BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716996.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 = 1,411,934 number of mapped reads = 1,255,348 (88.91%) number of supplementary alignments = 7,042 (0.5%) number of secondary alignments = 0 number of mapped bases = 72,271,789 bp number of sequenced bases = 72,251,416 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,235 duplication rate = 2.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.259 >>>>>>> ACTG content number of A's = 18,368,889 bp (25.42%) number of C's = 13,157,384 bp (18.21%) number of T's = 23,148,782 bp (32.04%) number of G's = 17,575,342 bp (24.33%) number of N's = 1,019 bp (0%) GC percentage = 42.54% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 403,681 number of insertions = 5,140 mapped reads with insertion percentage = 0.41% number of deletions = 11,901 mapped reads with deletion percentage = 0.94% homopolymer indels = 41.39% >>>>>>> Coverage mean coverageData = 0.0233X std coverageData = 0.2425X There is a 2.12% 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 5277184 0.02117220000828002 0.3862612686152128 chr2 243199373 5436365 0.022353532136778986 0.2798753404135363 chr3 198022430 4361750 0.022026545174705713 0.1583576552974006 chr4 191154276 4424784 0.023147711328204867 0.18848852856183318 chr5 180915260 3920724 0.02167160470598224 0.1583573784052704 chr6 171115067 3722010 0.02175150362416654 0.16737519186501554 chr7 159138663 4608873 0.028961365598503236 0.3217648019850701 chr8 146364022 3142968 0.021473637831570386 0.2132607397063363 chr9 141213431 3367051 0.02384370223254472 0.2583722782902925 chr10 135534747 2881437 0.02125976595507276 0.2652188079957764 chr11 135006516 2807679 0.020796618438772244 0.19684251617838916 chr12 133851895 5427171 0.040546090139403704 0.2346464849244229 chr13 115169878 2987775 0.025942330163795085 0.1702951044835917 chr14 107349540 2551788 0.023770833112093447 0.18619294661693422 chr15 102531392 1851770 0.018060517504726748 0.1430346190889782 chr16 90354753 2196028 0.024304510023949708 0.18621200113307845 chr17 81195210 2280642 0.028088381075681682 0.1845947990369327 chr18 78077248 2153976 0.02758775514218944 0.4723396240855994 chr19 59128983 1348925 0.022813262321795726 0.3239310957226545 chr20 63025520 1949497 0.03093186696436618 0.19628589185324105 chr21 48129895 877023 0.0182220011076276 0.171981105544963 chr22 51304566 730330 0.0142351852269835 0.12598882328343533 chrMT 16571 8633 0.5209703699233601 0.7794453276497212 chrX 155270560 3720617 0.023962153546686505 0.1950123908353525 chrY 59373566 236789 0.003988121582591149 0.11050827260306974