BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240254.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,102,864 number of mapped reads = 1,715,952 (81.6%) number of supplementary alignments = 6,657 (0.32%) number of secondary alignments = 0 number of mapped bases = 105,306,672 bp number of sequenced bases = 105,242,375 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 141,698 duplication rate = 6.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3477 >>>>>>> ACTG content number of A's = 28,405,838 bp (26.99%) number of C's = 18,127,991 bp (17.22%) number of T's = 34,482,111 bp (32.76%) number of G's = 24,201,811 bp (23%) number of N's = 24,624 bp (0.02%) GC percentage = 40.22% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 1,019,139 number of insertions = 7,231 mapped reads with insertion percentage = 0.42% number of deletions = 36,871 mapped reads with deletion percentage = 2.12% homopolymer indels = 50.42% >>>>>>> Coverage mean coverageData = 0.034X std coverageData = 0.3236X There is a 2.61% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 7732506 0.031023015986788655 0.4348339960800226 chr2 243199373 12541324 0.05156807702789595 0.38520712170619775 chr3 198022430 7060018 0.03565261773628371 0.23933856595141226 chr4 191154276 6811253 0.03563222933082596 0.2463110033069893 chr5 180915260 5488074 0.030335052996634998 0.22137144550281596 chr6 171115067 5736710 0.03352545220345792 0.27758497651295017 chr7 159138663 6692702 0.0420557887934499 0.651071393410703 chr8 146364022 6135233 0.04191763054994485 0.3945535751856772 chr9 141213431 3493368 0.024738213463562118 0.2720698280841776 chr10 135534747 4933116 0.03639742655807665 0.27833527997950563 chr11 135006516 4467862 0.033093676752609484 0.29214164618129435 chr12 133851895 5044252 0.03768532376773597 0.24684332544245113 chr13 115169878 1944037 0.0168797348209399 0.16338126532286049 chr14 107349540 3823886 0.035620888547822374 0.249562405682393 chr15 102531392 2826555 0.027567703362497996 0.22424992616897083 chr16 90354753 3171085 0.03509594011064365 0.2388794356093879 chr17 81195210 2794668 0.03441912398526958 0.2516852945569946 chr18 78077248 2244785 0.028750821237961667 0.4244652162463281 chr19 59128983 1941061 0.03282757290109319 0.3345621451456701 chr20 63025520 2043999 0.032431291324530126 0.23323055103891055 chr21 48129895 1820974 0.03783457246270743 0.25231515683077016 chr22 51304566 921633 0.017963956658360584 0.16452583776166868 chrMT 16571 51597 3.1136925954981596 3.7611134583174 chrX 155270560 5377134 0.03463073746884149 0.2572980732706585 chrY 59373566 208840 0.0035173902136853294 0.07631168305991107