BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716945.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 = 2,083,444 number of mapped reads = 1,433,890 (68.82%) number of supplementary alignments = 7,025 (0.34%) number of secondary alignments = 0 number of mapped bases = 82,238,172 bp number of sequenced bases = 82,217,571 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,196 duplication rate = 2.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2831 >>>>>>> ACTG content number of A's = 21,234,331 bp (25.83%) number of C's = 15,317,448 bp (18.63%) number of T's = 25,181,517 bp (30.63%) number of G's = 20,483,039 bp (24.91%) number of N's = 1,236 bp (0%) GC percentage = 43.54% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 390,836 number of insertions = 4,513 mapped reads with insertion percentage = 0.31% number of deletions = 13,273 mapped reads with deletion percentage = 0.92% homopolymer indels = 43.39% >>>>>>> Coverage mean coverageData = 0.0266X std coverageData = 0.2406X There is a 2.38% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% 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 8415273 0.033762295019517725 0.3976750677648 chr2 243199373 8496675 0.03493707609188614 0.31170370089972993 chr3 198022430 6173586 0.031176195545120824 0.19375017904372047 chr4 191154276 4082943 0.021359412331430138 0.1707063742128141 chr5 180915260 3895813 0.02153391040645217 0.16126847212525028 chr6 171115067 5785119 0.03380835540332635 0.24295149321589718 chr7 159138663 5112415 0.03212553696017919 0.325686076564977 chr8 146364022 4440955 0.030341848627253493 0.2161451712464825 chr9 141213431 3317241 0.023490973744558333 0.21190714019777496 chr10 135534747 4272569 0.03152379072209431 0.2429056183294363 chr11 135006516 2916211 0.021600520377846058 0.21503472663232015 chr12 133851895 3568111 0.026657157151193114 0.1822658097587731 chr13 115169878 1810815 0.015722991388425367 0.1364342254064794 chr14 107349540 1957907 0.01823861564753794 0.159155191144733 chr15 102531392 2702144 0.026354309127101287 0.18215304168750981 chr16 90354753 1885658 0.02086949426999153 0.16854699165530737 chr17 81195210 2323842 0.028620432165887617 0.192970125003688 chr18 78077248 1718728 0.022013173415128567 0.3552381182987055 chr19 59128983 1403581 0.023737614428443663 0.27227159711524107 chr20 63025520 1405400 0.022298903682190962 0.16593706405764472 chr21 48129895 812182 0.01687479268342472 0.14818840202473563 chr22 51304566 1438421 0.02803690026341905 0.18475610302265336 chrMT 16571 55569 3.3533884497012854 2.655460512737453 chrX 155270560 4063410 0.02616986761688758 0.1989466783390467 chrY 59373566 183604 0.0030923525799343094 0.07885374467477371