BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013255.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,194,850 number of mapped reads = 979,489 (81.98%) number of supplementary alignments = 6,805 (0.57%) number of secondary alignments = 0 number of mapped bases = 62,323,896 bp number of sequenced bases = 62,290,447 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,441 duplication rate = 6.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3836 >>>>>>> ACTG content number of A's = 16,915,343 bp (27.16%) number of C's = 10,916,842 bp (17.53%) number of T's = 20,522,707 bp (32.95%) number of G's = 13,934,842 bp (22.37%) number of N's = 713 bp (0%) GC percentage = 39.9% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 501,658 number of insertions = 4,396 mapped reads with insertion percentage = 0.45% number of deletions = 19,468 mapped reads with deletion percentage = 1.96% homopolymer indels = 47.42% >>>>>>> Coverage mean coverageData = 0.0201X std coverageData = 0.2276X There is a 1.48% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 4257163 0.017079849121017836 0.32745468318657805 chr2 243199373 6637743 0.02729342151716814 0.290106020784362 chr3 198022430 4000097 0.020200221762756876 0.18585169880521238 chr4 191154276 3916228 0.02048726338719203 0.1907174590321162 chr5 180915260 3853904 0.021302260516885087 0.19226903372462234 chr6 171115067 3114687 0.01820229541797158 0.19144936494930925 chr7 159138663 3246094 0.020397896644387417 0.23769459636389453 chr8 146364022 2865819 0.019580078224415015 0.31558145557295947 chr9 141213431 1973379 0.013974442700142312 0.19987643490782442 chr10 135534747 3026172 0.02232764709406954 0.21633393810788182 chr11 135006516 2582274 0.019127032357460435 0.20192494857183327 chr12 133851895 3413562 0.025502530240606607 0.20987133864422486 chr13 115169878 1263789 0.010973259865743715 0.13731401501853727 chr14 107349540 2031471 0.018923891057195028 0.18296288637486782 chr15 102531392 1933619 0.018858799849318344 0.18164067413173998 chr16 90354753 2310515 0.025571593339422886 0.20682108310629435 chr17 81195210 1842061 0.022686818594348113 0.19875423680478502 chr18 78077248 1743557 0.022331178988275815 0.29307551941635535 chr19 59128983 1231324 0.020824373049000353 0.2534367156178842 chr20 63025520 1797501 0.028520208956625825 0.2222056423997863 chr21 48129895 1209088 0.025121351293203528 0.21049747672045915 chr22 51304566 737106 0.014367259241604344 0.15219758861830512 chrMT 16571 20768 1.253273791563575 1.6063007603231194 chrX 155270560 3185937 0.020518616020963665 0.19513666355004672 chrY 59373566 130038 0.0021901665801915956 0.059657518072312093