BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716236.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 = 2,026,388 number of mapped reads = 1,825,737 (90.1%) number of supplementary alignments = 27,828 (1.37%) number of secondary alignments = 0 number of mapped bases = 142,999,762 bp number of sequenced bases = 142,937,411 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,967 duplication rate = 3.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6412 >>>>>>> ACTG content number of A's = 35,300,183 bp (24.7%) number of C's = 28,637,038 bp (20.03%) number of T's = 45,252,016 bp (31.66%) number of G's = 33,739,869 bp (23.6%) number of N's = 8,305 bp (0.01%) GC percentage = 43.64% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,248,863 number of insertions = 12,916 mapped reads with insertion percentage = 0.7% number of deletions = 36,382 mapped reads with deletion percentage = 1.96% homopolymer indels = 44.29% >>>>>>> Coverage mean coverageData = 0.0462X std coverageData = 0.5243X There is a 3.9% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.09% 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 0.01% 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 11322480 0.04542608541785739 0.7905383134566415 chr2 243199373 12316452 0.050643436486162326 0.8198434476343412 chr3 198022430 9316032 0.04704533723780685 0.24995941296154445 chr4 191154276 9232881 0.048300677302138925 0.2791491869222337 chr5 180915260 8617996 0.047635539423263686 0.25895937730823904 chr6 171115067 8353401 0.04881744867037337 0.3311423192962379 chr7 159138663 7932168 0.0498443800548959 0.6917338146554238 chr8 146364022 7267182 0.04965142321656069 0.726504938790778 chr9 141213431 6080112 0.04305618776446272 0.5922375118136534 chr10 135534747 6728155 0.049641550590713096 0.47268341171228295 chr11 135006516 6481145 0.04800616438394722 0.5195855716070483 chr12 133851895 6534411 0.04881821807603098 0.26201256631216885 chr13 115169878 4373089 0.03797077044746023 0.21992254190268132 chr14 107349540 4225344 0.0393606157977016 0.33106583972852294 chr15 102531392 4071189 0.03970675634638804 0.23167793666765218 chr16 90354753 4112805 0.04551841340322185 0.28941894344322494 chr17 81195210 3937002 0.048488106625994315 0.29434439680430596 chr18 78077248 4044420 0.05180023763132635 1.1206339688581797 chr19 59128983 3063307 0.05180719918690298 0.6173764654242617 chr20 63025520 2915283 0.04625559614581522 0.27592447264596454 chr21 48129895 1834632 0.038118346196267416 0.25104571104540807 chr22 51304566 1630488 0.03178056315689329 0.20489757142623438 chrMT 16571 9751 0.5884376320077244 0.8886235948935446 chrX 155270560 8227097 0.05298555630893583 0.40129766512954657 chrY 59373566 372940 0.006281246438861361 0.16764655158910804