BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716430.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 = 1,696,081 number of mapped reads = 1,558,400 (91.88%) number of supplementary alignments = 5,541 (0.33%) number of secondary alignments = 0 number of mapped bases = 90,607,461 bp number of sequenced bases = 90,577,615 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,288 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6363 >>>>>>> ACTG content number of A's = 22,920,711 bp (25.31%) number of C's = 16,129,099 bp (17.81%) number of T's = 28,552,804 bp (31.52%) number of G's = 22,973,295 bp (25.36%) number of N's = 1,706 bp (0%) GC percentage = 43.17% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 461,372 number of insertions = 6,626 mapped reads with insertion percentage = 0.42% number of deletions = 18,416 mapped reads with deletion percentage = 1.17% homopolymer indels = 42.5% >>>>>>> Coverage mean coverageData = 0.0293X std coverageData = 0.2791X There is a 2.64% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% 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 7625064 0.03059195587721324 0.4395130113156352 chr2 243199373 7160892 0.02944453314852913 0.4078251543590532 chr3 198022430 5189861 0.026208450224552846 0.17655779626215692 chr4 191154276 5644408 0.02952802374140979 0.22539588619353645 chr5 180915260 5184970 0.028659660882116855 0.18353161896725384 chr6 171115067 4802822 0.028067791365210405 0.21203203042166668 chr7 159138663 5138518 0.03228956372468707 0.360766903953556 chr8 146364022 4787361 0.03270859145972362 0.3606550953475278 chr9 141213431 2987751 0.021157697103188437 0.1994754167339309 chr10 135534747 4035504 0.029774682059944376 0.30200352772851713 chr11 135006516 3204338 0.023734691442596743 0.2096475441135588 chr12 133851895 4457581 0.03330233763220162 0.1997960895473687 chr13 115169878 2736339 0.023759155149925573 0.16589326825202683 chr14 107349540 3044826 0.028363661362684926 0.18640266893613489 chr15 102531392 3324114 0.032420451289688915 0.1962900829953529 chr16 90354753 3135038 0.03469699042838399 0.21248106533198338 chr17 81195210 3931053 0.04841483875711387 0.2490445884686469 chr18 78077248 1689168 0.021634574005477244 0.3340148729817402 chr19 59128983 2335899 0.03950514420313977 0.359815019742802 chr20 63025520 2997122 0.047554101893962954 0.24598962313143816 chr21 48129895 1166026 0.02422664749216677 0.21172053087272721 chr22 51304566 851601 0.0165989319547114 0.14140435247048577 chrMT 16571 3522 0.212539979482228 0.4831000780064504 chrX 155270560 4841069 0.0311782800293887 0.21051531067628848 chrY 59373566 332614 0.0056020552984808085 0.24381644020350413