BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006414.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 3,418,594 number of mapped reads = 2,988,807 (87.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,506,995 number of mapped paired reads (second in pair) = 1,481,812 number of mapped paired reads (both in pair) = 2,732,050 number of mapped paired reads (singletons) = 256,757 number of mapped bases = 115,682,723 bp number of sequenced bases = 115,666,345 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,755 duplication rate = 1.96% >>>>>>> Insert size mean insert size = 72,049.4431 std insert size = 2,523,550.4689 median insert size = 144 >>>>>>> Mapping quality mean mapping quality = 47.9905 >>>>>>> ACTG content number of A's = 32,144,203 bp (27.79%) number of C's = 25,006,966 bp (21.62%) number of T's = 32,740,933 bp (28.31%) number of G's = 25,769,289 bp (22.28%) number of N's = 4,954 bp (0%) GC percentage = 43.9% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 398,758 number of insertions = 3,082 mapped reads with insertion percentage = 0.1% number of deletions = 11,943 mapped reads with deletion percentage = 0.4% homopolymer indels = 42.15% >>>>>>> Coverage mean coverageData = 0.0374X std coverageData = 0.2649X There is a 3.31% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 9601991 0.03852343862364941 0.31544747992543043 chr2 243199373 9814187 0.04035449137444939 0.247875834503049 chr3 198022430 7822893 0.03950508535825967 0.21763509109767848 chr4 191154276 7270719 0.038035868996202836 0.2338951835693513 chr5 180915260 6953955 0.03843763649346108 0.21564953447128873 chr6 171115067 6588230 0.03850175274162152 0.22544322370834705 chr7 159138663 6166815 0.03875120529321024 0.27231467325394476 chr8 146364022 5794042 0.03958651805837913 0.5673592002920407 chr9 141213431 4766737 0.03375554978194673 0.21929267731757407 chr10 135534747 5500545 0.04058402086366827 0.2734049721761597 chr11 135006516 5337493 0.039535076958803976 0.23825439557436454 chr12 133851895 5226996 0.039050593941908705 0.2185113357345147 chr13 115169878 3620691 0.031437829603327354 0.1939823065143438 chr14 107349540 3527554 0.03286044821431 0.21841016063229646 chr15 102531392 3389185 0.033055095945639754 0.19982419794172865 chr16 90354753 3511279 0.03886103257899449 0.23986496436425397 chr17 81195210 3208198 0.03951215841427099 0.2245368544033032 chr18 78077248 2970087 0.0380403648448265 0.2954921619067516 chr19 59128983 2354188 0.039814451062011334 0.2682200648589267 chr20 63025520 2568713 0.04075671251899231 0.2269012250664534 chr21 48129895 1514881 0.03147484531183789 0.21031982159811552 chr22 51304566 1474894 0.028747811647017927 0.19155142855005955 chrMT 16571 1983 0.11966688793675699 0.5062937757038706 chrX 155270560 6392062 0.041167250250144005 0.23089262525819645 chrY 59373566 304405 0.005126944876445522 0.13733664154456976