BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008705.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 = 1,621,895 number of mapped reads = 579,715 (35.74%) number of supplementary alignments = 3,288 (0.2%) number of secondary alignments = 0 number of mapped bases = 38,406,920 bp number of sequenced bases = 38,388,685 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,506 duplication rate = 1.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4798 >>>>>>> ACTG content number of A's = 10,489,982 bp (27.33%) number of C's = 7,213,223 bp (18.79%) number of T's = 11,929,616 bp (31.08%) number of G's = 8,694,611 bp (22.65%) number of N's = 61,253 bp (0.16%) GC percentage = 41.44% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 319,940 number of insertions = 2,799 mapped reads with insertion percentage = 0.48% number of deletions = 10,438 mapped reads with deletion percentage = 1.78% homopolymer indels = 45.59% >>>>>>> Coverage mean coverageData = 0.0124X std coverageData = 0.1463X There is a 1.12% 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 2534139 0.010167031840614751 0.18295575787749777 chr2 243199373 3591574 0.014768023271178416 0.17924642284062717 chr3 198022430 2109998 0.010655348487542548 0.11195470238601896 chr4 191154276 2406174 0.01258760227785854 0.1251818245719146 chr5 180915260 2005010 0.011082591927292369 0.11396464029143138 chr6 171115067 2158265 0.012612945416431388 0.1286464239895016 chr7 159138663 1709413 0.010741657418599778 0.1470927590652963 chr8 146364022 2462593 0.016825125234670033 0.2046058894991959 chr9 141213431 1502996 0.010643435184292066 0.13025492042798398 chr10 135534747 1808967 0.013346887348378642 0.1500539587033034 chr11 135006516 2251399 0.016676224723849626 0.1548504449238181 chr12 133851895 1617528 0.012084460963365518 0.1250456448404535 chr13 115169878 1458353 0.012662625204830033 0.1214317959099351 chr14 107349540 1461583 0.013615177112077052 0.1387415791348463 chr15 102531392 1160257 0.011316114775853233 0.11490886400152261 chr16 90354753 807497 0.008936962065515247 0.1289344782477896 chr17 81195210 1063974 0.013103901079878973 0.1289803108211544 chr18 78077248 1041193 0.013335421350916466 0.20550485815713737 chr19 59128983 943150 0.015950722507775926 0.1657034383995912 chr20 63025520 536360 0.008510203485826059 0.1003802539972788 chr21 48129895 392637 0.008157861138072294 0.1449972125235368 chr22 51304566 584285 0.011388557501880047 0.11451946880204339 chrMT 16571 13903 0.8389958360992095 1.0302868353407524 chrX 155270560 2687590 0.017309076492027852 0.15327855558534625 chrY 59373566 98082 0.0016519472655558535 0.05318667411829619