BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237799.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 = 3,849,357 number of mapped reads = 3,656,323 (94.99%) number of supplementary alignments = 38,371 (1%) number of secondary alignments = 0 number of mapped bases = 263,290,794 bp number of sequenced bases = 263,158,939 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 317,638 duplication rate = 6.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.4175 >>>>>>> ACTG content number of A's = 80,033,770 bp (30.41%) number of C's = 51,451,083 bp (19.55%) number of T's = 78,817,927 bp (29.95%) number of G's = 52,400,082 bp (19.91%) number of N's = 456,077 bp (0.17%) GC percentage = 39.46% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 2,270,085 number of insertions = 20,814 mapped reads with insertion percentage = 0.57% number of deletions = 71,961 mapped reads with deletion percentage = 1.94% homopolymer indels = 46.69% >>>>>>> Coverage mean coverageData = 0.0851X std coverageData = 1.0304X There is a 2.46% of reference with a coverageData >= 1X There is a 1.45% of reference with a coverageData >= 2X There is a 1.04% of reference with a coverageData >= 3X There is a 0.78% of reference with a coverageData >= 4X There is a 0.6% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.28% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 20825974 0.08355435150550738 1.8360497571342225 chr2 243199373 22543972 0.09269749227519596 1.038750431407715 chr3 198022430 17789887 0.08983773706847249 0.8081293146496671 chr4 191154276 18572502 0.09715975173895665 0.8781424438796962 chr5 180915260 17632261 0.09746143581254561 0.8319606652246627 chr6 171115067 17820025 0.10414059563790487 0.888033433762962 chr7 159138663 17878068 0.11234270580745045 1.280846382408899 chr8 146364022 12610926 0.08616137919467669 1.1248252584803937 chr9 141213431 10561479 0.07479089577534591 0.9032686996911153 chr10 135534747 11715844 0.08644162666271846 1.1804931621506611 chr11 135006516 11385959 0.08433636640175204 0.868352370053471 chr12 133851895 12006829 0.08970234601460068 0.8002512629451547 chr13 115169878 8768042 0.07613138220047433 0.7187047852902336 chr14 107349540 7352799 0.06849399634129778 0.7159554339976724 chr15 102531392 6076255 0.0592623866844605 0.6377511621358227 chr16 90354753 6584953 0.07287887777193082 0.7468865869549618 chr17 81195210 5553687 0.06839919497714213 0.7915110919446368 chr18 78077248 6672828 0.0854644364514487 1.3949827696539578 chr19 59128983 3539647 0.05986314697819173 1.2086667971821135 chr20 63025520 5583947 0.08859819006650005 0.8155454893764595 chr21 48129895 3845947 0.07990765406822517 0.7975123248527256 chr22 51304566 2840967 0.05537454502587547 0.6162035755750339 chrMT 16571 204071 12.314947800374147 9.912730580553998 chrX 155270560 14097571 0.09079358636949593 0.8207968905994707 chrY 59373566 826354 0.013917877191341346 0.4445558292195898