BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173976.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 11,569,914 number of mapped reads = 11,331,737 (97.94%) number of supplementary alignments = 1,568,120 (13.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,663,282 number of mapped paired reads (second in pair) = 5,668,455 number of mapped paired reads (both in pair) = 11,177,950 number of mapped paired reads (singletons) = 153,787 number of mapped bases = 1,285,312,040 bp number of sequenced bases = 1,284,460,811 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,229,743 duplication rate = 65.12% >>>>>>> Insert size mean insert size = 923,571.3911 std insert size = 9,092,079.4583 median insert size = 152 >>>>>>> Mapping quality mean mapping quality = 52.4489 >>>>>>> ACTG content number of A's = 384,593,367 bp (29.94%) number of C's = 254,387,753 bp (19.81%) number of T's = 381,433,924 bp (29.7%) number of G's = 264,036,090 bp (20.56%) number of N's = 9,677 bp (0%) GC percentage = 40.36% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 10,714,634 number of insertions = 142,797 mapped reads with insertion percentage = 1.21% number of deletions = 352,202 mapped reads with deletion percentage = 3.03% homopolymer indels = 41.51% >>>>>>> Coverage mean coverageData = 0.4152X std coverageData = 6.9799X There is a 8.52% of reference with a coverageData >= 1X There is a 6.43% of reference with a coverageData >= 2X There is a 4.84% of reference with a coverageData >= 3X There is a 3.92% of reference with a coverageData >= 4X There is a 2.99% of reference with a coverageData >= 5X There is a 2.49% of reference with a coverageData >= 6X There is a 1.9% of reference with a coverageData >= 7X There is a 1.65% of reference with a coverageData >= 8X There is a 1.26% of reference with a coverageData >= 9X There is a 1.13% of reference with a coverageData >= 10X There is a 0.86% of reference with a coverageData >= 11X There is a 0.79% of reference with a coverageData >= 12X There is a 0.59% of reference with a coverageData >= 13X There is a 0.55% of reference with a coverageData >= 14X There is a 0.41% of reference with a coverageData >= 15X There is a 0.38% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.2% of reference with a coverageData >= 19X There is a 0.19% of reference with a coverageData >= 20X There is a 0.14% of reference with a coverageData >= 21X There is a 0.13% of reference with a coverageData >= 22X There is a 0.1% of reference with a coverageData >= 23X There is a 0.09% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 103996526 0.41723677791759645 3.277210210932721 chr2 243199373 114916343 0.47251907594350584 22.891992945374906 chr3 198022430 96664319 0.48814833248940537 2.1523326658033968 chr4 191154276 86344682 0.4517015460329017 3.4144755209728213 chr5 180915260 79918878 0.44174757839664824 2.053210158407454 chr6 171115067 73445242 0.4292155172986608 2.5515446122356518 chr7 159138663 70058270 0.4402341246262701 2.960475567385514 chr8 146364022 66211893 0.45237820124948463 3.673550151552693 chr9 141213431 53961956 0.3821304787927715 3.0148229697400573 chr10 135534747 63320645 0.4671912288293127 4.332745850886355 chr11 135006516 57004002 0.4222314869602294 2.1222392365499485 chr12 133851895 58170890 0.4345914564750839 2.132469314295987 chr13 115169878 42182909 0.3662668549496944 1.879042707349922 chr14 107349540 39156519 0.36475721274632383 1.9029275613028733 chr15 102531392 36683992 0.35778302902588116 1.9140717151651836 chr16 90354753 39974996 0.44242272456878945 2.9251366467653352 chr17 81195210 35149787 0.4329046873577887 2.421546134271405 chr18 78077248 34717699 0.44465833375684555 4.108734663462647 chr19 59128983 23820752 0.4028608440635619 2.68884536236549 chr20 63025520 27232905 0.43209330125320666 2.161413798430104 chr21 48129895 17892395 0.3717522134631709 2.9355897396264545 chr22 51304566 15813692 0.3082316688927843 2.2352977748869405 chrMT 16571 3573579 215.65258584273732 175.9198773161496 chrX 155270560 34711644 0.2235558627469367 1.4709292359027049 chrY 59373566 10387525 0.17495201484108264 2.8958655785625433