BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524674.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 = 867,994 number of mapped reads = 801,858 (92.38%) number of supplementary alignments = 3,494 (0.4%) number of secondary alignments = 0 number of mapped bases = 47,393,675 bp number of sequenced bases = 47,379,720 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,871 duplication rate = 1.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8612 >>>>>>> ACTG content number of A's = 12,420,174 bp (26.21%) number of C's = 8,830,960 bp (18.64%) number of T's = 15,188,794 bp (32.06%) number of G's = 10,933,536 bp (23.08%) number of N's = 6,256 bp (0.01%) GC percentage = 41.72% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 236,201 number of insertions = 3,960 mapped reads with insertion percentage = 0.49% number of deletions = 8,783 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.45% >>>>>>> Coverage mean coverageData = 0.0153X std coverageData = 0.1729X There is a 1.43% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% 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 3810329 0.015287139445080861 0.2865408998214717 chr2 243199373 4001900 0.016455223344675318 0.22834978758688765 chr3 198022430 3148513 0.01589977963607456 0.13145469393174988 chr4 191154276 3054138 0.015977345963215598 0.14222520168056185 chr5 180915260 2849548 0.01575073324384024 0.13113067844381 chr6 171115067 2741642 0.01602221270205271 0.1443961089958183 chr7 159138663 2651764 0.01666322909851266 0.19709162855292467 chr8 146364022 2371480 0.01620261569472312 0.17843294552641292 chr9 141213431 1967426 0.013932286653384975 0.15020105209000326 chr10 135534747 2298188 0.016956448813823365 0.1803916662404592 chr11 135006516 2136938 0.015828406385955476 0.1550176483767991 chr12 133851895 2159849 0.016136110736422522 0.1340464501193035 chr13 115169878 1474102 0.012799371029984073 0.11834577055475254 chr14 107349540 1441924 0.013432046378587184 0.12525414157739947 chr15 102531392 1364672 0.013309796866895166 0.12062305690230166 chr16 90354753 1352004 0.014963285882702817 0.13374156790238534 chr17 81195210 1271986 0.015665776343210393 0.13440011503425306 chr18 78077248 1250524 0.016016496892923275 0.23250549435832063 chr19 59128983 971570 0.016431366661591323 0.20346580644453172 chr20 63025520 1016462 0.016127784427641373 0.13405388542091276 chr21 48129895 627864 0.013045197792349224 0.1329272330340611 chr22 51304566 558602 0.010887958783239683 0.10858204417283536 chrMT 16571 48586 2.9319896204212177 2.347690764130662 chrX 155270560 2664553 0.01716070966704828 0.14529408480633382 chrY 59373566 159111 0.0026798289326263477 0.10755304631016381