BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063571.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,441,131 number of mapped reads = 3,063,802 (89.03%) number of supplementary alignments = 29,243 (0.85%) number of secondary alignments = 0 number of mapped bases = 203,238,691 bp number of sequenced bases = 203,156,219 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 605,166 duplication rate = 12.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8273 >>>>>>> ACTG content number of A's = 56,663,248 bp (27.89%) number of C's = 37,523,233 bp (18.47%) number of T's = 65,024,923 bp (32.01%) number of G's = 43,939,585 bp (21.63%) number of N's = 5,230 bp (0%) GC percentage = 40.1% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,687,462 number of insertions = 15,534 mapped reads with insertion percentage = 0.5% number of deletions = 47,456 mapped reads with deletion percentage = 1.53% homopolymer indels = 46.93% >>>>>>> Coverage mean coverageData = 0.0657X std coverageData = 1.1053X There is a 2.31% of reference with a coverageData >= 1X There is a 1.42% of reference with a coverageData >= 2X There is a 0.95% of reference with a coverageData >= 3X There is a 0.63% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.16% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 12955719 0.05197868293375285 1.9303964031993521 chr2 243199373 17999911 0.07401298275551065 0.887007529558152 chr3 198022430 14636312 0.07391239467165411 0.5810567098156958 chr4 191154276 15216651 0.07960403145781578 0.6147412639880564 chr5 180915260 6655327 0.036786985243809724 0.40854783998369276 chr6 171115067 7915558 0.046258685098723655 0.4747387351012947 chr7 159138663 21408163 0.13452521591186173 1.5713736132265546 chr8 146364022 4491559 0.030687589331208732 2.9970078876343482 chr9 141213431 9601152 0.0679903599254663 0.8188371687722473 chr10 135534747 5914397 0.04363749614702125 0.5415767275772415 chr11 135006516 15203134 0.11261037208011501 0.8765698365180294 chr12 133851895 9000387 0.06724138645926529 0.5871473010770314 chr13 115169878 5590520 0.04854151186997003 0.4803830314119805 chr14 107349540 4540067 0.04229237498362825 0.5143418388697795 chr15 102531392 1652320 0.016115259607516107 0.26590483069539894 chr16 90354753 4461824 0.04938117643905241 0.4996573438398066 chr17 81195210 9142770 0.11260233208338274 0.7312234492271598 chr18 78077248 6327202 0.08103771792776303 1.1746277699209902 chr19 59128983 5966029 0.10089855595858972 1.2696100951957074 chr20 63025520 4265777 0.06768332891184396 0.5794427844693398 chr21 48129895 5045214 0.10482495338915657 0.7004987137554294 chr22 51304566 919707 0.017926416140037125 0.26991286243190216 chrMT 16571 56762 3.4253816909057995 5.187967308164544 chrX 155270560 13585512 0.08749573647444822 0.6929296416018593 chrY 59373566 686717 0.011566039338112183 0.2757269455436901