BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238258.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 = 2,599,766 number of mapped reads = 2,324,533 (89.41%) number of supplementary alignments = 19,173 (0.74%) number of secondary alignments = 0 number of mapped bases = 150,301,471 bp number of sequenced bases = 150,231,959 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,162 duplication rate = 2.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.1467 >>>>>>> ACTG content number of A's = 41,548,549 bp (27.66%) number of C's = 30,770,587 bp (20.48%) number of T's = 43,292,757 bp (28.82%) number of G's = 34,585,370 bp (23.02%) number of N's = 34,696 bp (0.02%) GC percentage = 43.5% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,364,919 number of insertions = 13,604 mapped reads with insertion percentage = 0.58% number of deletions = 41,970 mapped reads with deletion percentage = 1.78% homopolymer indels = 43.51% >>>>>>> Coverage mean coverageData = 0.0486X std coverageData = 0.4578X There is a 4.21% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 0.01% 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 15271274 0.061268750058600656 0.7198884832388859 chr2 243199373 10270462 0.042230626967940416 0.6563840512621438 chr3 198022430 8531877 0.04308540704202044 0.23245610149874005 chr4 191154276 7230805 0.037827063831938554 0.2633327590303369 chr5 180915260 11049383 0.06107490877220639 0.2785201017275408 chr6 171115067 9092675 0.053137781256866176 0.34390457231714117 chr7 159138663 6993235 0.04394428649937822 0.6496474047563816 chr8 146364022 7016841 0.04794102337526636 0.4844552663628459 chr9 141213431 6583463 0.0466206574925582 0.49818267017030354 chr10 135534747 5975399 0.0440875799915722 0.47681637198152765 chr11 135006516 7078220 0.05242872869928737 0.42871101644528575 chr12 133851895 8068017 0.06027570248445119 0.2836757794457059 chr13 115169878 2674069 0.02321847558091535 0.1677876522005827 chr14 107349540 4050875 0.03773537362153578 0.30050396180864203 chr15 102531392 3781153 0.03687800317779749 0.22452102878723856 chr16 90354753 4808986 0.053223387152638225 0.3219192875927097 chr17 81195210 4519663 0.05566415802114435 0.31149936445808696 chr18 78077248 4236830 0.054264591907747566 0.8808479727138945 chr19 59128983 3592719 0.060760710191819126 0.5972690260680602 chr20 63025520 3910964 0.06205365699481734 0.2886114901763064 chr21 48129895 1848855 0.038413858995536974 0.2742935934917861 chr22 51304566 2249205 0.04384025000815717 0.23649559432831413 chrMT 16571 7040 0.4248385734113813 0.6985456146116564 chrX 155270560 10969224 0.07064587131005388 0.3758371112836997 chrY 59373566 490237 0.008256822573196968 0.21040387371529073