BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472739.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 = 17,411,618 number of mapped reads = 17,256,417 (99.11%) number of supplementary alignments = 57,088 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,657,182 number of mapped paired reads (second in pair) = 8,599,235 number of mapped paired reads (both in pair) = 17,162,072 number of mapped paired reads (singletons) = 94,345 number of mapped bases = 1,700,843,572 bp number of sequenced bases = 1,700,604,417 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,749,304 duplication rate = 46.11% >>>>>>> Insert size mean insert size = 22,204.7372 std insert size = 1,501,402.5183 median insert size = 248 >>>>>>> Mapping quality mean mapping quality = 55.1455 >>>>>>> ACTG content number of A's = 469,168,410 bp (27.59%) number of C's = 383,726,291 bp (22.56%) number of T's = 465,659,989 bp (27.38%) number of G's = 381,720,200 bp (22.45%) number of N's = 329,527 bp (0.02%) GC percentage = 45.01% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 10,565,992 number of insertions = 100,013 mapped reads with insertion percentage = 0.57% number of deletions = 94,812 mapped reads with deletion percentage = 0.54% homopolymer indels = 45.42% >>>>>>> Coverage mean coverageData = 0.5494X std coverageData = 18.1163X There is a 4.98% of reference with a coverageData >= 1X There is a 2.08% of reference with a coverageData >= 2X There is a 0.93% of reference with a coverageData >= 3X There is a 0.67% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 174769290 0.7011789551368861 22.981777625735187 chr2 243199373 162690913 0.6689610708823661 26.89065170740859 chr3 198022430 195786929 0.9887108697736918 21.235361165008623 chr4 191154276 75082433 0.39278448053131704 17.05614138287887 chr5 180915260 74322103 0.4108116860899407 13.570026283218489 chr6 171115067 102680974 0.600069741374674 17.883209605317443 chr7 159138663 51295533 0.32233231091051706 8.906939226842638 chr8 146364022 68164368 0.46571805740621147 13.524767417838078 chr9 141213431 102268725 0.7242138674472118 17.14161090947854 chr10 135534747 43513971 0.32105398772758986 10.073134817785954 chr11 135006516 82719084 0.6127043823573671 18.512871071966455 chr12 133851895 96810645 0.72326689883621 22.6323043740897 chr13 115169878 48488289 0.4210153717450322 18.589589038737284 chr14 107349540 33504709 0.3121085474609393 10.051153866904185 chr15 102531392 36045004 0.35155090842812314 11.944025335538518 chr16 90354753 54966622 0.6083423414372015 16.142219669515974 chr17 81195210 67927390 0.8365935626005524 22.165891195966054 chr18 78077248 31044415 0.39761154235354196 13.609524216168271 chr19 59128983 49651577 0.8397164043900434 29.28994341518899 chr20 63025520 26769544 0.4247413428719033 13.690223455347423 chr21 48129895 8093138 0.16815199783834975 8.322061468202092 chr22 51304566 22541673 0.43936972393451296 13.325413942544925 chrMT 16571 1182 0.07132943093355863 0.350494586851578 chrX 155270560 90318835 0.5816867988368175 17.540698738217554 chrY 59373566 1386226 0.023347528090194213 0.7252584943838121