BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716398.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 = 1,273,620 number of mapped reads = 1,198,848 (94.13%) number of supplementary alignments = 19,327 (1.52%) number of secondary alignments = 0 number of mapped bases = 95,224,991 bp number of sequenced bases = 95,183,745 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,572 duplication rate = 2.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2248 >>>>>>> ACTG content number of A's = 22,909,025 bp (24.07%) number of C's = 18,463,002 bp (19.4%) number of T's = 29,569,402 bp (31.07%) number of G's = 24,236,790 bp (25.46%) number of N's = 5,526 bp (0.01%) GC percentage = 44.86% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 777,195 number of insertions = 8,345 mapped reads with insertion percentage = 0.69% number of deletions = 23,439 mapped reads with deletion percentage = 1.93% homopolymer indels = 44.85% >>>>>>> Coverage mean coverageData = 0.0308X std coverageData = 0.4265X There is a 2.7% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8362383 0.033550098958429475 0.5941995961210337 chr2 243199373 8413905 0.03459673804339948 0.7887178707253661 chr3 198022430 7076203 0.03573435090156201 0.21262671413349832 chr4 191154276 3863360 0.020210690970888876 0.16751791946298975 chr5 180915260 5723438 0.03163601566833003 0.19905601307483448 chr6 171115067 6745949 0.03942346584827624 0.27721115605483204 chr7 159138663 4901138 0.030797908613823154 0.5908049078253366 chr8 146364022 6729618 0.045978635378030264 0.5933331012045782 chr9 141213431 4180665 0.029605292997944368 0.4145601733855889 chr10 135534747 4606319 0.03398625888902128 0.3520728154793816 chr11 135006516 3807749 0.02820418682606401 0.28279542450815526 chr12 133851895 3587743 0.026803826722064713 0.1856100339415413 chr13 115169878 3328071 0.028897061087448578 0.18548100410340843 chr14 107349540 2260502 0.02105739810342923 0.20533360562953232 chr15 102531392 2084268 0.020328096199064574 0.16140306355988893 chr16 90354753 2439271 0.02699659861833721 0.22040489035350982 chr17 81195210 2922801 0.03599720968761581 0.2503848639966331 chr18 78077248 2938560 0.03763657243656949 0.9499906669428628 chr19 59128983 1892275 0.032002495290676655 0.5173651150511215 chr20 63025520 1750906 0.02778090525869521 0.231105275532244 chr21 48129895 2113365 0.04390961168728916 0.24064556371693915 chr22 51304566 1417935 0.027637598571635905 0.1851116724012064 chrMT 16571 2384 0.1438657896324905 0.5764798400161912 chrX 155270560 3857012 0.02484058793888552 0.25235815721135313 chrY 59373566 219171 0.0036913902055335534 0.10644482353914597