BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525208.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 = 1,196,028 number of mapped reads = 1,088,388 (91%) number of supplementary alignments = 3,341 (0.28%) number of secondary alignments = 0 number of mapped bases = 63,999,634 bp number of sequenced bases = 63,978,013 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,114 duplication rate = 1.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0074 >>>>>>> ACTG content number of A's = 16,667,223 bp (26.05%) number of C's = 11,944,049 bp (18.67%) number of T's = 20,451,088 bp (31.97%) number of G's = 14,914,191 bp (23.31%) number of N's = 1,462 bp (0%) GC percentage = 41.98% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 323,866 number of insertions = 4,866 mapped reads with insertion percentage = 0.45% number of deletions = 13,474 mapped reads with deletion percentage = 1.23% homopolymer indels = 43.13% >>>>>>> Coverage mean coverageData = 0.0207X std coverageData = 0.2318X There is a 1.91% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 6050503 0.02427477602954498 0.41447997122675356 chr2 243199373 5174007 0.021274754684503235 0.2680198611487543 chr3 198022430 3897912 0.019684194361214536 0.15020458322313296 chr4 191154276 3657759 0.019135114717496564 0.1526874279734317 chr5 180915260 2809542 0.015529602091056333 0.13282609531527978 chr6 171115067 3860376 0.0225601173974937 0.17339377589094343 chr7 159138663 5052042 0.03174616340719163 0.44604357852640747 chr8 146364022 4122795 0.02816809037947864 0.21710158361841259 chr9 141213431 2085013 0.01476497656940295 0.16146372058923972 chr10 135534747 4298957 0.031718486182735116 0.25102369842728894 chr11 135006516 2912874 0.02157580305235045 0.18152310319230333 chr12 133851895 2827945 0.02112741847995503 0.1549442098416918 chr13 115169878 1961541 0.01703171900555456 0.13894293490163315 chr14 107349540 1487626 0.013857777126944373 0.12964177450690365 chr15 102531392 1733149 0.016903593779356862 0.13980463385940475 chr16 90354753 1674252 0.01852976124011982 0.15841012014388864 chr17 81195210 1114753 0.01372929511482266 0.12683040772281093 chr18 78077248 1465246 0.018766619438226103 0.2885453876781448 chr19 59128983 1295516 0.021909999703529484 0.2930038314326836 chr20 63025520 1116480 0.017714728890773135 0.14142700167055444 chr21 48129895 878193 0.018246310323344773 0.14697542384464862 chr22 51304566 711844 0.013874866420271444 0.12592049358452603 chrMT 16571 106738 6.441252791020458 3.9639154064787783 chrX 155270560 3505842 0.022578922881452867 0.16968221503202427 chrY 59373566 198729 0.0033470955744851166 0.09880701607159775