BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716959.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 = 1,558,527 number of mapped reads = 1,288,910 (82.7%) number of supplementary alignments = 3,988 (0.26%) number of secondary alignments = 0 number of mapped bases = 72,191,440 bp number of sequenced bases = 72,169,948 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,133 duplication rate = 1.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.9632 >>>>>>> ACTG content number of A's = 16,938,986 bp (23.47%) number of C's = 13,522,759 bp (18.74%) number of T's = 23,217,512 bp (32.17%) number of G's = 18,489,645 bp (25.62%) number of N's = 1,046 bp (0%) GC percentage = 44.36% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 381,333 number of insertions = 4,627 mapped reads with insertion percentage = 0.36% number of deletions = 13,724 mapped reads with deletion percentage = 1.06% homopolymer indels = 42.06% >>>>>>> Coverage mean coverageData = 0.0233X std coverageData = 0.231X There is a 2.14% of reference with a coverageData >= 1X There is a 0.13% 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 5902407 0.02368061101039343 0.26275222184771824 chr2 243199373 7010094 0.028824473984149623 0.3615191738796701 chr3 198022430 5131111 0.025911766661988744 0.17826816253955702 chr4 191154276 4764074 0.02492266508335916 0.17287060698103227 chr5 180915260 3886364 0.02148168153421663 0.15719171715985658 chr6 171115067 3998063 0.023364763080740283 0.1885403030067936 chr7 159138663 3619843 0.022746471107401474 0.45036666365171785 chr8 146364022 5820660 0.0397683796910145 0.24859175940617395 chr9 141213431 2974829 0.021066190226622282 0.175014844050771 chr10 135534747 3421661 0.02524563682551457 0.262928505166944 chr11 135006516 2156612 0.01597413268556608 0.16672190673895132 chr12 133851895 3367321 0.02515706632319251 0.17601819765884855 chr13 115169878 1915251 0.016629790994482082 0.1391910391680864 chr14 107349540 2293290 0.021362830245942366 0.161628911479618 chr15 102531392 1701317 0.016593132764646364 0.1423280007388155 chr16 90354753 1975562 0.021864505567294284 0.16467919179602591 chr17 81195210 2935948 0.03615912810620232 0.21128049712812705 chr18 78077248 1701937 0.02179811716724442 0.2556812030970188 chr19 59128983 1513933 0.025603907308874227 0.26067988166613226 chr20 63025520 1558224 0.024723699225329677 0.17060095879210954 chr21 48129895 727863 0.015122887760299498 0.13522180517304705 chr22 51304566 1066958 0.020796550544838446 0.1556414462667726 chrMT 16571 47448 2.8633154305714803 2.573741076153697 chrX 155270560 2541675 0.016369329768630963 0.1552558254772756 chrY 59373566 158995 0.002677875201230123 0.06930214011619744