BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716142.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 = 1,747,978 number of mapped reads = 1,583,547 (90.59%) number of supplementary alignments = 9,017 (0.52%) number of secondary alignments = 0 number of mapped bases = 92,205,344 bp number of sequenced bases = 92,179,424 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,314 duplication rate = 3.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8034 >>>>>>> ACTG content number of A's = 22,929,573 bp (24.87%) number of C's = 17,695,999 bp (19.2%) number of T's = 29,135,564 bp (31.61%) number of G's = 22,417,625 bp (24.32%) number of N's = 663 bp (0%) GC percentage = 43.52% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 454,014 number of insertions = 7,205 mapped reads with insertion percentage = 0.45% number of deletions = 16,386 mapped reads with deletion percentage = 1.03% homopolymer indels = 39.6% >>>>>>> Coverage mean coverageData = 0.0298X std coverageData = 0.2579X There is a 2.63% of reference with a coverageData >= 1X There is a 0.26% 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% 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 10946209 0.043916476340494254 0.4055961369018625 chr2 243199373 9761149 0.04013640693062149 0.3839329933919825 chr3 198022430 6032086 0.03046163002847708 0.1937429001553693 chr4 191154276 4849299 0.025368509151215638 0.1935235242014652 chr5 180915260 6273835 0.034678307402040046 0.2063315491644885 chr6 171115067 3142244 0.018363339097427347 0.16840650329125167 chr7 159138663 5302050 0.0333171706991154 0.36530266207339734 chr8 146364022 4267050 0.02915368095036361 0.24533653614988948 chr9 141213431 2584825 0.018304384941967736 0.19334377607585895 chr10 135534747 4202958 0.031010188110654754 0.23675485904463847 chr11 135006516 4056187 0.030044379487579695 0.2368476900236968 chr12 133851895 3523776 0.02632593285287444 0.1813847894523927 chr13 115169878 2753675 0.02390968061978845 0.17258295835194415 chr14 107349540 2064235 0.019229099630981187 0.16259421935953672 chr15 102531392 3382379 0.03298871627530425 0.203099768521647 chr16 90354753 2836594 0.03139396551723184 0.202226592996708 chr17 81195210 3532929 0.04351154458495766 0.24824906948346995 chr18 78077248 2913550 0.03731624864646869 0.3655302188393989 chr19 59128983 1478760 0.02500905520394288 0.3080466278102926 chr20 63025520 2550250 0.040463767692833 0.2266212443327328 chr21 48129895 1199338 0.0249187744955604 0.18118514955526013 chr22 51304566 795186 0.015499322224068711 0.13655786509909165 chrMT 16571 8189 0.4941765735320741 0.7698905536072289 chrX 155270560 3540196 0.022800175384181005 0.18336621456343696 chrY 59373566 208395 0.0035098952958291236 0.09460444366765103