BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717027.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 = 2,579,635 number of mapped reads = 2,390,685 (92.68%) number of supplementary alignments = 46,253 (1.79%) number of secondary alignments = 0 number of mapped bases = 185,127,145 bp number of sequenced bases = 185,057,052 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 154,738 duplication rate = 5.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3965 >>>>>>> ACTG content number of A's = 46,662,099 bp (25.21%) number of C's = 37,903,995 bp (20.48%) number of T's = 55,272,839 bp (29.87%) number of G's = 45,210,941 bp (24.43%) number of N's = 7,178 bp (0%) GC percentage = 44.91% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,213,729 number of insertions = 15,068 mapped reads with insertion percentage = 0.62% number of deletions = 33,311 mapped reads with deletion percentage = 1.37% homopolymer indels = 38.95% >>>>>>> Coverage mean coverageData = 0.0598X std coverageData = 0.4696X There is a 4.62% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 22641997 0.09084028320234355 0.8696765978153526 chr2 243199373 17637726 0.07252373138313971 0.5167725141399856 chr3 198022430 12474494 0.06299535865709759 0.3220625761305372 chr4 191154276 9906583 0.05182506615755747 0.4163512247480961 chr5 180915260 7085867 0.03916677343857008 0.24266361805536757 chr6 171115067 11736103 0.06858602930623287 0.3543211408454339 chr7 159138663 12039402 0.07565353241656932 0.6161353572663025 chr8 146364022 11974907 0.08181591921544763 0.5209236814426499 chr9 141213431 5659900 0.04008046515065553 0.3224109707113488 chr10 135534747 9569502 0.07060552523848368 0.6961360879733954 chr11 135006516 6124979 0.04536802505147233 0.3767187789694654 chr12 133851895 7332456 0.0547803675099258 0.29339466377618695 chr13 115169878 3388645 0.029423014583726485 0.206694683096817 chr14 107349540 3763756 0.035060755733093966 0.2524818648879956 chr15 102531392 4167002 0.040641231126560734 0.24725539863013601 chr16 90354753 6141368 0.06796950681720086 0.3510530608371277 chr17 81195210 4584146 0.056458330485258924 0.3219130254034782 chr18 78077248 5605318 0.0717919514786177 0.5099052336694428 chr19 59128983 5457271 0.09229434911809661 0.6701207899907045 chr20 63025520 3997715 0.06343009942639109 0.33210369164055376 chr21 48129895 2915296 0.06057141824223801 0.37803017946103934 chr22 51304566 3587727 0.06992997465371796 0.3557938747749301 chrMT 16571 285350 17.219841892462735 12.63642183332377 chrX 155270560 6523601 0.04201441020113536 0.2711870300319353 chrY 59373566 526034 0.008859733976564588 0.3518485982996543