BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716844.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 = 1,325,715 number of mapped reads = 1,164,688 (87.85%) number of supplementary alignments = 19,884 (1.5%) number of secondary alignments = 0 number of mapped bases = 91,519,072 bp number of sequenced bases = 91,478,590 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,122 duplication rate = 2.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9027 >>>>>>> ACTG content number of A's = 23,357,506 bp (25.53%) number of C's = 17,329,802 bp (18.94%) number of T's = 28,839,115 bp (31.53%) number of G's = 21,946,802 bp (23.99%) number of N's = 5,365 bp (0.01%) GC percentage = 42.94% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 765,835 number of insertions = 9,284 mapped reads with insertion percentage = 0.79% number of deletions = 23,385 mapped reads with deletion percentage = 1.98% homopolymer indels = 43.51% >>>>>>> Coverage mean coverageData = 0.0296X std coverageData = 0.3564X There is a 2.64% of reference with a coverageData >= 1X There is a 0.2% 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 0.01% 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 7303917 0.029303505727273593 0.5614876506345872 chr2 243199373 7854497 0.0322965347447668 0.5314293099417873 chr3 198022430 6116091 0.03088584964844639 0.19233096689892562 chr4 191154276 5889166 0.030808445007005754 0.2054876577300435 chr5 180915260 5491622 0.0303546643881782 0.19390326554916024 chr6 171115067 5248363 0.030671542208495294 0.22939287026618843 chr7 159138663 5040918 0.031676262103571905 0.45379843270169157 chr8 146364022 4648499 0.0317598473756071 0.4615615399609836 chr9 141213431 3820101 0.02705196646627756 0.37843541789812557 chr10 135534747 4377774 0.03230001233558211 0.37094962172160306 chr11 135006516 4168304 0.030874835700522782 0.350722840634785 chr12 133851895 4098255 0.030617833240239145 0.1934512716259521 chr13 115169878 2852970 0.02477184181787533 0.16876058897527094 chr14 107349540 2759591 0.02570659361931127 0.23799942294447435 chr15 102531392 2573404 0.025098693676176755 0.17275255498309636 chr16 90354753 2684587 0.02971163011203185 0.2179248197615898 chr17 81195210 2510891 0.030924127174497117 0.21603334167669389 chr18 78077248 2551653 0.03268113394570464 0.7150216016398044 chr19 59128983 1915973 0.03240328013082856 0.44149382038069174 chr20 63025520 1858467 0.02948753139997893 0.20198883533729656 chr21 48129895 1184568 0.024611896618515375 0.1852537542157648 chr22 51304566 1016164 0.019806502212688048 0.15211944502784194 chrMT 16571 2380 0.14362440407941585 0.44372861382753387 chrX 155270560 5293151 0.03408985579751886 0.2781282827413801 chrY 59373566 257766 0.004341426957579068 0.12579883112557627