BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716516.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 = 534,909 number of mapped reads = 451,967 (84.49%) number of supplementary alignments = 1,997 (0.37%) number of secondary alignments = 0 number of mapped bases = 25,877,275 bp number of sequenced bases = 25,869,908 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,684 duplication rate = 1.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3926 >>>>>>> ACTG content number of A's = 6,836,427 bp (26.43%) number of C's = 4,778,593 bp (18.47%) number of T's = 7,953,252 bp (30.74%) number of G's = 6,300,868 bp (24.36%) number of N's = 768 bp (0%) GC percentage = 42.83% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 130,907 number of insertions = 2,129 mapped reads with insertion percentage = 0.47% number of deletions = 4,702 mapped reads with deletion percentage = 1.03% homopolymer indels = 42.91% >>>>>>> Coverage mean coverageData = 0.0084X std coverageData = 0.1121X There is a 0.8% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% 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 2791415 0.011199229870725178 0.17822463348125442 chr2 243199373 2371455 0.009751073659223619 0.13328504383265652 chr3 198022430 2291258 0.011570699339463716 0.11108933135224956 chr4 191154276 1200533 0.006280440203179132 0.08318157326704485 chr5 180915260 1134920 0.006273213215955359 0.0819236299768544 chr6 171115067 1879204 0.010982107145480065 0.11720110507131991 chr7 159138663 1488464 0.009353251887003726 0.12564178889230648 chr8 146364022 1860961 0.012714606872445744 0.12005286552659003 chr9 141213431 985873 0.006981439322156262 0.09844852415960634 chr10 135534747 1332532 0.009831663315090704 0.125091944319098 chr11 135006516 848159 0.006282356030874836 0.09162038807784696 chr12 133851895 1120281 0.008369556516177825 0.09529479100398704 chr13 115169878 595446 0.00517015395292856 0.07426077703520129 chr14 107349540 566861 0.005280516339427258 0.07774842842976731 chr15 102531392 754737 0.0073610333896568965 0.0886179026399262 chr16 90354753 549611 0.006082812267773008 0.08399541542013048 chr17 81195210 615301 0.0075780455521945195 0.09099718486617964 chr18 78077248 503177 0.006444604707379031 0.1419136567549449 chr19 59128983 492630 0.008331447202465836 0.13300929913762655 chr20 63025520 400745 0.006358456066685368 0.08241891212701333 chr21 48129895 249697 0.005187981399086784 0.07585168571953393 chr22 51304566 408988 0.007971766099726874 0.0923536902241128 chrMT 16571 6446 0.388992818779796 0.6837911592667115 chrX 155270560 1363882 0.008783905976767264 0.10194142542802015 chrY 59373566 64699 0.0010896936862441445 0.039926654844671984