BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819042.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,969,405 number of mapped reads = 2,644,684 (89.06%) number of supplementary alignments = 11,346 (0.38%) number of secondary alignments = 0 number of mapped bases = 150,359,252 bp number of sequenced bases = 150,318,116 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,095 duplication rate = 2.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9433 >>>>>>> ACTG content number of A's = 37,896,888 bp (25.21%) number of C's = 27,707,577 bp (18.43%) number of T's = 46,143,217 bp (30.7%) number of G's = 38,567,091 bp (25.66%) number of N's = 3,343 bp (0%) GC percentage = 44.09% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 740,671 number of insertions = 9,210 mapped reads with insertion percentage = 0.35% number of deletions = 24,123 mapped reads with deletion percentage = 0.91% homopolymer indels = 40.93% >>>>>>> Coverage mean coverageData = 0.0486X std coverageData = 0.3367X There is a 4.17% of reference with a coverageData >= 1X There is a 0.5% 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% 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 16829471 0.06752027711096455 0.5129215563063484 chr2 243199373 12473026 0.051287245711772456 0.39279761346646386 chr3 198022430 9911703 0.050053435865825904 0.25658106430507593 chr4 191154276 9575829 0.05009476743277247 0.2892922124196471 chr5 180915260 7621774 0.04212897242609606 0.2368937442258781 chr6 171115067 7905785 0.046201571484058734 0.2687394213958145 chr7 159138663 6446892 0.04051116101182778 0.2956304003217779 chr8 146364022 9470907 0.06470788975722462 0.34483337691801813 chr9 141213431 5433742 0.03847893193672208 0.35338836306475907 chr10 135534747 7206015 0.05316728853302836 0.3836012397648502 chr11 135006516 5935242 0.04396263362577255 0.32952564843778814 chr12 133851895 6806221 0.05084889534063003 0.261740662234378 chr13 115169878 4616919 0.04008790388750781 0.22549358175516698 chr14 107349540 4072347 0.03793539310927648 0.2433337577152244 chr15 102531392 4253610 0.04148592852421237 0.232593938304295 chr16 90354753 4438669 0.04912490879146114 0.28695506917668495 chr17 81195210 3427155 0.04220883226978537 0.24400000481769515 chr18 78077248 3670775 0.047014656561665695 0.6747354606255953 chr19 59128983 2859709 0.04836391317604769 0.3707311698395436 chr20 63025520 4858535 0.07708837626409112 0.33199153837117806 chr21 48129895 1937025 0.04024577655945437 0.2671686162262752 chr22 51304566 1790656 0.03490246852492622 0.21245186223016196 chrMT 16571 16276 0.9821978154607447 1.1012537098312245 chrX 155270560 8365284 0.05387553184583092 0.3140167843890996 chrY 59373566 435685 0.007338029856586347 0.15643628295129414