BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716349.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 = 628,803 number of mapped reads = 589,642 (93.77%) number of supplementary alignments = 11,745 (1.87%) number of secondary alignments = 0 number of mapped bases = 46,876,922 bp number of sequenced bases = 46,854,220 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,074 duplication rate = 1.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7583 >>>>>>> ACTG content number of A's = 11,991,076 bp (25.59%) number of C's = 8,945,167 bp (19.09%) number of T's = 14,094,550 bp (30.08%) number of G's = 11,820,196 bp (25.23%) number of N's = 3,231 bp (0.01%) GC percentage = 44.32% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 299,844 number of insertions = 3,954 mapped reads with insertion percentage = 0.66% number of deletions = 11,793 mapped reads with deletion percentage = 1.97% homopolymer indels = 42.81% >>>>>>> Coverage mean coverageData = 0.0151X std coverageData = 0.1627X There is a 1.41% of reference with a coverageData >= 1X There is a 0.07% 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 3788396 0.015199143676356176 0.24984003851369496 chr2 243199373 3966116 0.01630808480743904 0.18225110900769237 chr3 198022430 3051747 0.015411117821349834 0.12913692397686455 chr4 191154276 3039292 0.01589968094671343 0.14808507632948226 chr5 180915260 2851460 0.015761301727670735 0.13135495972067446 chr6 171115067 2511264 0.014675878892651808 0.13060055755945338 chr7 159138663 2516008 0.015810161732978743 0.19376064360210749 chr8 146364022 2346359 0.01603098198544995 0.1929163831528586 chr9 141213431 1977639 0.014004609802306977 0.15174073680890438 chr10 135534747 2302104 0.016985341773648643 0.173402926424612 chr11 135006516 2192559 0.01624039390809848 0.15840701800286489 chr12 133851895 2145754 0.01603080778198919 0.13237976449828148 chr13 115169878 1474794 0.012805379545509287 0.1177577346920536 chr14 107349540 1427379 0.01329655441467192 0.12423525705212374 chr15 102531392 1379007 0.013449607706486615 0.12105591692437145 chr16 90354753 1368148 0.015141959383143905 0.13231255178594453 chr17 81195210 1312255 0.016161729244865555 0.14091795333774446 chr18 78077248 1267856 0.01623848217601112 0.22209373949373568 chr19 59128983 940477 0.01590551625080377 0.18499988297412417 chr20 63025520 1026561 0.01628802110637088 0.13680323666080532 chr21 48129895 627337 0.013034248256722772 0.1298013356615664 chr22 51304566 571592 0.011141152621776394 0.11051294106844572 chrMT 16571 3557 0.21465210307163116 0.4600694501294144 chrX 155270560 2644870 0.017033943846148297 0.14521653432379458 chrY 59373566 144391 0.002431907155450289 0.09537153096821424