 8,903,056 bp (23.71%) number of N's = 491 bp (0%) GC percentage = 42.65% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 186,286 number of insertions = 2,329 mapped reads with insertion percentage = 0.35% number of deletions = 6,234 mapped reads with deletion percentage = 0.94% homopolymer indels = 41% >>>>>>> Coverage mean coverageData = 0.0121X std coverageData = 0.1403X There is a 1.14% 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 4389555 0.01761100928209924 0.2207711627380274 chr2 243199373 3184745 0.013095202346594866 0.1777807924833712 chr3 198022430 3359646 0.016965987135901726 0.13654714393996767 chr4 191154276 1726387 0.009031380496034523 0.10131104556061495 chr5 180915260 1649327 0.009116572034885282 0.10040403916796328 chr6 171115067 2635672 0.015402921824528754 0.14867961747705816 chr7 159138663 2202302 0.01383888715968413 0.16770724605587314 chr8 146364022 2444552 0.01670186406875318 0.14213329014550588 chr9 141213431 1396059 0.009886163023685756 0.12001531779053727 chr10 135534747 1948442 0.014375959251246472 0.15059569428371963 chr11 135006516 1228159 0.009097034990518532 0.11289627561891827 chr12 133851895 1654674 0.012361976645904042 0.11678001720385288 chr13 115169878 858086 0.007450611348220756 0.09055842799113246 chr14 107349540 817261 0.007613083390948857 0.09713898505437588 chr15 102531392 1119030 0.010914023287619075 0.1102956684104793 chr16 90354753 803793 0.008895968095889766 0.10249544098399778 chr17 81195210 840558 0.01035231019169727 0.10827982593116116 chr18 78077248 744002 0.009529049999303254 0.16923829955238617 chr19 59128983 838395 0.0141790870984539 0.1680960901065549 chr20 63025520 590893 0.009375456164423554 0.10120962432276062 chr21 48129895 345830 0.007185347069633125 0.09178837172852125 chr22 51304566 616002 0.01200676758477988 0.11452163179567215 chrMT 16571 60838 3.671353569488866 2.75141224424691 chrX 155270560 2011567 0.01295523761877332 0.12794833377024026 chrY 59373566 91460 0.0015404161508507002 0.04685464657928266