BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240054.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 = 3,777,255 number of mapped reads = 3,136,044 (83.02%) number of supplementary alignments = 14,556 (0.39%) number of secondary alignments = 0 number of mapped bases = 194,004,115 bp number of sequenced bases = 193,898,644 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 354,081 duplication rate = 9.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0345 >>>>>>> ACTG content number of A's = 52,584,688 bp (27.12%) number of C's = 33,849,898 bp (17.46%) number of T's = 63,045,250 bp (32.51%) number of G's = 44,295,867 bp (22.84%) number of N's = 122,941 bp (0.06%) GC percentage = 40.3% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 1,902,333 number of insertions = 13,707 mapped reads with insertion percentage = 0.43% number of deletions = 61,291 mapped reads with deletion percentage = 1.93% homopolymer indels = 49.16% >>>>>>> Coverage mean coverageData = 0.0627X std coverageData = 0.5566X There is a 4.18% of reference with a coverageData >= 1X There is a 1.29% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% 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% 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 13385757 0.05370400661910487 0.8836824836718039 chr2 243199373 19955885 0.08205565974053725 0.67868744067586 chr3 198022430 12839328 0.06483774590585521 0.35992722513093545 chr4 191154276 11766936 0.06155727324666282 0.3618011451889838 chr5 180915260 9861022 0.05450630311671884 0.3367473834721171 chr6 171115067 10982216 0.06418029804470696 0.5000036394367607 chr7 159138663 11583119 0.07278632848637166 0.8744738656350545 chr8 146364022 11661155 0.07967227765850818 0.814413904108127 chr9 141213431 6421161 0.04547131922600195 0.48584559627865825 chr10 135534747 9376121 0.06917872506893011 0.49232943072284935 chr11 135006516 9298453 0.06887410530614685 0.5283217499887605 chr12 133851895 9641281 0.07202946958651575 0.38456015500413676 chr13 115169878 3638441 0.031591949763114274 0.24699820019281807 chr14 107349540 8076693 0.07523733217673778 0.40694874933104 chr15 102531392 4309722 0.042033195062834997 0.30869975484360673 chr16 90354753 6847813 0.0757880772470265 0.40094883642664897 chr17 81195210 5322298 0.06554940864122404 0.40353109336298154 chr18 78077248 4377788 0.05606995779359437 0.8601441580905581 chr19 59128983 3836709 0.06488711297469804 0.6530836893867329 chr20 63025520 4255699 0.067523425431476 0.37730659797839206 chr21 48129895 3984491 0.08278619764285794 0.4301850398733346 chr22 51304566 1847849 0.036017242597861564 0.25731403030948385 chrMT 16571 57080 3.444571842375234 3.3912896760663775 chrX 155270560 10269931 0.06614216500539445 0.41874000551827456 chrY 59373566 407167 0.006857715098331807 0.13050247257979375