BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716334.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 = 435,247 number of mapped reads = 390,829 (89.79%) number of supplementary alignments = 1,750 (0.4%) number of secondary alignments = 0 number of mapped bases = 22,495,978 bp number of sequenced bases = 22,489,590 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,813 duplication rate = 1.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2359 >>>>>>> ACTG content number of A's = 5,706,098 bp (25.37%) number of C's = 4,181,879 bp (18.59%) number of T's = 7,187,954 bp (31.96%) number of G's = 5,413,260 bp (24.07%) number of N's = 399 bp (0%) GC percentage = 42.66% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 121,649 number of insertions = 1,464 mapped reads with insertion percentage = 0.37% number of deletions = 3,830 mapped reads with deletion percentage = 0.97% homopolymer indels = 41.97% >>>>>>> Coverage mean coverageData = 0.0073X std coverageData = 0.0998X There is a 0.69% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% 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 1919520 0.007701164363397915 0.1380909342967697 chr2 243199373 1921984 0.007902915111545127 0.10793002311160574 chr3 198022430 1491710 0.007533035525319026 0.08920046730379796 chr4 191154276 1472931 0.007705456717065539 0.09278219094947719 chr5 180915260 1372959 0.007588961815603615 0.08958349798399745 chr6 171115067 1308572 0.007647321904154705 0.09257438769460581 chr7 159138663 1207454 0.007587433356782695 0.10362381633403185 chr8 146364022 1134980 0.00775450130770525 0.10112736533829911 chr9 141213431 929271 0.006580613426211562 0.09850220599604 chr10 135534747 1071645 0.00790679160673093 0.10456497412332257 chr11 135006516 997691 0.007389947015594417 0.0977181200209795 chr12 133851895 1111607 0.00830475354868902 0.0944550005258032 chr13 115169878 670231 0.005819499088120941 0.07847550979716456 chr14 107349540 660470 0.00615251821293319 0.08358952008157827 chr15 102531392 598720 0.005839382342531739 0.07829020563375255 chr16 90354753 640055 0.007083800007731746 0.08911722753301149 chr17 81195210 609134 0.00750209279586813 0.09040909443262568 chr18 78077248 608639 0.007795343913760895 0.1440880264417 chr19 59128983 420366 0.007109305431483575 0.11590095476715047 chr20 63025520 479389 0.007606268064111172 0.09043234992686099 chr21 48129895 288331 0.005990684168332385 0.08275885094316146 chr22 51304566 257219 0.0050135693575499695 0.07289096190888227 chrMT 16571 8126 0.4903747510711484 0.7279499371904606 chrX 155270560 1251464 0.008059892358216521 0.09668578925861893 chrY 59373566 63510 0.0010696679394328445 0.03983574670739007