BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231867.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 = 5,754,586 number of mapped reads = 5,132,548 (89.19%) number of supplementary alignments = 46,498 (0.81%) number of secondary alignments = 0 number of mapped bases = 338,488,478 bp number of sequenced bases = 338,342,474 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 314,815 duplication rate = 4.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7514 >>>>>>> ACTG content number of A's = 99,450,675 bp (29.39%) number of C's = 64,589,769 bp (19.09%) number of T's = 101,585,491 bp (30.02%) number of G's = 72,690,434 bp (21.48%) number of N's = 26,105 bp (0.01%) GC percentage = 40.57% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 2,080,505 number of insertions = 23,615 mapped reads with insertion percentage = 0.46% number of deletions = 85,730 mapped reads with deletion percentage = 1.65% homopolymer indels = 45.67% >>>>>>> Coverage mean coverageData = 0.1093X std coverageData = 3.89X There is a 8.27% of reference with a coverageData >= 1X There is a 1.79% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 38351581 0.15386754442629855 2.293034252880793 chr2 243199373 30521192 0.12549864591961757 13.414526582699267 chr3 198022430 33217395 0.1677456185140239 0.5119529383776859 chr4 191154276 15068057 0.07882668028833423 0.38976668868699094 chr5 180915260 13638441 0.07538579664313558 0.3523677779076407 chr6 171115067 26898587 0.15719590023010657 0.720250850017533 chr7 159138663 25950104 0.1630659923289666 1.9059321954286395 chr8 146364022 19776509 0.1351186495817941 1.474480964678866 chr9 141213431 12647328 0.08956179246151168 0.6670381212880344 chr10 135534747 15680628 0.11569452370763639 0.7517619661375465 chr11 135006516 9146952 0.06775192984018638 0.5854075758144969 chr12 133851895 7682924 0.057398694280719746 0.3138937768768218 chr13 115169878 13353289 0.11594428362596686 0.4192474143281192 chr14 107349540 16422997 0.15298618885558335 0.5640586939660652 chr15 102531392 6348938 0.061921894125849766 0.3093486343673766 chr16 90354753 7155061 0.07918854030844398 0.48882127149120674 chr17 81195210 5273416 0.06494737805345907 0.3735426603659716 chr18 78077248 7252239 0.09288543315461119 1.6016024253508692 chr19 59128983 6082495 0.10286824990715636 1.3890042155106521 chr20 63025520 3345543 0.05308235457636843 0.34445372436641064 chr21 48129895 7286735 0.1513972760588819 0.5151240399406753 chr22 51304566 1617962 0.03153641334769307 0.21198062575494925 chrMT 16571 253701 15.309939050147849 8.41314983608645 chrX 155270560 14716465 0.09477949329222488 0.46813198243019893 chrY 59373566 799939 0.01347298223589939 0.25796276843040433