BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013338.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,044,662 number of mapped reads = 1,608,148 (78.65%) number of supplementary alignments = 21,731 (1.06%) number of secondary alignments = 0 number of mapped bases = 104,469,967 bp number of sequenced bases = 104,430,575 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 208,085 duplication rate = 9.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0036 >>>>>>> ACTG content number of A's = 28,197,611 bp (27%) number of C's = 19,884,282 bp (19.04%) number of T's = 32,451,725 bp (31.07%) number of G's = 23,884,810 bp (22.87%) number of N's = 12,147 bp (0.01%) GC percentage = 41.91% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 777,329 number of insertions = 6,798 mapped reads with insertion percentage = 0.42% number of deletions = 22,637 mapped reads with deletion percentage = 1.39% homopolymer indels = 46.58% >>>>>>> Coverage mean coverageData = 0.0337X std coverageData = 0.3625X There is a 1.83% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 4547256 0.01824370981206101 0.4082875369421349 chr2 243199373 10164692 0.04179571630721268 0.5406080077898425 chr3 198022430 7648891 0.03862638691990599 0.33160657019576345 chr4 191154276 6980256 0.036516347664647585 0.32226672190843736 chr5 180915260 9393974 0.051924718788232675 0.38362055448999294 chr6 171115067 4153702 0.024274320624261568 0.28741825670697546 chr7 159138663 4102781 0.025781170475210037 0.30054544328968436 chr8 146364022 4082478 0.0278926333412729 0.3836350862164154 chr9 141213431 7137633 0.050545000921335875 0.42374259283375376 chr10 135534747 6629525 0.04891384052238648 0.4106227530282837 chr11 135006516 3347866 0.024797810499753953 0.2796888658745015 chr12 133851895 3779939 0.028239712258089435 0.2816795794944992 chr13 115169878 2504030 0.021742056547112084 0.24635706020599396 chr14 107349540 2950141 0.02748163615791926 0.2870995108075138 chr15 102531392 1573631 0.015347797092231032 0.20032574065515973 chr16 90354753 2224965 0.024624769877905593 0.2696224172372893 chr17 81195210 2869398 0.0353394984753411 0.31798489508338906 chr18 78077248 1832835 0.02347463629865643 0.4001208268848547 chr19 59128983 1698546 0.028726115583621658 0.36668183949558886 chr20 63025520 3170364 0.05030286144406266 0.38840494928250247 chr21 48129895 1734558 0.03603909794525835 0.32635761094664856 chr22 51304566 1122197 0.021873238339059336 0.24295699112786207 chrMT 16571 34919 2.1072355319534126 2.44995623612191 chrX 155270560 10540405 0.06788411789073215 0.4545218826364131 chrY 59373566 244985 0.0041261628112416225 0.10976459587285314