BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716942.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 = 1,745,976 number of mapped reads = 1,255,078 (71.88%) number of supplementary alignments = 1,152 (0.07%) number of secondary alignments = 0 number of mapped bases = 64,983,842 bp number of sequenced bases = 64,967,554 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 105,961 duplication rate = 7.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3987 >>>>>>> ACTG content number of A's = 13,589,760 bp (20.92%) number of C's = 11,203,198 bp (17.24%) number of T's = 21,885,987 bp (33.69%) number of G's = 18,287,518 bp (28.15%) number of N's = 1,091 bp (0%) GC percentage = 45.39% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 451,839 number of insertions = 3,886 mapped reads with insertion percentage = 0.31% number of deletions = 9,561 mapped reads with deletion percentage = 0.76% homopolymer indels = 39.38% >>>>>>> Coverage mean coverageData = 0.021X std coverageData = 0.2026X There is a 1.77% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.02% 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 6457226 0.025906559326084887 0.23092581217539734 chr2 243199373 5453023 0.022422027379157758 0.3250971732346039 chr3 198022430 4333362 0.02188318767727474 0.17560983537402822 chr4 191154276 4120126 0.02155393060629206 0.18570413315956358 chr5 180915260 3905015 0.021584773998611282 0.17214897686248923 chr6 171115067 2786969 0.016287104630009 0.18206216803824937 chr7 159138663 3723317 0.023396683934689085 0.21273861417621842 chr8 146364022 4010980 0.027404138976175444 0.20494974495945875 chr9 141213431 2875176 0.020360499561829924 0.1858563117474567 chr10 135534747 3380822 0.02494431926006399 0.22368854398173546 chr11 135006516 2812816 0.02083466845407669 0.19693027382434194 chr12 133851895 3089012 0.023077835394112275 0.18374581880484403 chr13 115169878 1119526 0.009720649352428766 0.11811588983041797 chr14 107349540 2071454 0.019296347240984918 0.16619298174519384 chr15 102531392 1273118 0.012416860584512497 0.1324890268161964 chr16 90354753 1784507 0.01975000695314833 0.18136966943458796 chr17 81195210 2627009 0.03235423616737983 0.2280314007790735 chr18 78077248 1725314 0.02209752577344939 0.20180434482397067 chr19 59128983 1822382 0.03082045229832551 0.24935570367696805 chr20 63025520 1754601 0.027839532303739818 0.21190245526648857 chr21 48129895 896903 0.018635050003745074 0.17380325840073013 chr22 51304566 757846 0.014771511759791517 0.14998306979778442 chrMT 16571 4897 0.2955162633516384 0.6201929060734986 chrX 155270560 1999501 0.012877528103202564 0.13951482714522614 chrY 59373566 198940 0.003350649344524801 0.09680778255110122