BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525109.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 = 1,729,663 number of mapped reads = 1,573,107 (90.95%) number of supplementary alignments = 42,310 (2.45%) number of secondary alignments = 0 number of mapped bases = 121,502,603 bp number of sequenced bases = 121,454,423 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,829 duplication rate = 1.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.602 >>>>>>> ACTG content number of A's = 32,256,364 bp (26.56%) number of C's = 22,285,535 bp (18.35%) number of T's = 37,766,109 bp (31.09%) number of G's = 29,141,774 bp (23.99%) number of N's = 4,641 bp (0%) GC percentage = 42.34% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 900,058 number of insertions = 10,503 mapped reads with insertion percentage = 0.66% number of deletions = 28,394 mapped reads with deletion percentage = 1.78% homopolymer indels = 42.68% >>>>>>> Coverage mean coverageData = 0.0392X std coverageData = 0.3953X There is a 3.48% of reference with a coverageData >= 1X There is a 0.3% 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 9628395 0.03862937216112292 0.5575758345022739 chr2 243199373 10510735 0.04321859415320121 0.6115138722989198 chr3 198022430 8187940 0.041348548242742 0.22204564753768852 chr4 191154276 7989126 0.04179412654101444 0.23342894058349575 chr5 180915260 7448084 0.041168909687330967 0.22680046122965036 chr6 171115067 7117223 0.04159319880346948 0.2645390844918447 chr7 159138663 6815635 0.04282827863144734 0.6287739314374116 chr8 146364022 6426503 0.04390766878488759 0.5623747539758378 chr9 141213431 5160806 0.036546141280286576 0.39369244520323043 chr10 135534747 5637103 0.04159157061030261 0.3639454178628636 chr11 135006516 5487125 0.04064340864851294 0.40269779017705665 chr12 133851895 5517474 0.04122073878744862 0.2245126707909776 chr13 115169878 3926393 0.03409218684767557 0.19935670549574938 chr14 107349540 3647040 0.033973503752321624 0.24117194061691283 chr15 102531392 3404007 0.0331996565500642 0.19838946474701105 chr16 90354753 3330045 0.036855227748782624 0.23035625687929653 chr17 81195210 3087215 0.03802213209375282 0.27719331501017236 chr18 78077248 3364709 0.04309461573235778 0.6580303440436482 chr19 59128983 2252865 0.0381008582542338 0.4414972966768146 chr20 63025520 2408813 0.03821964499459901 0.22296206334191873 chr21 48129895 1591432 0.03306535366428703 0.21422630877094373 chr22 51304566 1214740 0.02367703490562614 0.1668234079874616 chrMT 16571 7988 0.48204694949007304 0.8022572802983473 chrX 155270560 7067247 0.045515692092564106 0.3334354777083645 chrY 59373566 273960 0.004614174597496805 0.1048801414470832