BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525226.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 = 2,852,869 number of mapped reads = 2,640,222 (92.55%) number of supplementary alignments = 10,781 (0.38%) number of secondary alignments = 0 number of mapped bases = 154,392,903 bp number of sequenced bases = 154,344,771 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 152,364 duplication rate = 4.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9167 >>>>>>> ACTG content number of A's = 39,124,708 bp (25.35%) number of C's = 31,657,465 bp (20.51%) number of T's = 46,953,047 bp (30.42%) number of G's = 36,606,344 bp (23.72%) number of N's = 3,207 bp (0%) GC percentage = 44.23% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 755,665 number of insertions = 10,476 mapped reads with insertion percentage = 0.39% number of deletions = 29,439 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.32% >>>>>>> Coverage mean coverageData = 0.0499X std coverageData = 0.4294X There is a 4.25% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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% 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 13101948 0.052565357500152426 0.7116561162942624 chr2 243199373 12003578 0.04935694468258354 0.6338600292566271 chr3 198022430 8730792 0.044089914460700236 0.24246348821594366 chr4 191154276 9453204 0.0494532698813392 0.34322312018827145 chr5 180915260 8658730 0.047860694559430754 0.24953450250374573 chr6 171115067 8169367 0.04774195015801852 0.30820843500410444 chr7 159138663 8691673 0.054616978904742965 0.5684175156109436 chr8 146364022 8118748 0.05546956068206434 0.5733217655280894 chr9 141213431 5105837 0.036156879440171666 0.29400187269389005 chr10 135534747 6849404 0.05053614775257595 0.477230492078677 chr11 135006516 5447329 0.040348637690939305 0.3047103227645294 chr12 133851895 7694829 0.057487635867986775 0.27836158659097654 chr13 115169878 4627187 0.04017705914388483 0.23187456690656047 chr14 107349540 5258490 0.048984746464679776 0.2585906530834997 chr15 102531392 5759584 0.05617385941663603 0.2731696014288884 chr16 90354753 5376702 0.05950657626168266 0.2968067972235372 chr17 81195210 6848770 0.08434943391365082 0.35742505052787077 chr18 78077248 2843401 0.03641779228694126 0.5312432128176473 chr19 59128983 4093672 0.06923291746790233 0.5706129137172039 chr20 63025520 5294195 0.08400081427332928 0.3596415117981653 chr21 48129895 1968900 0.040908046859441514 0.33155328005070595 chr22 51304566 1450850 0.02827915940269332 0.19119985094201505 chrMT 16571 26561 1.6028604188039346 1.7230844387090103 chrX 155270560 8229551 0.05300136097918369 0.2906643530863371 chrY 59373566 589601 0.009930361939183507 0.4129357419060408