BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525251.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 = 1,223,197 number of mapped reads = 1,122,319 (91.75%) number of supplementary alignments = 4,417 (0.36%) number of secondary alignments = 0 number of mapped bases = 65,139,835 bp number of sequenced bases = 65,118,431 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,997 duplication rate = 2.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0913 >>>>>>> ACTG content number of A's = 16,161,951 bp (24.82%) number of C's = 12,431,533 bp (19.09%) number of T's = 20,754,828 bp (31.87%) number of G's = 15,768,738 bp (24.22%) number of N's = 1,381 bp (0%) GC percentage = 43.31% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 326,074 number of insertions = 4,366 mapped reads with insertion percentage = 0.39% number of deletions = 13,209 mapped reads with deletion percentage = 1.17% homopolymer indels = 44.66% >>>>>>> Coverage mean coverageData = 0.021X std coverageData = 0.2205X There is a 1.94% of reference with a coverageData >= 1X There is a 0.12% 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 7101161 0.028490043360814735 0.39786741977538154 chr2 243199373 5571433 0.022908911858091015 0.29055798400660604 chr3 198022430 5180339 0.026160364762719053 0.17257902495580876 chr4 191154276 3770914 0.01972707113284769 0.15593592304305057 chr5 180915260 2996519 0.016563108054013797 0.1372963466257297 chr6 171115067 3341916 0.019530226406070952 0.16395670724267788 chr7 159138663 3910653 0.02457387115285743 0.3000741739430835 chr8 146364022 3103652 0.021205019905779852 0.2206667044384184 chr9 141213431 2184445 0.015469102227252025 0.16277231361931163 chr10 135534747 3605893 0.0266049340100218 0.2365334553577769 chr11 135006516 3049755 0.02258968744886358 0.1878543505611072 chr12 133851895 3016172 0.022533651839594798 0.16069086502498786 chr13 115169878 2086032 0.018112652685105736 0.14437425717419294 chr14 107349540 2520336 0.023477846295382354 0.16624512089564913 chr15 102531392 1809744 0.017650633281171096 0.14339138518181216 chr16 90354753 1760785 0.01948746404076828 0.160258655816366 chr17 81195210 1311095 0.016147442687813728 0.14004597615611522 chr18 78077248 1437297 0.018408653440244206 0.30241396921039454 chr19 59128983 1159235 0.019605190909507103 0.26803722997953966 chr20 63025520 1237209 0.019630286271338976 0.15036248748002612 chr21 48129895 863587 0.017942839891921643 0.15301755617047375 chr22 51304566 526444 0.010261152974181674 0.10747400833942959 chrMT 16571 1371 0.08273489831633576 0.30520305038082224 chrX 155270560 3405463 0.021932444888457928 0.16877189465128245 chrY 59373566 188385 0.003172876629980419 0.09319825410068165