BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716245.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 = 1,484,886 number of mapped reads = 1,367,827 (92.12%) number of supplementary alignments = 20,478 (1.38%) number of secondary alignments = 0 number of mapped bases = 108,091,966 bp number of sequenced bases = 108,043,829 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,775 duplication rate = 2.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7144 >>>>>>> ACTG content number of A's = 27,456,579 bp (25.41%) number of C's = 21,144,554 bp (19.57%) number of T's = 33,520,236 bp (31.02%) number of G's = 25,915,843 bp (23.99%) number of N's = 6,617 bp (0.01%) GC percentage = 43.56% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 908,787 number of insertions = 9,977 mapped reads with insertion percentage = 0.72% number of deletions = 27,816 mapped reads with deletion percentage = 2.01% homopolymer indels = 44.43% >>>>>>> Coverage mean coverageData = 0.0349X std coverageData = 0.4192X There is a 3.06% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8497844 0.03409357202765003 0.6576360843031684 chr2 243199373 9322367 0.038332199976518856 0.620395537794921 chr3 198022430 7123284 0.03597210679618466 0.21212769766502193 chr4 191154276 7084135 0.03705977783097041 0.2301326826335975 chr5 180915260 6631455 0.03665503396452018 0.2163547409366659 chr6 171115067 6221407 0.03635803152272967 0.2617694048130756 chr7 159138663 5930063 0.037263496426383824 0.5288887030188348 chr8 146364022 5518037 0.03770077457969828 0.5679674604653672 chr9 141213431 4591754 0.03251641127535525 0.4842715394563834 chr10 135534747 5082636 0.037500612296859935 0.39269859835776183 chr11 135006516 4953911 0.03669386594644069 0.3958323942470812 chr12 133851895 4948365 0.03696895736888895 0.21924889036639303 chr13 115169878 3321943 0.028843852730312 0.18492798475471292 chr14 107349540 3216404 0.029961972822612933 0.2674078587272656 chr15 102531392 3059125 0.029835984280794706 0.20153542214421824 chr16 90354753 3125462 0.0345910081786179 0.24443257737948593 chr17 81195210 2987756 0.036797195302530776 0.240039518099626 chr18 78077248 2968523 0.038020333401095285 0.9047153991235173 chr19 59128983 2303580 0.03895855945974921 0.5165871233124304 chr20 63025520 2131292 0.03381633344714966 0.21608321818606407 chr21 48129895 1371425 0.028494244585407884 0.20619997445305835 chr22 51304566 1174749 0.022897552627187217 0.16737082032260708 chrMT 16571 14806 0.8934886247058114 1.1684655631205805 chrX 155270560 6221235 0.04006706100628477 0.32989330070598016 chrY 59373566 290408 0.004891200235471792 0.1384827875847744