BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716840.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 = 3,263,115 number of mapped reads = 2,901,294 (88.91%) number of supplementary alignments = 14,793 (0.45%) number of secondary alignments = 0 number of mapped bases = 166,260,647 bp number of sequenced bases = 166,215,031 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 123,286 duplication rate = 3.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7505 >>>>>>> ACTG content number of A's = 42,515,402 bp (25.58%) number of C's = 30,536,611 bp (18.37%) number of T's = 51,285,791 bp (30.86%) number of G's = 41,876,083 bp (25.19%) number of N's = 1,144 bp (0%) GC percentage = 43.57% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 849,156 number of insertions = 10,866 mapped reads with insertion percentage = 0.37% number of deletions = 29,384 mapped reads with deletion percentage = 1.01% homopolymer indels = 41.39% >>>>>>> Coverage mean coverageData = 0.0537X std coverageData = 0.4424X There is a 4.6% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 19794203 0.07941485931142374 0.7403323186292539 chr2 243199373 17232434 0.07085723037616548 0.6404486852587284 chr3 198022430 10782130 0.05444903387964686 0.26807030489042566 chr4 191154276 7027584 0.03676393825477386 0.23608764478238944 chr5 180915260 11094320 0.061323295779471564 0.2845541480488834 chr6 171115067 6701792 0.0391654114245825 0.27386918831345863 chr7 159138663 11251361 0.07070161824848309 0.7990820377827456 chr8 146364022 7534815 0.05147996684595071 0.3516291771044612 chr9 141213431 4746301 0.033610832669308914 0.33318207820263257 chr10 135534747 7459059 0.05503429316173807 0.3810384701358428 chr11 135006516 7179697 0.053180373901360434 0.4258278891394965 chr12 133851895 6736195 0.05032573502227966 0.2610740343421383 chr13 115169878 3627500 0.03149695096490421 0.20356015810053438 chr14 107349540 3583483 0.03338144718645278 0.2265311318786908 chr15 102531392 7234736 0.07056117993599463 0.3156920775997005 chr16 90354753 5214785 0.05771456206625898 0.30491890319744774 chr17 81195210 5989785 0.07377017683678631 0.34544820704548446 chr18 78077248 5378000 0.06888050152587345 0.7315395829024414 chr19 59128983 2632275 0.04451750844420916 0.6064391697576355 chr20 63025520 4336690 0.06880847631245247 0.30313450194043656 chr21 48129895 2126830 0.04418937543911118 0.24993226088462162 chr22 51304566 1911694 0.037261673746543336 0.218908179172064 chrMT 16571 11085 0.6689397139581196 0.9003454807660577 chrX 155270560 6320543 0.04070664136201995 0.2932461150235578 chrY 59373566 353350 0.005951301628067952 0.11792707925938181