BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173940.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 3,660,348 number of mapped reads = 3,563,702 (97.36%) number of supplementary alignments = 346,462 (9.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,787,020 number of mapped paired reads (second in pair) = 1,776,682 number of mapped paired reads (both in pair) = 3,500,514 number of mapped paired reads (singletons) = 63,188 number of mapped bases = 418,813,642 bp number of sequenced bases = 418,561,377 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,695,881 duplication rate = 63.39% >>>>>>> Insert size mean insert size = 850,999.7468 std insert size = 8,757,395.9188 median insert size = 190 >>>>>>> Mapping quality mean mapping quality = 52.7846 >>>>>>> ACTG content number of A's = 126,563,264 bp (30.24%) number of C's = 81,594,617 bp (19.49%) number of T's = 126,141,262 bp (30.14%) number of G's = 84,256,955 bp (20.13%) number of N's = 5,279 bp (0%) GC percentage = 39.62% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 4,332,527 number of insertions = 42,083 mapped reads with insertion percentage = 1.15% number of deletions = 103,982 mapped reads with deletion percentage = 2.85% homopolymer indels = 42.24% >>>>>>> Coverage mean coverageData = 0.1353X std coverageData = 2.1031X There is a 3% of reference with a coverageData >= 1X There is a 2.3% of reference with a coverageData >= 2X There is a 1.72% of reference with a coverageData >= 3X There is a 1.4% of reference with a coverageData >= 4X There is a 1.04% of reference with a coverageData >= 5X There is a 0.84% of reference with a coverageData >= 6X There is a 0.61% of reference with a coverageData >= 7X There is a 0.5% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.2% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 37738087 0.1514061904784582 1.654587244897746 chr2 243199373 32277606 0.13272076157860818 5.963620484870424 chr3 198022430 35861933 0.18110035817659645 1.2184982561511963 chr4 191154276 17260626 0.09029683437476439 0.9857724110566601 chr5 180915260 30504138 0.16861008850220816 1.1888647841836952 chr6 171115067 29003917 0.16949949240881285 1.21641656917925 chr7 159138663 31448723 0.19761836883096096 2.1495336365250637 chr8 146364022 16742351 0.114388432151721 1.1129131821146507 chr9 141213431 16947950 0.12001655848160789 1.1279961230861015 chr10 135534747 17756389 0.13100986568411124 2.0639303919336576 chr11 135006516 16753442 0.12409358078687106 1.0197535015123922 chr12 133851895 15025925 0.11225784289419287 0.9506670281483774 chr13 115169878 13921883 0.12088128633773494 0.9990759522698357 chr14 107349540 14758351 0.1374794060598676 1.0589825960274044 chr15 102531392 13806399 0.13465533560687443 1.0356423116300115 chr16 90354753 17285103 0.19130264237455222 1.578465719482098 chr17 81195210 9699332 0.11945694826086416 1.079670987956998 chr18 78077248 6722765 0.08610402098188706 1.4268821798559712 chr19 59128983 7619938 0.1288697625663543 1.6234893122522707 chr20 63025520 10832208 0.17187018845699328 1.1639413926320978 chr21 48129895 6479375 0.13462267058758387 1.0728267710431614 chr22 51304566 3656866 0.0712775934991829 0.7105483109599543 chrMT 16571 1243111 75.01725906704483 61.07717512324527 chrX 155270560 14912567 0.09604246291119192 0.8886321334764062 chrY 59373566 554657 0.009341817198582953 0.39386190152123973