BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472639.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 = 16,381,364 number of mapped reads = 16,264,734 (99.29%) number of supplementary alignments = 21,128 (0.13%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,168,159 number of mapped paired reads (second in pair) = 8,096,575 number of mapped paired reads (both in pair) = 16,185,384 number of mapped paired reads (singletons) = 79,350 number of mapped bases = 1,603,120,383 bp number of sequenced bases = 1,602,911,304 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,264,769 duplication rate = 49.01% >>>>>>> Insert size mean insert size = 16,622.5368 std insert size = 1,326,314.6649 median insert size = 215 >>>>>>> Mapping quality mean mapping quality = 54.766 >>>>>>> ACTG content number of A's = 419,357,901 bp (26.16%) number of C's = 381,783,640 bp (23.82%) number of T's = 427,246,861 bp (26.65%) number of G's = 374,158,071 bp (23.34%) number of N's = 364,831 bp (0.02%) GC percentage = 47.16% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 6,712,317 number of insertions = 66,726 mapped reads with insertion percentage = 0.4% number of deletions = 80,804 mapped reads with deletion percentage = 0.49% homopolymer indels = 43.23% >>>>>>> Coverage mean coverageData = 0.5179X std coverageData = 11.6688X There is a 3.43% of reference with a coverageData >= 1X There is a 1.5% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.52% of reference with a coverageData >= 6X There is a 0.49% of reference with a coverageData >= 7X There is a 0.47% of reference with a coverageData >= 8X There is a 0.46% of reference with a coverageData >= 9X There is a 0.44% of reference with a coverageData >= 10X There is a 0.43% of reference with a coverageData >= 11X There is a 0.42% of reference with a coverageData >= 12X There is a 0.41% of reference with a coverageData >= 13X There is a 0.4% of reference with a coverageData >= 14X There is a 0.39% of reference with a coverageData >= 15X There is a 0.39% of reference with a coverageData >= 16X There is a 0.38% of reference with a coverageData >= 17X There is a 0.37% of reference with a coverageData >= 18X There is a 0.36% of reference with a coverageData >= 19X There is a 0.36% of reference with a coverageData >= 20X There is a 0.35% of reference with a coverageData >= 21X There is a 0.35% of reference with a coverageData >= 22X There is a 0.34% of reference with a coverageData >= 23X There is a 0.33% of reference with a coverageData >= 24X There is a 0.33% of reference with a coverageData >= 25X There is a 0.32% of reference with a coverageData >= 26X There is a 0.32% of reference with a coverageData >= 27X There is a 0.32% of reference with a coverageData >= 28X There is a 0.31% of reference with a coverageData >= 29X There is a 0.31% of reference with a coverageData >= 30X There is a 0.3% of reference with a coverageData >= 31X There is a 0.3% of reference with a coverageData >= 32X There is a 0.29% of reference with a coverageData >= 33X There is a 0.29% of reference with a coverageData >= 34X There is a 0.29% of reference with a coverageData >= 35X There is a 0.28% of reference with a coverageData >= 36X There is a 0.28% of reference with a coverageData >= 37X There is a 0.28% of reference with a coverageData >= 38X There is a 0.27% of reference with a coverageData >= 39X There is a 0.27% of reference with a coverageData >= 40X There is a 0.27% of reference with a coverageData >= 41X There is a 0.26% of reference with a coverageData >= 42X There is a 0.26% of reference with a coverageData >= 43X There is a 0.26% of reference with a coverageData >= 44X There is a 0.25% of reference with a coverageData >= 45X There is a 0.25% of reference with a coverageData >= 46X There is a 0.25% of reference with a coverageData >= 47X There is a 0.24% of reference with a coverageData >= 48X There is a 0.24% of reference with a coverageData >= 49X There is a 0.24% of reference with a coverageData >= 50X There is a 0.24% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 204506884 0.8204869587867546 16.074912584714674 chr2 243199373 103199901 0.4243427921995506 9.91857644418175 chr3 198022430 121243683 0.6122724733758695 11.805788771270244 chr4 191154276 36785784 0.19244028838779417 5.6224184404459425 chr5 180915260 68301873 0.3775351675696124 8.90551267937692 chr6 171115067 133970196 0.7829246035943754 14.246571674129418 chr7 159138663 96107640 0.6039238874339418 13.157436955858046 chr8 146364022 88250157 0.602949794588181 12.783150288622538 chr9 141213431 75780226 0.5366361079350873 10.14262830930206 chr10 135534747 37726514 0.27835307797490483 7.249079917712324 chr11 135006516 48213337 0.357118592705555 7.81453575105239 chr12 133851895 69718631 0.5208639817912178 9.49667289225644 chr13 115169878 62370686 0.541553808019142 15.538641606647918 chr14 107349540 27272647 0.25405462380183463 5.966482599475064 chr15 102531392 23500581 0.22920376424812414 5.566026485856533 chr16 90354753 92169971 1.0200899005279778 21.55221029314305 chr17 81195210 76924450 0.9474013306942614 15.157123196065873 chr18 78077248 17321638 0.22185256836921302 5.678590378033131 chr19 59128983 53396863 0.9030573551383422 12.861384201189383 chr20 63025520 63615975 1.009368506598597 20.96329080669095 chr21 48129895 12395840 0.25754969962016333 11.494144660107457 chr22 51304566 31407391 0.6121753568678469 12.97537358636859 chrMT 16571 18795 1.1342103675095045 1.4068832874288324 chrX 155270560 56683013 0.3650596288182383 6.387115027641093 chrY 59373566 2237707 0.03768860708147461 1.2173124326792637