BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867869.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 = 2,044,452 number of mapped reads = 1,886,575 (92.28%) number of supplementary alignments = 7,487 (0.37%) number of secondary alignments = 0 number of mapped bases = 111,351,746 bp number of sequenced bases = 111,318,217 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,393 duplication rate = 3.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8359 >>>>>>> ACTG content number of A's = 28,061,512 bp (25.21%) number of C's = 20,817,570 bp (18.7%) number of T's = 35,655,239 bp (32.03%) number of G's = 26,768,130 bp (24.05%) number of N's = 15,766 bp (0.01%) GC percentage = 42.75% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 558,789 number of insertions = 7,880 mapped reads with insertion percentage = 0.42% number of deletions = 20,887 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.63% >>>>>>> Coverage mean coverageData = 0.036X std coverageData = 0.3399X There is a 3.2% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8945675 0.035890281693621136 0.647296580921614 chr2 243199373 9362274 0.03849629168246252 0.4660966993683398 chr3 198022430 7350200 0.037118017388232234 0.21211027730059848 chr4 191154276 7144032 0.03737312159315756 0.2467912634179143 chr5 180915260 6721897 0.03715494757048134 0.21401922841645524 chr6 171115067 6382688 0.037300561031250394 0.25008704059691017 chr7 159138663 6160955 0.038714382060630985 0.3857525093631811 chr8 146364022 5677627 0.038791138166454596 0.35035054184531617 chr9 141213431 4658144 0.032986550691484866 0.2767182231261181 chr10 135534747 5403233 0.03986603523891921 0.35145153610557883 chr11 135006516 5073403 0.03757894915235054 0.28275344462197927 chr12 133851895 5007832 0.03741323199047723 0.21589764153284516 chr13 115169878 3508480 0.030463521025871017 0.1928260576383068 chr14 107349540 3334509 0.031062163843459414 0.202198626338648 chr15 102531392 3220749 0.03141232101871786 0.19474378424291244 chr16 90354753 3278523 0.03628500871448345 0.22819186605756728 chr17 81195210 3023889 0.0372422092386977 0.226931813133203 chr18 78077248 2970777 0.038049202246472624 0.515470236699593 chr19 59128983 2319799 0.03923285810615075 0.45937801029473657 chr20 63025520 2381058 0.03777926782674701 0.21725215178044793 chr21 48129895 1484476 0.03084311735980309 0.23192737709496442 chr22 51304566 1338106 0.026081616205466 0.17681466350154312 chrMT 16571 33249 2.006457063544747 1.8181186797914468 chrX 155270560 6195830 0.03990344338295682 0.24363001358592473 chrY 59373566 374341 0.006304842798224381 0.2356390911064531