BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716916.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 = 1,057,213 number of mapped reads = 735,960 (69.61%) number of supplementary alignments = 3,504 (0.33%) number of secondary alignments = 0 number of mapped bases = 40,980,365 bp number of sequenced bases = 40,968,168 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,570 duplication rate = 1.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.1354 >>>>>>> ACTG content number of A's = 9,788,337 bp (23.89%) number of C's = 8,439,573 bp (20.6%) number of T's = 11,837,135 bp (28.89%) number of G's = 10,901,974 bp (26.61%) number of N's = 1,149 bp (0%) GC percentage = 47.21% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 218,728 number of insertions = 3,363 mapped reads with insertion percentage = 0.45% number of deletions = 7,216 mapped reads with deletion percentage = 0.97% homopolymer indels = 33.62% >>>>>>> Coverage mean coverageData = 0.0132X std coverageData = 0.1391X There is a 1.23% of reference with a coverageData >= 1X There is a 0.07% 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 3999434 0.016045833643078464 0.16751327470636757 chr2 243199373 3573560 0.01469395235653013 0.1652461629031581 chr3 198022430 2741396 0.013843866071131437 0.13167150845453057 chr4 191154276 2669164 0.013963402001009907 0.1370527764779457 chr5 180915260 2479924 0.013707655175135586 0.1244980117161 chr6 171115067 1760538 0.010288620580676276 0.10999257680759164 chr7 159138663 2366557 0.01487103734181806 0.15408692880875915 chr8 146364022 2516391 0.017192688241376694 0.1446018402517421 chr9 141213431 1730580 0.012255066587823363 0.12535665664926274 chr10 135534747 2199549 0.016228672341860793 0.2068084707458724 chr11 135006516 1740307 0.012890540779528004 0.13753208220420055 chr12 133851895 1921594 0.014356120994775606 0.12767310272878232 chr13 115169878 741943 0.006442161899311902 0.08574081286982668 chr14 107349540 1311426 0.012216410056344908 0.11990689597981127 chr15 102531392 830303 0.008098036940725431 0.09742067469107676 chr16 90354753 1055462 0.0116813113306834 0.12105970849256024 chr17 81195210 1629635 0.020070580518235005 0.1564974579028572 chr18 78077248 1098331 0.014067235054186337 0.14998608414599607 chr19 59128983 1085939 0.018365595768829644 0.1633628975826653 chr20 63025520 1067148 0.016931998339720165 0.1448667600148758 chr21 48129895 548907 0.011404699719373999 0.12286571323457648 chr22 51304566 432795 0.00843579887217056 0.0987553857673824 chrMT 16571 34106 2.0581739182909904 1.9793378113960574 chrX 155270560 1311170 0.008444421144613634 0.10478899347914597 chrY 59373566 134206 0.0022603661703593817 0.07404975203523158