BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173868.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 = 5,337,544 number of mapped reads = 5,185,170 (97.15%) number of supplementary alignments = 516,415 (9.68%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,596,652 number of mapped paired reads (second in pair) = 2,588,518 number of mapped paired reads (both in pair) = 5,086,748 number of mapped paired reads (singletons) = 98,422 number of mapped bases = 609,221,390 bp number of sequenced bases = 608,867,492 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,930,729 duplication rate = 64% >>>>>>> Insert size mean insert size = 702,136.1509 std insert size = 7,789,121.2372 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 52.756 >>>>>>> ACTG content number of A's = 183,632,136 bp (30.16%) number of C's = 118,741,605 bp (19.5%) number of T's = 183,388,239 bp (30.12%) number of G's = 123,098,258 bp (20.22%) number of N's = 7,254 bp (0%) GC percentage = 39.72% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 6,278,353 number of insertions = 62,285 mapped reads with insertion percentage = 1.16% number of deletions = 145,922 mapped reads with deletion percentage = 2.75% homopolymer indels = 42.51% >>>>>>> Coverage mean coverageData = 0.1968X std coverageData = 2.9332X There is a 4.35% of reference with a coverageData >= 1X There is a 3.38% of reference with a coverageData >= 2X There is a 2.55% of reference with a coverageData >= 3X There is a 2.06% of reference with a coverageData >= 4X There is a 1.53% of reference with a coverageData >= 5X There is a 1.23% of reference with a coverageData >= 6X There is a 0.89% of reference with a coverageData >= 7X There is a 0.73% of reference with a coverageData >= 8X There is a 0.53% of reference with a coverageData >= 9X There is a 0.44% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% 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 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 48731622 0.19551253996675097 2.1043218985766456 chr2 243199373 52637539 0.21643780718135322 8.944003958662446 chr3 198022430 49105530 0.2479796354382683 1.4142768959856253 chr4 191154276 30957897 0.16195241690539008 1.2861931736908814 chr5 180915260 39708723 0.2194879691188018 1.3101194645172745 chr6 171115067 31125252 0.18189661813941843 1.3935453494690113 chr7 159138663 33044944 0.2076487471809412 1.8431256610295272 chr8 146364022 37364472 0.2552845398030945 1.82768602497943 chr9 141213431 21534370 0.15249519714594287 1.3844209625221728 chr10 135534747 32797721 0.2419875472966353 2.681456332169104 chr11 135006516 21130064 0.1565114383071703 1.1251199673594834 chr12 133851895 28369880 0.21194978225747196 1.2960772412096142 chr13 115169878 15939332 0.13839844477390173 1.0437463295471807 chr14 107349540 18446679 0.17183752254550883 1.166341178972539 chr15 102531392 20792875 0.20279520832019915 1.252403665701774 chr16 90354753 19611601 0.2170511273491058 1.6880536222699092 chr17 81195210 23904436 0.29440697302217705 1.6541589387831626 chr18 78077248 11599719 0.1485672112828567 2.105982918659232 chr19 59128983 9690722 0.1638912341854417 1.5326883231855335 chr20 63025520 25814591 0.4095894964452495 1.9678971752837697 chr21 48129895 7416124 0.15408560521480463 1.1442894570993305 chr22 51304566 4362055 0.0850227443693803 0.7908986687001001 chrMT 16571 1045979 63.121054854866934 46.103322206849946 chrX 155270560 23039836 0.14838508987151203 1.0769470574722748 chrY 59373566 1049427 0.017674986878840997 0.6151972489069424