BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716884.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 = 996,245 number of mapped reads = 876,174 (87.95%) number of supplementary alignments = 3,955 (0.4%) number of secondary alignments = 0 number of mapped bases = 50,615,611 bp number of sequenced bases = 50,601,053 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,459 duplication rate = 1.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7099 >>>>>>> ACTG content number of A's = 12,965,535 bp (25.62%) number of C's = 9,822,290 bp (19.41%) number of T's = 15,918,939 bp (31.46%) number of G's = 11,892,810 bp (23.5%) number of N's = 1,479 bp (0%) GC percentage = 42.91% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 248,822 number of insertions = 4,128 mapped reads with insertion percentage = 0.47% number of deletions = 9,274 mapped reads with deletion percentage = 1.05% homopolymer indels = 41% >>>>>>> Coverage mean coverageData = 0.0164X std coverageData = 0.166X There is a 1.53% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% 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 5911195 0.02371586869586977 0.2414326699768919 chr2 243199373 4271223 0.017562639851049288 0.20872279161608814 chr3 198022430 4446743 0.022455754128459085 0.15774297922650393 chr4 191154276 2318612 0.012129532482966795 0.12039308137412198 chr5 180915260 3133203 0.017318621989101418 0.13921885530799546 chr6 171115067 3752450 0.02192939561540773 0.18292288828628278 chr7 159138663 2832812 0.017800903605681293 0.2026889972197564 chr8 146364022 3612736 0.0246832244060634 0.17695072175783427 chr9 141213431 2104670 0.014904177209602677 0.16341926999299836 chr10 135534747 2545670 0.018782415995508516 0.191158561482392 chr11 135006516 1623652 0.01202647137416686 0.13592580280367772 chr12 133851895 2199027 0.016428807376989322 0.1380512834763322 chr13 115169878 1161158 0.010082132760442796 0.10626285772078876 chr14 107349540 1090729 0.010160537250555522 0.11634292373350577 chr15 102531392 1484086 0.014474454808923301 0.1278968596626845 chr16 90354753 1070052 0.011842785957258939 0.12367290888737068 chr17 81195210 1146440 0.014119552126289223 0.12855452202511308 chr18 78077248 953765 0.012215658523210245 0.22219469377464462 chr19 59128983 764294 0.012925877652926993 0.18480293335071768 chr20 63025520 852079 0.013519586986350926 0.12275166038228506 chr21 48129895 453781 0.009428256596030388 0.10868468212869056 chr22 51304566 622449 0.01213242891480653 0.11596760149760511 chrMT 16571 1776 0.10717518556514392 0.3234900325658063 chrX 155270560 2152743 0.013864463424360677 0.13680303888798293 chrY 59373566 110266 0.0018571564322075586 0.056642779667068176