BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524467.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 = 2,449,375 number of mapped reads = 2,242,560 (91.56%) number of supplementary alignments = 5,186 (0.21%) number of secondary alignments = 0 number of mapped bases = 130,593,098 bp number of sequenced bases = 130,552,755 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,291 duplication rate = 4.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4193 >>>>>>> ACTG content number of A's = 33,611,832 bp (25.75%) number of C's = 24,144,140 bp (18.49%) number of T's = 41,842,376 bp (32.05%) number of G's = 30,951,543 bp (23.71%) number of N's = 2,864 bp (0%) GC percentage = 42.2% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 607,459 number of insertions = 8,915 mapped reads with insertion percentage = 0.4% number of deletions = 23,454 mapped reads with deletion percentage = 1.04% homopolymer indels = 42.84% >>>>>>> Coverage mean coverageData = 0.0422X std coverageData = 0.3685X There is a 3.58% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 12806912 0.051381665364035344 0.6771549706724779 chr2 243199373 10397858 0.04275446055529099 0.43555697051196757 chr3 198022430 7247449 0.03659913172462332 0.221489059281555 chr4 191154276 7347742 0.038438805313463144 0.2649943111704588 chr5 180915260 7033392 0.03887672051545016 0.22771720460488915 chr6 171115067 5669824 0.03313456903242775 0.2844325665646926 chr7 159138663 6525770 0.041006816803531895 0.5070846528403963 chr8 146364022 12084979 0.0825679619544754 0.3973756888521513 chr9 141213431 5478550 0.03879623886484282 0.3208796119566753 chr10 135534747 6743824 0.04975715932092307 0.37262409448993505 chr11 135006516 4586280 0.033970804786933394 0.3511512132829139 chr12 133851895 6048897 0.04519097021375753 0.24619666332186152 chr13 115169878 2922433 0.025374976953609345 0.18679762696540256 chr14 107349540 3168087 0.029511882398378233 0.20511134978139817 chr15 102531392 3393388 0.03309608826923953 0.23022319965620147 chr16 90354753 4093842 0.04530854065861925 0.2674760868906733 chr17 81195210 4456029 0.05488044183887202 0.28617192829758004 chr18 78077248 3138812 0.04020136570387317 0.5677144948189807 chr19 59128983 2625879 0.044409338141330794 0.471212721506736 chr20 63025520 3636212 0.05769428003132699 0.27981636866634474 chr21 48129895 1764113 0.03665316535596016 0.23987993072299443 chr22 51304566 1017504 0.019832620745685675 0.16027831307658283 chrMT 16571 10626 0.6412407217428037 0.9747328676838841 chrX 155270560 7973990 0.0513554533454378 0.3046026566107962 chrY 59373566 420706 0.007085745868792856 0.18356903054554638