BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236114.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 = 1,655,363 number of mapped reads = 1,419,968 (85.78%) number of supplementary alignments = 8,614 (0.52%) number of secondary alignments = 0 number of mapped bases = 94,677,644 bp number of sequenced bases = 94,616,264 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,684 duplication rate = 3.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8715 >>>>>>> ACTG content number of A's = 26,547,203 bp (28.06%) number of C's = 16,776,396 bp (17.73%) number of T's = 30,607,455 bp (32.35%) number of G's = 20,633,239 bp (21.81%) number of N's = 51,971 bp (0.05%) GC percentage = 39.54% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 798,269 number of insertions = 6,638 mapped reads with insertion percentage = 0.46% number of deletions = 35,408 mapped reads with deletion percentage = 2.46% homopolymer indels = 46.18% >>>>>>> Coverage mean coverageData = 0.0306X std coverageData = 0.2755X There is a 2.67% of reference with a coverageData >= 1X There is a 0.3% 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 9956356 0.0399451602569929 0.4029731341030068 chr2 243199373 8714884 0.03583431935903881 0.28707695219280427 chr3 198022430 6209431 0.031357210392782275 0.19582055479159372 chr4 191154276 2739808 0.014332967367154267 0.13743857722697178 chr5 180915260 4182996 0.023121299994262507 0.1695130944125742 chr6 171115067 11214630 0.06553853028032885 0.34724267318681007 chr7 159138663 4040333 0.025388757978945693 0.21967097251732062 chr8 146364022 4797582 0.0327784241949842 0.6671270690658607 chr9 141213431 3505572 0.02482463583793244 0.20683930774990242 chr10 135534747 5045021 0.03722308198944733 0.2437109959808558 chr11 135006516 4361097 0.03230286307069801 0.2183143600583021 chr12 133851895 4114718 0.030740827389855032 0.19590372211536813 chr13 115169878 4106203 0.03565344577338182 0.21144106280733263 chr14 107349540 2486184 0.023159707996885687 0.17310928077833665 chr15 102531392 2609631 0.025452019611710723 0.18067103127233033 chr16 90354753 1492430 0.01651744872790477 0.15025943830978142 chr17 81195210 1622630 0.019984306956038415 0.162210277726346 chr18 78077248 2760283 0.03535323119995213 0.29530740605148886 chr19 59128983 1406268 0.023783057455934935 0.23538139277708414 chr20 63025520 1589518 0.025220228250397617 0.1759732770127584 chr21 48129895 777712 0.016158605789603323 0.14465231097884887 chr22 51304566 495754 0.009662960602765844 0.10669370888545997 chrMT 16571 47081 2.8411683060768813 2.446262021344156 chrX 155270560 6230182 0.04012468300494312 0.2323070027820146 chrY 59373566 171340 0.002885796012319691 0.0698569411338015