BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525249.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 = 1,101,836 number of mapped reads = 1,005,742 (91.28%) number of supplementary alignments = 3,943 (0.36%) number of secondary alignments = 0 number of mapped bases = 58,208,849 bp number of sequenced bases = 58,190,156 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,543 duplication rate = 2.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1873 >>>>>>> ACTG content number of A's = 15,441,270 bp (26.54%) number of C's = 10,532,854 bp (18.1%) number of T's = 18,143,041 bp (31.18%) number of G's = 14,071,751 bp (24.18%) number of N's = 1,240 bp (0%) GC percentage = 42.28% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 296,161 number of insertions = 4,640 mapped reads with insertion percentage = 0.46% number of deletions = 11,788 mapped reads with deletion percentage = 1.16% homopolymer indels = 42.51% >>>>>>> Coverage mean coverageData = 0.0188X std coverageData = 0.2034X There is a 1.75% of reference with a coverageData >= 1X There is a 0.09% 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 6287924 0.02522731528119242 0.35833786871112944 chr2 243199373 5020054 0.02064172262483588 0.26577227372956036 chr3 198022430 4336667 0.02189987770577303 0.15818062342629152 chr4 191154276 3468319 0.018144082740791004 0.14727899458830548 chr5 180915260 2737673 0.015132349808413065 0.13010040262880496 chr6 171115067 3011010 0.017596404879998088 0.15352482793246064 chr7 159138663 3511962 0.022068565449742405 0.2924707245223025 chr8 146364022 2849779 0.019470488451048443 0.20217957537749914 chr9 141213431 2003872 0.01419037825091864 0.1476908682810916 chr10 135534747 3221390 0.023768000983541142 0.229283258808122 chr11 135006516 2761571 0.02045509418226895 0.17567854297062713 chr12 133851895 2645552 0.019764770607095253 0.1497956294122315 chr13 115169878 1908205 0.016568611803166104 0.13803391417849395 chr14 107349540 2231435 0.020786628428962062 0.15455428178843536 chr15 102531392 1651140 0.01610375093707886 0.13561801170596177 chr16 90354753 1585117 0.01754326083985864 0.1543116670168713 chr17 81195210 1173326 0.014450680033957669 0.12959934801991865 chr18 78077248 1287397 0.016488759952195037 0.24402656805624107 chr19 59128983 998905 0.01689366110017485 0.25787757283882495 chr20 63025520 1035684 0.016432771994582512 0.13662719653161276 chr21 48129895 767944 0.015955655004026084 0.13722802631133454 chr22 51304566 454832 0.008865331791326331 0.09886724931384303 chrMT 16571 2343 0.14139158771347535 0.4066105966362952 chrX 155270560 3090083 0.01990128070640049 0.15996423665410117 chrY 59373566 166665 0.0028070572685494418 0.08093892064163674