BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525099.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 = 1,660,028 number of mapped reads = 1,531,682 (92.27%) number of supplementary alignments = 5,520 (0.33%) number of secondary alignments = 0 number of mapped bases = 89,419,507 bp number of sequenced bases = 89,391,215 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,335 duplication rate = 2.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6108 >>>>>>> ACTG content number of A's = 21,285,092 bp (23.81%) number of C's = 15,994,545 bp (17.89%) number of T's = 29,512,107 bp (33.01%) number of G's = 22,597,675 bp (25.28%) number of N's = 1,796 bp (0%) GC percentage = 43.17% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 454,820 number of insertions = 6,824 mapped reads with insertion percentage = 0.44% number of deletions = 17,517 mapped reads with deletion percentage = 1.14% homopolymer indels = 42.29% >>>>>>> Coverage mean coverageData = 0.0289X std coverageData = 0.2725X There is a 2.61% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 7515691 0.03015314854521466 0.4321171651753222 chr2 243199373 7007623 0.028814313596112768 0.3878270241711717 chr3 198022430 5143308 0.02597336069454354 0.17558569777944383 chr4 191154276 5540711 0.028985545685622015 0.2204428600407561 chr5 180915260 5101145 0.028196322410834775 0.18179790168747847 chr6 171115067 4733308 0.027661550107682804 0.21200357832137112 chr7 159138663 5101439 0.03205656566311607 0.3518767206686487 chr8 146364022 4688525 0.03203331622029354 0.3412902379844868 chr9 141213431 2988485 0.021162894909054365 0.1942355443351667 chr10 135534747 3935217 0.02903474634441897 0.288901865074062 chr11 135006516 3166861 0.02345709743372683 0.2156855510423457 chr12 133851895 4450932 0.03325266332613371 0.1985315416158661 chr13 115169878 2704450 0.023482268514689233 0.16663128717896755 chr14 107349540 3014369 0.02807994333278 0.18504589505665942 chr15 102531392 3296277 0.032148953951585874 0.1963587558472844 chr16 90354753 3068540 0.0339610247177589 0.21044384898466065 chr17 81195210 3914335 0.04820893991160316 0.2486433441012426 chr18 78077248 1681197 0.021532482804721805 0.32090113808548454 chr19 59128983 2307005 0.039016483676034136 0.34722808426285834 chr20 63025520 2941483 0.04667130076832369 0.24407963508194488 chr21 48129895 1132286 0.023525627886784296 0.20886099138467498 chr22 51304566 830324 0.01618421253188264 0.13799612683992818 chrMT 16571 13740 0.8291593748114175 0.9646253642848648 chrX 155270560 4808260 0.030966977899738367 0.20636849185375294 chrY 59373566 333996 0.005625331650115137 0.26086571340656733