BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524750.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 = 1,239,432 number of mapped reads = 1,131,513 (91.29%) number of supplementary alignments = 3,839 (0.31%) number of secondary alignments = 0 number of mapped bases = 65,733,188 bp number of sequenced bases = 65,713,060 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,080 duplication rate = 2.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7986 >>>>>>> ACTG content number of A's = 16,104,013 bp (24.51%) number of C's = 12,932,401 bp (19.68%) number of T's = 20,350,299 bp (30.97%) number of G's = 16,318,565 bp (24.83%) number of N's = 7,782 bp (0.01%) GC percentage = 44.51% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 325,858 number of insertions = 3,907 mapped reads with insertion percentage = 0.34% number of deletions = 12,376 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.64% >>>>>>> Coverage mean coverageData = 0.0212X std coverageData = 0.1962X There is a 1.93% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% 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 5279551 0.021181696474088223 0.24057327522458236 chr2 243199373 5517381 0.022686657995619093 0.28723245302487865 chr3 198022430 4267354 0.02154985170114315 0.15976168079331057 chr4 191154276 4202443 0.021984561831093957 0.1808286950064354 chr5 180915260 3891697 0.021511159423478154 0.1574963935827757 chr6 171115067 3702071 0.021634979694686966 0.16741021634455602 chr7 159138663 3595792 0.022595338758124417 0.23267304285849014 chr8 146364022 3282775 0.022428838420414546 0.18546808538426493 chr9 141213431 2798693 0.019818886774304066 0.1770783326046178 chr10 135534747 3211966 0.023698468998507076 0.2492669356836666 chr11 135006516 2957591 0.02190702410245147 0.18134072236246435 chr12 133851895 2982198 0.022279833991143718 0.1618336388290624 chr13 115169878 2030533 0.017630764530288032 0.14316765743889034 chr14 107349540 1962398 0.018280450945574615 0.14850065441399368 chr15 102531392 1922510 0.01875045254432906 0.1483667303171206 chr16 90354753 2018507 0.022339798770740927 0.17764585448357456 chr17 81195210 1896255 0.02335427176061248 0.17458262203024957 chr18 78077248 1741056 0.022299146609265737 0.25535793773428384 chr19 59128983 1431533 0.024210343682048448 0.21263044071214202 chr20 63025520 1435856 0.022782136505974087 0.16896483138399718 chr21 48129895 867818 0.018030747833545035 0.1603966627633987 chr22 51304566 858221 0.016727965304296696 0.14088208936651656 chrMT 16571 14127 0.8525134270713898 1.001711557338943 chrX 155270560 3625554 0.023349912565524333 0.17361966155300423 chrY 59373566 239308 0.004030547870410883 0.11853681993687719