BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524957.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 = 699,623 number of mapped reads = 647,646 (92.57%) number of supplementary alignments = 1,624 (0.23%) number of secondary alignments = 0 number of mapped bases = 37,954,383 bp number of sequenced bases = 37,941,902 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,844 duplication rate = 1.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5297 >>>>>>> ACTG content number of A's = 9,836,141 bp (25.92%) number of C's = 7,381,193 bp (19.45%) number of T's = 11,746,914 bp (30.96%) number of G's = 8,977,263 bp (23.66%) number of N's = 391 bp (0%) GC percentage = 43.11% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 187,277 number of insertions = 3,020 mapped reads with insertion percentage = 0.46% number of deletions = 7,432 mapped reads with deletion percentage = 1.14% homopolymer indels = 42.29% >>>>>>> Coverage mean coverageData = 0.0123X std coverageData = 0.1419X There is a 1.16% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 4133866 0.0165851783374293 0.24240284555121333 chr2 243199373 3570342 0.014680720414521793 0.15734963651333161 chr3 198022430 2158507 0.010900315686460367 0.10831473203381912 chr4 191154276 2535077 0.01326194241137457 0.12197135154264882 chr5 180915260 1702802 0.009412152407707344 0.10094401408099865 chr6 171115067 2300026 0.013441399640161436 0.14543383547047356 chr7 159138663 2446885 0.015375804684245714 0.18431982189762303 chr8 146364022 2340607 0.01599168271011301 0.14966966025191455 chr9 141213431 1114536 0.007892563703802367 0.11025627228395869 chr10 135534747 1985218 0.01464729926415106 0.14497437860771684 chr11 135006516 1616479 0.011973340605278637 0.1283317146135371 chr12 133851895 2119372 0.015833709339714615 0.1303346812429765 chr13 115169878 766596 0.006656219606310601 0.08538206053942159 chr14 107349540 894576 0.008333300729560648 0.09651974567932403 chr15 102531392 1074672 0.010481394810284055 0.11063018240962333 chr16 90354753 990879 0.010966539856514244 0.1119063262665973 chr17 81195210 960279 0.011826793723422848 0.1280565004598842 chr18 78077248 759620 0.00972908266438899 0.1495728874614219 chr19 59128983 959970 0.01623518537431973 0.17641591117178984 chr20 63025520 720876 0.01143784295631357 0.11140865052595612 chr21 48129895 566650 0.01177334793686959 0.11379289014693045 chr22 51304566 503345 0.009810920143053155 0.1018307783452998 chrMT 16571 6844 0.41301068131072355 0.6604046227836229 chrX 155270560 1625698 0.010470098130643698 0.11499692365653383 chrY 59373566 100661 0.001695384104097773 0.05033047223805908