BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004132.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 = 2,615,844 number of mapped reads = 2,336,324 (89.31%) number of supplementary alignments = 23,651 (0.9%) number of secondary alignments = 0 number of mapped bases = 154,556,594 bp number of sequenced bases = 154,494,421 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 98,728 duplication rate = 3.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9559 >>>>>>> ACTG content number of A's = 43,075,186 bp (27.88%) number of C's = 28,758,807 bp (18.61%) number of T's = 48,380,430 bp (31.32%) number of G's = 34,268,965 bp (22.18%) number of N's = 11,033 bp (0.01%) GC percentage = 40.8% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,370,507 number of insertions = 11,676 mapped reads with insertion percentage = 0.5% number of deletions = 38,449 mapped reads with deletion percentage = 1.63% homopolymer indels = 46.17% >>>>>>> Coverage mean coverageData = 0.0499X std coverageData = 0.4561X There is a 4.22% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 13483098 0.05409454125291828 0.9377302166629947 chr2 243199373 7173577 0.02949669200010643 0.43719105954565896 chr3 198022430 12119045 0.06120036502935551 0.2806260484617485 chr4 191154276 15375858 0.08043690322679467 0.33394777689359595 chr5 180915260 11412883 0.06308413673893512 0.2905603068065169 chr6 171115067 11042602 0.06453319508094515 0.3558173938042386 chr7 159138663 8062284 0.05066200663002931 0.6537558831674506 chr8 146364022 11678431 0.07979031213012171 0.6243841715021367 chr9 141213431 5699691 0.040362244296719904 0.3901868545251037 chr10 135534747 6722497 0.04959980483823827 0.4053188042434827 chr11 135006516 3898778 0.028878443170846656 0.2503230355744282 chr12 133851895 6060881 0.04528050200559357 0.2569268821072783 chr13 115169878 4539414 0.03941494146585794 0.22836674981631985 chr14 107349540 3936171 0.0366668641523755 0.2621545787014967 chr15 102531392 3999607 0.03900860918771102 0.22803560729760164 chr16 90354753 4087081 0.045233713383069064 0.27740891141217966 chr17 81195210 3049111 0.03755284332659525 0.23932703483400103 chr18 78077248 4434742 0.05679941485642527 0.7185889176593949 chr19 59128983 2530189 0.04279101164313954 0.6155704590007257 chr20 63025520 2942436 0.046686421627302715 0.25983505878162433 chr21 48129895 1968796 0.04090588604026666 0.25047838069827777 chr22 51304566 1081722 0.02108432220243321 0.16175859386043637 chrMT 16571 37166 2.2428338663930965 1.971165208325249 chrX 155270560 8842342 0.05694796231816257 0.30827853603360583 chrY 59373566 378192 0.006369703312076623 0.12698233689077354