BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237597.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 = 815,515 number of mapped reads = 583,314 (71.53%) number of supplementary alignments = 2,750 (0.34%) number of secondary alignments = 0 number of mapped bases = 35,413,435 bp number of sequenced bases = 35,392,755 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,793 duplication rate = 7.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0434 >>>>>>> ACTG content number of A's = 9,185,778 bp (25.95%) number of C's = 5,794,531 bp (16.37%) number of T's = 11,962,480 bp (33.8%) number of G's = 8,388,857 bp (23.7%) number of N's = 61,109 bp (0.17%) GC percentage = 40.07% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 356,953 number of insertions = 2,866 mapped reads with insertion percentage = 0.49% number of deletions = 13,207 mapped reads with deletion percentage = 2.24% homopolymer indels = 48.58% >>>>>>> Coverage mean coverageData = 0.0114X std coverageData = 0.1445X There is a 0.9% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 3441569 0.01380766469584844 0.18363173133643815 chr2 243199373 2849386 0.01171625553491867 0.15668147639692326 chr3 198022430 2347338 0.011853899580971711 0.13664629238398882 chr4 191154276 2112608 0.011051847984818295 0.13182820237080745 chr5 180915260 2227745 0.012313748436699037 0.13673271737306458 chr6 171115067 2334483 0.01364276706270407 0.14969266013709517 chr7 159138663 1869221 0.01174586341723884 0.16069069014584134 chr8 146364022 1918896 0.013110435022071203 0.15874349479203437 chr9 141213431 1321772 0.009360101164881406 0.13210882140162789 chr10 135534747 1926877 0.014216848761299566 0.16220911429903637 chr11 135006516 1463173 0.010837795414259856 0.13995620732466274 chr12 133851895 2191830 0.01637503899365788 0.15878452751371563 chr13 115169878 1116107 0.00969096277066474 0.12615477572748113 chr14 107349540 911259 0.008488708940904637 0.11438810814779517 chr15 102531392 829190 0.00808718172869437 0.11167649019560656 chr16 90354753 757538 0.008384041512459228 0.11434272720466059 chr17 81195210 794165 0.009780934121606435 0.12146735465458512 chr18 78077248 839491 0.010752056732327452 0.17179136387503938 chr19 59128983 460880 0.007794485489459543 0.12930237740795622 chr20 63025520 637140 0.010109238289505584 0.12641671336519483 chr21 48129895 434415 0.009025887133142509 0.12038334920222497 chr22 51304566 288587 0.0056249769270048985 0.0928485912923542 chrMT 16571 31917 1.926075674370889 2.099667912786091 chrX 155270560 2207289 0.014215759896789191 0.1510453986389162 chrY 59373566 100559 0.0016936661678700585 0.050987006923837466