BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472674.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 = 20,627,986 number of mapped reads = 20,442,567 (99.1%) number of supplementary alignments = 111,625 (0.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,250,819 number of mapped paired reads (second in pair) = 10,191,748 number of mapped paired reads (both in pair) = 20,324,042 number of mapped paired reads (singletons) = 118,525 number of mapped bases = 2,012,240,279 bp number of sequenced bases = 2,012,001,985 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,894,543 duplication rate = 49.79% >>>>>>> Insert size mean insert size = 20,928.5387 std insert size = 1,442,879.8514 median insert size = 221 >>>>>>> Mapping quality mean mapping quality = 54.7749 >>>>>>> ACTG content number of A's = 525,274,099 bp (26.11%) number of C's = 484,134,719 bp (24.06%) number of T's = 526,406,859 bp (26.16%) number of G's = 475,822,114 bp (23.65%) number of N's = 364,194 bp (0.02%) GC percentage = 47.71% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 12,619,938 number of insertions = 125,064 mapped reads with insertion percentage = 0.61% number of deletions = 100,184 mapped reads with deletion percentage = 0.48% homopolymer indels = 47.1% >>>>>>> Coverage mean coverageData = 0.65X std coverageData = 31.6379X There is a 3.82% of reference with a coverageData >= 1X There is a 1.76% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.32% 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 0.26% 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 0.21% 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 0.2% 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 0.17% 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 0.16% 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 327715348 1.3148025336314006 55.48833051542632 chr2 243199373 121434683 0.4993215299120035 20.255022392466735 chr3 198022430 157931580 0.7975438943962055 26.214408614788216 chr4 191154276 40920009 0.21406797617229342 12.53586146007443 chr5 180915260 47420812 0.26211615316474685 9.941071412288153 chr6 171115067 148077297 0.8653667943805322 31.322490347851936 chr7 159138663 120769933 0.7588974968326836 26.987055315328565 chr8 146364022 70718571 0.48316908782405554 15.795241670782142 chr9 141213431 162096669 1.147884219313388 50.98927795453188 chr10 135534747 26277427 0.19387963294755697 7.297311035755054 chr11 135006516 37407973 0.27708272243689336 11.322868303225825 chr12 133851895 60429643 0.4514664734481346 16.242297174534478 chr13 115169878 75358156 0.6543217489559205 29.497584835946874 chr14 107349540 26502135 0.2468770243449576 16.868523839244272 chr15 102531392 20513303 0.20006851170029955 11.89052437838241 chr16 90354753 115277882 1.2758363912521569 54.28197407465931 chr17 81195210 61832792 0.7615325091221514 24.084786840045247 chr18 78077248 11712055 0.1500059915021595 7.6604885140013685 chr19 59128983 79652631 1.3470996279438798 62.43700066423223 chr20 63025520 129764062 2.058912992705177 79.04788262052698 chr21 48129895 7534949 0.15655444500761947 9.241617270439601 chr22 51304566 26713989 0.5206941814886418 16.941930997984763 chrMT 16571 4449 0.2684810814072778 0.6097258356363034 chrX 155270560 134512063 0.8663075794922103 35.25752069129244 chrY 59373566 1661868 0.02799003179293627 2.0775230709128008