BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716198.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 = 3,016,377 number of mapped reads = 2,735,469 (90.69%) number of supplementary alignments = 73,724 (2.44%) number of secondary alignments = 0 number of mapped bases = 203,209,021 bp number of sequenced bases = 203,137,145 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 111,586 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5134 >>>>>>> ACTG content number of A's = 51,750,453 bp (25.48%) number of C's = 42,818,876 bp (21.08%) number of T's = 59,588,485 bp (29.33%) number of G's = 48,955,778 bp (24.1%) number of N's = 23,553 bp (0.01%) GC percentage = 45.18% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 1,476,611 number of insertions = 15,853 mapped reads with insertion percentage = 0.57% number of deletions = 41,444 mapped reads with deletion percentage = 1.5% homopolymer indels = 41.12% >>>>>>> Coverage mean coverageData = 0.0656X std coverageData = 0.488X There is a 5.35% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 16219417 0.06507272453295111 0.5604532697511403 chr2 243199373 17363685 0.0713969151556982 0.7419812281408128 chr3 198022430 13406396 0.06770140130085263 0.3079535543125991 chr4 191154276 12770492 0.06680725258795675 0.34637561879647927 chr5 180915260 12152744 0.06717368120301184 0.3111985961786213 chr6 171115067 11663892 0.06816402672477696 0.37105046649430234 chr7 159138663 11132298 0.06995344682517535 0.6444508842570993 chr8 146364022 10323464 0.07053279801234213 0.628521934451093 chr9 141213431 8675524 0.06143554432864109 0.5215699960341811 chr10 135534747 9753758 0.07196499949935348 0.5008325067767777 chr11 135006516 9146255 0.0677467671264104 0.5431718384593438 chr12 133851895 9186312 0.06863042170602067 0.3164325775798389 chr13 115169878 6258954 0.0543454079199424 0.27467866461959484 chr14 107349540 6124358 0.057050621735314375 0.3625400049898356 chr15 102531392 5948776 0.05801906990592696 0.2876982438955254 chr16 90354753 6127251 0.06781326711169251 0.35992552932835564 chr17 81195210 5788004 0.07128504255361862 0.3550106777398908 chr18 78077248 5508557 0.07055265318777629 0.9976555278300193 chr19 59128983 4351664 0.073596124594262 0.5035360974257553 chr20 63025520 4373517 0.0693927951724952 0.3354939566435122 chr21 48129895 2689585 0.055881796542460775 0.31919697861463103 chr22 51304566 2444056 0.04763817707765036 0.26098607508278765 chrMT 16571 13437 0.8108744191660129 1.078580319724532 chrX 155270560 11255156 0.07248737944913704 0.4204345278239694 chrY 59373566 531469 0.008951273029482515 0.2401870304170917