BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716690.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 = 487,577 number of mapped reads = 448,599 (92.01%) number of supplementary alignments = 1,893 (0.39%) number of secondary alignments = 0 number of mapped bases = 26,089,133 bp number of sequenced bases = 26,081,610 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,593 duplication rate = 2.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.899 >>>>>>> ACTG content number of A's = 6,615,082 bp (25.36%) number of C's = 5,128,803 bp (19.66%) number of T's = 8,159,012 bp (31.28%) number of G's = 6,178,196 bp (23.69%) number of N's = 517 bp (0%) GC percentage = 43.35% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 128,264 number of insertions = 1,664 mapped reads with insertion percentage = 0.37% number of deletions = 4,543 mapped reads with deletion percentage = 1% homopolymer indels = 44.42% >>>>>>> Coverage mean coverageData = 0.0084X std coverageData = 0.1121X There is a 0.79% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% 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 2084987 0.008365022288149084 0.14419479758975876 chr2 243199373 2196205 0.009030471472473739 0.15144541416443505 chr3 198022430 1686377 0.008516090828700567 0.09626342096656297 chr4 191154276 1670685 0.008739982358542689 0.10503217140474125 chr5 180915260 1561270 0.008629841396463736 0.09727323922985472 chr6 171115067 1487234 0.008691426337109169 0.10129041735140867 chr7 159138663 1417518 0.008907439419671384 0.11892156563441449 chr8 146364022 1311710 0.008961970175976717 0.12096633551403593 chr9 141213431 1091944 0.0077325789216182985 0.10139897314025051 chr10 135534747 1261054 0.009304285638279902 0.12164072672736294 chr11 135006516 1184116 0.008770806292045933 0.10506507646001269 chr12 133851895 1200704 0.008970392238376602 0.09951821722015258 chr13 115169878 811185 0.007043378130521246 0.0877178176442434 chr14 107349540 778038 0.007247706883513427 0.09010879478559569 chr15 102531392 742856 0.007245156683330701 0.08925029927680016 chr16 90354753 794609 0.008794324300792456 0.10004122630607247 chr17 81195210 757352 0.009327545307167751 0.10399710589097436 chr18 78077248 675421 0.008650676314820933 0.1292724404446197 chr19 59128983 583213 0.009863403197717776 0.12277311801186697 chr20 63025520 574822 0.009120464218303951 0.1008884953728911 chr21 48129895 348778 0.007246597982397427 0.09780806685197825 chr22 51304566 325049 0.006335673904735887 0.08400517190357684 chrMT 16571 1419 0.08563152495323155 0.29657071502493565 chrX 155270560 1441327 0.009282680502987816 0.103161757338529 chrY 59373566 101260 0.0017054727688075868 0.0805817740571192