BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525209.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 = 371,447 number of mapped reads = 346,879 (93.39%) number of supplementary alignments = 1,053 (0.28%) number of secondary alignments = 0 number of mapped bases = 21,262,288 bp number of sequenced bases = 21,255,101 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,530 duplication rate = 0.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9681 >>>>>>> ACTG content number of A's = 5,604,676 bp (26.37%) number of C's = 4,152,353 bp (19.54%) number of T's = 6,235,653 bp (29.34%) number of G's = 5,261,901 bp (24.76%) number of N's = 518 bp (0%) GC percentage = 44.29% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 113,893 number of insertions = 1,255 mapped reads with insertion percentage = 0.36% number of deletions = 4,408 mapped reads with deletion percentage = 1.26% homopolymer indels = 46.07% >>>>>>> Coverage mean coverageData = 0.0069X std coverageData = 0.1003X There is a 0.66% of reference with a coverageData >= 1X There is a 0.02% 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 2189907 0.008785964067868862 0.1530319320925068 chr2 243199373 1626452 0.006687731057596106 0.10546678745354901 chr3 198022430 1449430 0.0073195243589324705 0.088081707027306 chr4 191154276 1258010 0.006581124034076015 0.08395711561472735 chr5 180915260 992699 0.005487093791866977 0.07559374688987502 chr6 171115067 1401034 0.008187671749560196 0.09563117907551667 chr7 159138663 1658190 0.010419780892591764 0.14976069779011109 chr8 146364022 1125843 0.007692074764111087 0.09916213407919787 chr9 141213431 731126 0.005177453694188622 0.07891401672370127 chr10 135534747 1037323 0.007653557651898668 0.11179847298217241 chr11 135006516 1017533 0.007536917699587181 0.0930864909174426 chr12 133851895 997480 0.007452117132895279 0.08835842526175125 chr13 115169878 508708 0.004417022999711783 0.06777831481761391 chr14 107349540 1012116 0.009428228569959406 0.09991505453891164 chr15 102531392 420439 0.0041005880423431685 0.06508875746843573 chr16 90354753 489166 0.00541383805232692 0.07838411025140661 chr17 81195210 377363 0.004647601748920903 0.07047107750296641 chr18 78077248 467948 0.005993397718116294 0.11834065531335698 chr19 59128983 365062 0.0061739942322363295 0.120736905004235 chr20 63025520 405757 0.00643797940897592 0.08237502658253769 chr21 48129895 278063 0.005777344829029858 0.07845200025598205 chr22 51304566 183504 0.0035767576710423786 0.06094357380453906 chrMT 16571 19844 1.197513728803331 1.2795428691031934 chrX 155270560 1187272 0.007646472067853687 0.09134945611681802 chrY 59373566 62019 0.0010445557539865468 0.04208539302806653