BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068092.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 = 2,313,573 number of mapped reads = 2,051,645 (88.68%) number of supplementary alignments = 22,012 (0.95%) number of secondary alignments = 0 number of mapped bases = 133,461,622 bp number of sequenced bases = 133,403,068 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 146,082 duplication rate = 5.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7415 >>>>>>> ACTG content number of A's = 37,148,348 bp (27.85%) number of C's = 24,865,718 bp (18.64%) number of T's = 41,914,470 bp (31.42%) number of G's = 29,471,770 bp (22.09%) number of N's = 2,762 bp (0%) GC percentage = 40.73% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,044,950 number of insertions = 10,646 mapped reads with insertion percentage = 0.51% number of deletions = 35,903 mapped reads with deletion percentage = 1.73% homopolymer indels = 45.93% >>>>>>> Coverage mean coverageData = 0.0431X std coverageData = 0.4045X There is a 3.13% of reference with a coverageData >= 1X There is a 0.79% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 11246372 0.04512073813448994 0.6664376382927129 chr2 243199373 13706709 0.05635996849383325 0.5933373414646469 chr3 198022430 3524829 0.01780015021530642 0.17862444312249964 chr4 191154276 5420711 0.02835778049767508 0.2311690680253813 chr5 180915260 8037827 0.04442868445702148 0.28568429757847413 chr6 171115067 7413836 0.043326611326400616 0.32702406953720903 chr7 159138663 11292950 0.07096295637471832 0.3760241686567983 chr8 146364022 3065243 0.02094259885807183 0.4506003239108564 chr9 141213431 9082753 0.06431932809563985 0.49631313912595737 chr10 135534747 4545746 0.03353934028445119 0.30862299653513925 chr11 135006516 8059911 0.05970016291658101 0.34605110122314936 chr12 133851895 2728065 0.020381220602069174 0.21077309303401623 chr13 115169878 3599770 0.031256176202600475 0.23553171618429666 chr14 107349540 3206628 0.029870905827821898 0.27035630237845704 chr15 102531392 3898658 0.03802404243180469 0.2589231597496319 chr16 90354753 4961863 0.054915351271006184 0.35017803759267363 chr17 81195210 6786227 0.08357915448460568 0.3938022154030822 chr18 78077248 5933866 0.07599993790764756 0.7724387715552 chr19 59128983 5678347 0.09603322620989439 0.6109205265332962 chr20 63025520 2386455 0.03786489980566602 0.25941404198022283 chr21 48129895 2668792 0.05544977814724092 0.32751764286825635 chr22 51304566 802477 0.015641434331595358 0.15657371892562122 chrMT 16571 30861 1.8623498883591818 2.0393223378885272 chrX 155270560 5093407 0.03280343034764607 0.2743611098802553 chrY 59373566 289319 0.004872858739864134 0.159210982122875