BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716599.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 = 1,064,993 number of mapped reads = 979,855 (92.01%) number of supplementary alignments = 6,183 (0.58%) number of secondary alignments = 0 number of mapped bases = 57,468,322 bp number of sequenced bases = 57,451,157 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,490 duplication rate = 2.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2128 >>>>>>> ACTG content number of A's = 14,812,785 bp (25.78%) number of C's = 11,182,158 bp (19.46%) number of T's = 17,028,315 bp (29.64%) number of G's = 14,427,188 bp (25.11%) number of N's = 711 bp (0%) GC percentage = 44.58% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 287,173 number of insertions = 4,219 mapped reads with insertion percentage = 0.43% number of deletions = 10,764 mapped reads with deletion percentage = 1.09% homopolymer indels = 41.15% >>>>>>> Coverage mean coverageData = 0.0186X std coverageData = 0.179X There is a 1.71% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4652220 0.018664828120929736 0.264718337194488 chr2 243199373 4869317 0.020021914283471446 0.2117533536500526 chr3 198022430 3816210 0.019271604736897735 0.14760973135908248 chr4 191154276 3652495 0.019107576751251958 0.1586659213081261 chr5 180915260 3428194 0.018949169904186082 0.1463448375913768 chr6 171115067 3269251 0.019105570639200344 0.15487750873346892 chr7 159138663 3141227 0.01973893044457713 0.22276734525446656 chr8 146364022 2919970 0.019950053026009357 0.19149854488415388 chr9 141213431 2395810 0.016965879116696767 0.15670167030168383 chr10 135534747 2737902 0.02020073863420426 0.18565259761254643 chr11 135006516 2609909 0.019331726181275575 0.1691924729043781 chr12 133851895 2598924 0.019416415434387387 0.1485176754072931 chr13 115169878 1800144 0.015630336953209242 0.13254800005799466 chr14 107349540 1763365 0.016426386177341795 0.13967252138183706 chr15 102531392 1688703 0.01647010702829432 0.13782966416227485 chr16 90354753 1698907 0.01880263011731104 0.15134139244572128 chr17 81195210 1600483 0.019711544560325665 0.15680607860427612 chr18 78077248 1492915 0.01912099924423566 0.248405992713845 chr19 59128983 1237394 0.020927029981219192 0.21908555213879627 chr20 63025520 1256502 0.01993640036607393 0.15212028606381353 chr21 48129895 746699 0.015514245356238571 0.1438915460336272 chr22 51304566 725166 0.014134531417729954 0.12619720091609504 chrMT 16571 5025 0.30324060105002715 0.5945265592770549 chrX 155270560 3186988 0.020525384850804945 0.1590264620333244 chrY 59373566 174602 0.0029407362865824837 0.09123000050430057