BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716275.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 = 1,380,924 number of mapped reads = 715,869 (51.84%) number of supplementary alignments = 2,642 (0.19%) number of secondary alignments = 0 number of mapped bases = 41,685,457 bp number of sequenced bases = 41,673,098 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,317 duplication rate = 2.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.25 >>>>>>> ACTG content number of A's = 10,274,188 bp (24.65%) number of C's = 8,544,378 bp (20.5%) number of T's = 13,294,875 bp (31.9%) number of G's = 9,558,514 bp (22.94%) number of N's = 1,143 bp (0%) GC percentage = 43.44% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 204,035 number of insertions = 3,611 mapped reads with insertion percentage = 0.5% number of deletions = 7,744 mapped reads with deletion percentage = 1.07% homopolymer indels = 41.6% >>>>>>> Coverage mean coverageData = 0.0135X std coverageData = 0.1491X There is a 1.23% of reference with a coverageData >= 1X There is a 0.09% 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 3361797 0.013487617348804921 0.21770729936928934 chr2 243199373 3509743 0.014431546252382814 0.1823440893861475 chr3 198022430 2741680 0.013845300252097703 0.12624298429972192 chr4 191154276 2608218 0.013644570524804792 0.13120577555944482 chr5 180915260 2531979 0.013995386569380604 0.1276031229747868 chr6 171115067 2378370 0.013899243600798753 0.13685403855454775 chr7 159138663 2276590 0.014305700180477198 0.1707223632389519 chr8 146364022 2054534 0.014037151835032246 0.14931318997487467 chr9 141213431 1761722 0.012475598018718205 0.13604264204035352 chr10 135534747 2015993 0.01487436280823249 0.15456310745447632 chr11 135006516 1915636 0.014189211430357925 0.14063270024841296 chr12 133851895 1880590 0.014049782410626313 0.12836521365161768 chr13 115169878 1286321 0.011168901299001116 0.11459039861417696 chr14 107349540 1255997 0.011700068766014274 0.11782435777948515 chr15 102531392 1189764 0.011603899808558143 0.11609692740660792 chr16 90354753 1219672 0.013498703272422205 0.12870024808183828 chr17 81195210 1165959 0.014359948080681114 0.13261825108731598 chr18 78077248 1085295 0.013900272202216964 0.18929513499049258 chr19 59128983 910029 0.015390574196075722 0.17344375658127661 chr20 63025520 933927 0.014818235533796468 0.13327374404062875 chr21 48129895 560328 0.011641995063567041 0.12232990139225113 chr22 51304566 532237 0.010374066900790077 0.1095529204014204 chrMT 16571 8089 0.4881419347052079 0.7604341770969065 chrX 155270560 2361629 0.015209766745222017 0.13985523056747318 chrY 59373566 139358 0.002347138792371002 0.07174912208055416