BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173995.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 = 6,766,378 number of mapped reads = 6,623,515 (97.89%) number of supplementary alignments = 912,285 (13.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,310,767 number of mapped paired reads (second in pair) = 3,312,748 number of mapped paired reads (both in pair) = 6,532,290 number of mapped paired reads (singletons) = 91,225 number of mapped bases = 753,516,530 bp number of sequenced bases = 752,991,754 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,419,981 duplication rate = 65.05% >>>>>>> Insert size mean insert size = 1,188,890.4389 std insert size = 10,062,774.2181 median insert size = 157 >>>>>>> Mapping quality mean mapping quality = 52.4427 >>>>>>> ACTG content number of A's = 224,675,953 bp (29.84%) number of C's = 149,965,515 bp (19.92%) number of T's = 222,766,962 bp (29.58%) number of G's = 155,577,656 bp (20.66%) number of N's = 5,668 bp (0%) GC percentage = 40.58% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 6,392,146 number of insertions = 84,706 mapped reads with insertion percentage = 1.23% number of deletions = 215,276 mapped reads with deletion percentage = 3.17% homopolymer indels = 41.25% >>>>>>> Coverage mean coverageData = 0.2434X std coverageData = 4.1241X There is a 5% of reference with a coverageData >= 1X There is a 3.77% of reference with a coverageData >= 2X There is a 2.86% of reference with a coverageData >= 3X There is a 2.32% of reference with a coverageData >= 4X There is a 1.77% of reference with a coverageData >= 5X There is a 1.47% of reference with a coverageData >= 6X There is a 1.12% of reference with a coverageData >= 7X There is a 0.96% of reference with a coverageData >= 8X There is a 0.74% of reference with a coverageData >= 9X There is a 0.66% of reference with a coverageData >= 10X There is a 0.5% of reference with a coverageData >= 11X There is a 0.46% of reference with a coverageData >= 12X There is a 0.35% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.23% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.16% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.11% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 65100378 0.26118441646731144 2.1905329630556634 chr2 243199373 63418365 0.2607669757438067 13.16220030805355 chr3 198022430 53120141 0.2682531519282942 1.6074232671914441 chr4 191154276 49499585 0.25895096900683506 2.129195797808823 chr5 180915260 44144345 0.24400564662151772 1.5266964620972217 chr6 171115067 47067099 0.27506110259711963 1.861911238959676 chr7 159138663 44071424 0.2769372518857972 2.0709526276263226 chr8 146364022 39378054 0.2690418961020352 2.545049444315357 chr9 141213431 30550439 0.21634230387051498 1.9700116711212987 chr10 135534747 35107817 0.25903185549901825 2.7908915935481997 chr11 135006516 36886490 0.27322007183712527 1.6873332936735481 chr12 133851895 32711754 0.24438767938249958 1.6014122225398686 chr13 115169878 26616816 0.2311091794331848 1.5126359066857056 chr14 107349540 23501805 0.21892785940209897 1.4686123642354199 chr15 102531392 21363113 0.2083568025683295 1.452741713843906 chr16 90354753 22090056 0.2444813943545394 1.8194690404126492 chr17 81195210 21558102 0.2655095294414535 1.698385382406179 chr18 78077248 20642067 0.26438005345680216 2.7901520572051344 chr19 59128983 13807827 0.23352045476581257 1.8133746504082209 chr20 63025520 16013143 0.25407395290034895 1.6248886211952396 chr21 48129895 11160857 0.2318903251295271 1.902740951386692 chr22 51304566 9494869 0.1850686934960136 1.6480428159099336 chrMT 16571 1003228 60.541186409993365 50.92316567380813 chrX 155270560 19059597 0.12275087434475666 1.0903486898108095 chrY 59373566 6149159 0.10356728447134202 1.583053892737303