BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716221.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 = 1,931,949 number of mapped reads = 1,765,182 (91.37%) number of supplementary alignments = 7,950 (0.41%) number of secondary alignments = 0 number of mapped bases = 102,276,752 bp number of sequenced bases = 102,249,302 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,125 duplication rate = 3.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4439 >>>>>>> ACTG content number of A's = 26,656,615 bp (26.07%) number of C's = 19,984,052 bp (19.54%) number of T's = 31,812,453 bp (31.11%) number of G's = 23,794,527 bp (23.27%) number of N's = 1,655 bp (0%) GC percentage = 42.82% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 529,481 number of insertions = 7,730 mapped reads with insertion percentage = 0.44% number of deletions = 16,688 mapped reads with deletion percentage = 0.94% homopolymer indels = 41.26% >>>>>>> Coverage mean coverageData = 0.033X std coverageData = 0.2965X There is a 2.9% of reference with a coverageData >= 1X There is a 0.29% 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 7347964 0.029480223441449318 0.474545370638956 chr2 243199373 8614012 0.03541954855286572 0.346893994942587 chr3 198022430 6149124 0.031052664084568603 0.19332744658215764 chr4 191154276 5943674 0.031093596880877518 0.21666841668928846 chr5 180915260 5503470 0.030420153612249184 0.19450831058481846 chr6 171115067 5370930 0.031387826298195004 0.2154203326130159 chr7 159138663 6543519 0.04111834846821605 0.4067134760025748 chr8 146364022 4359028 0.02978210041262736 0.2933434432470484 chr9 141213431 4085083 0.028928431035713593 0.30805702645623145 chr10 135534747 3918971 0.02891488040332565 0.28072685325868474 chr11 135006516 3949285 0.029252551039832774 0.24660330546718837 chr12 133851895 7665089 0.05726544999605721 0.2988101877545193 chr13 115169878 3789163 0.032900642648939854 0.19892498707842998 chr14 107349540 3626659 0.03378364732629502 0.21994655337278454 chr15 102531392 2572926 0.025094031689338617 0.17477117905225384 chr16 90354753 2864550 0.03170336816702935 0.21212344986634488 chr17 81195210 4144555 0.0510443288464923 0.2644136471410242 chr18 78077248 3179135 0.04071781577137555 0.5538213055561401 chr19 59128983 1756900 0.02971300893167738 0.3774957002061867 chr20 63025520 3133758 0.049722049100110556 0.2537666708265237 chr21 48129895 1229151 0.025538202399984458 0.20586568878680633 chr22 51304566 1006657 0.019621197068502638 0.15226988050780096 chrMT 16571 8635 0.5210910626998974 0.7976558299791808 chrX 155270560 5237863 0.033733780569864626 0.24243900456783674 chrY 59373566 276651 0.004659497797386804 0.11008798942682285