BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237791.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 = 2,135,607 number of mapped reads = 1,410,676 (66.06%) number of supplementary alignments = 6,726 (0.31%) number of secondary alignments = 0 number of mapped bases = 78,716,727 bp number of sequenced bases = 78,686,695 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,738 duplication rate = 3.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8633 >>>>>>> ACTG content number of A's = 23,090,541 bp (29.34%) number of C's = 14,659,222 bp (18.63%) number of T's = 23,499,721 bp (29.86%) number of G's = 17,372,789 bp (22.08%) number of N's = 64,422 bp (0.08%) GC percentage = 40.71% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 643,301 number of insertions = 5,166 mapped reads with insertion percentage = 0.36% number of deletions = 20,018 mapped reads with deletion percentage = 1.41% homopolymer indels = 46.5% >>>>>>> Coverage mean coverageData = 0.0254X std coverageData = 0.243X There is a 2.15% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 6530789 0.026201696002996117 0.29615999817543615 chr2 243199373 5916855 0.024329236243549032 0.22534654026182596 chr3 198022430 6591999 0.03328915315300393 0.21470645596546553 chr4 191154276 6498019 0.03399358432348121 0.21856497878817135 chr5 180915260 5980547 0.033057172733798136 0.32934409649373136 chr6 171115067 6626461 0.038725175498426447 0.25237090971471565 chr7 159138663 4692719 0.029488239448134612 0.2948547398474391 chr8 146364022 4226610 0.028877383541701253 0.24627169015484263 chr9 141213431 4163449 0.02948337824891458 0.2267854193779136 chr10 135534747 1888003 0.01393002932303404 0.2183315167766479 chr11 135006516 1745926 0.012932160992881261 0.15027582020565122 chr12 133851895 7201629 0.05380296633080914 0.43833561744501065 chr13 115169878 3177872 0.02759290931957052 0.19455117777658115 chr14 107349540 1063194 0.009904038713160764 0.19766100890008625 chr15 102531392 843599 0.00822771429846578 0.1071650835170983 chr16 90354753 1830818 0.020262553315817264 0.17564866080718564 chr17 81195210 1841071 0.022674625756864228 0.21997226391169275 chr18 78077248 744562 0.009536222383247934 0.2621003658659849 chr19 59128983 714284 0.012080099534267315 0.2008551170943458 chr20 63025520 1635763 0.025953978642302356 0.1901913488723001 chr21 48129895 1142087 0.023729264316907403 0.18431295169305037 chr22 51304566 514935 0.010036825962040103 0.11336724468953362 chrMT 16571 49133 2.964999094804176 3.4689939264559455 chrX 155270560 2925389 0.01884059025741905 0.17665103400653545 chrY 59373566 171014 0.0028803053533958192 0.07613442112043202