BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237846.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,132,819 number of mapped reads = 2,700,745 (65.35%) number of supplementary alignments = 14,270 (0.35%) number of secondary alignments = 0 number of mapped bases = 160,573,554 bp number of sequenced bases = 160,480,084 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 278,395 duplication rate = 7.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6717 >>>>>>> ACTG content number of A's = 43,870,426 bp (27.34%) number of C's = 30,632,130 bp (19.09%) number of T's = 49,709,183 bp (30.98%) number of G's = 36,129,599 bp (22.51%) number of N's = 138,746 bp (0.09%) GC percentage = 41.6% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 1,564,666 number of insertions = 12,471 mapped reads with insertion percentage = 0.46% number of deletions = 59,032 mapped reads with deletion percentage = 2.15% homopolymer indels = 46.04% >>>>>>> Coverage mean coverageData = 0.0519X std coverageData = 0.456X There is a 3.29% of reference with a coverageData >= 1X There is a 1.05% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 13229777 0.05307821078608266 0.6806975715379397 chr2 243199373 13863804 0.05700591999470327 0.5233454407646344 chr3 198022430 10946887 0.05528104568760216 0.3681976105789596 chr4 191154276 9511440 0.04975792432704984 0.3647096477427682 chr5 180915260 9553027 0.05280387624570752 0.3446766229607652 chr6 171115067 9251372 0.0540652098158019 0.38663086792086376 chr7 159138663 9029855 0.056742056454250844 0.616958921594896 chr8 146364022 9471393 0.06471121024537027 0.5320177943846544 chr9 141213431 6475785 0.04585813795573029 0.39876351630199935 chr10 135534747 7538130 0.05561769337275555 0.5603818449655895 chr11 135006516 7206105 0.05337597927495588 0.44092808611836204 chr12 133851895 8264725 0.06174529691940484 0.38633829171132716 chr13 115169878 5332230 0.046298824767358006 0.3322587359706783 chr14 107349540 4739710 0.04415212212367189 0.3304715236610507 chr15 102531392 4437527 0.0432796913554046 0.3164433460152985 chr16 90354753 4643732 0.05139444075509785 0.4050112670659048 chr17 81195210 3771966 0.046455523669438135 0.35026785399811855 chr18 78077248 3960270 0.050722458865353454 0.6049957880075013 chr19 59128983 2800581 0.04736392980072057 0.49884505421384145 chr20 63025520 3298591 0.05233738650629142 0.3588461769031973 chr21 48129895 2088565 0.04339433942251484 0.342496231800488 chr22 51304566 1492886 0.02909850168111743 0.2650484965988968 chrMT 16571 159460 9.622835073320863 7.016069709901282 chrX 155270560 8972261 0.0577846888682568 0.3906488706259428 chrY 59373566 533475 0.008985059108627567 0.20991820545069584