BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472438.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 14,262,076 number of mapped reads = 14,117,962 (98.99%) number of supplementary alignments = 48,798 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,078,057 number of mapped paired reads (second in pair) = 7,039,905 number of mapped paired reads (both in pair) = 14,047,674 number of mapped paired reads (singletons) = 70,288 number of mapped bases = 1,382,543,069 bp number of sequenced bases = 1,382,391,005 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,622,778 duplication rate = 46.9% >>>>>>> Insert size mean insert size = 15,644.7732 std insert size = 1,223,041.7217 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 54.7909 >>>>>>> ACTG content number of A's = 363,414,684 bp (26.29%) number of C's = 329,188,868 bp (23.81%) number of T's = 363,879,471 bp (26.32%) number of G's = 325,736,966 bp (23.56%) number of N's = 171,016 bp (0.01%) GC percentage = 47.38% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 7,100,916 number of insertions = 77,288 mapped reads with insertion percentage = 0.54% number of deletions = 60,566 mapped reads with deletion percentage = 0.42% homopolymer indels = 44.5% >>>>>>> Coverage mean coverageData = 0.4466X std coverageData = 14.6328X There is a 3.95% of reference with a coverageData >= 1X There is a 1.81% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.43% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 174474291 0.6999954114457352 19.822902485290683 chr2 243199373 115370409 0.474386128454369 18.41801291943834 chr3 198022430 81382422 0.4109757768349777 9.840657413613389 chr4 191154276 41828833 0.2188223767487158 9.045488221257514 chr5 180915260 50343955 0.27827367906941625 10.599242282535638 chr6 171115067 107471196 0.6280638980785953 14.279032939329495 chr7 159138663 89548140 0.5627051171090962 16.497817964509494 chr8 146364022 104757196 0.7157305092367576 20.493150994133387 chr9 141213431 60175086 0.4261286307815862 15.660173012340758 chr10 135534747 26882385 0.19834312303692866 8.752336638587048 chr11 135006516 38902670 0.2881540176920053 9.28954442563919 chr12 133851895 68406249 0.5110592494786869 13.708180867625718 chr13 115169878 51427386 0.44653503930949723 15.785792954761783 chr14 107349540 22498278 0.20957964049030858 6.370319500995088 chr15 102531392 19588126 0.1910451581501985 6.571619202229129 chr16 90354753 63971839 0.7080074581134652 19.28485701724726 chr17 81195210 46957677 0.5783306305876911 13.55233350806094 chr18 78077248 7154167 0.09162934380064215 4.577437810570898 chr19 59128983 43387852 0.7337831601128671 17.062431146515717 chr20 63025520 66952760 1.0623119015916092 29.17913610155993 chr21 48129895 10810487 0.22461064999206834 13.058898816955107 chr22 51304566 14029836 0.2734617421770998 9.084064949612323 chrMT 16571 3839 0.23166978456339388 0.6227061434622386 chrX 155270560 75980682 0.48934377514964844 14.946283881820356 chrY 59373566 237308 0.003996862846338049 0.26939476848143606