BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472616.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 = 15,447,326 number of mapped reads = 15,306,908 (99.09%) number of supplementary alignments = 80,020 (0.52%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,668,760 number of mapped paired reads (second in pair) = 7,638,148 number of mapped paired reads (both in pair) = 15,222,078 number of mapped paired reads (singletons) = 84,830 number of mapped bases = 1,503,346,715 bp number of sequenced bases = 1,503,094,500 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,621,105 duplication rate = 48.71% >>>>>>> Insert size mean insert size = 20,569.1176 std insert size = 1,356,336.3751 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 54.8603 >>>>>>> ACTG content number of A's = 401,585,577 bp (26.72%) number of C's = 352,437,775 bp (23.45%) number of T's = 401,559,459 bp (26.72%) number of G's = 347,238,744 bp (23.1%) number of N's = 272,945 bp (0.02%) GC percentage = 46.55% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 9,432,913 number of insertions = 84,759 mapped reads with insertion percentage = 0.55% number of deletions = 76,410 mapped reads with deletion percentage = 0.49% homopolymer indels = 46.01% >>>>>>> Coverage mean coverageData = 0.4856X std coverageData = 24.8105X There is a 3.11% of reference with a coverageData >= 1X There is a 1.45% of reference with a coverageData >= 2X There is a 0.7% of reference with a coverageData >= 3X There is a 0.53% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.37% of reference with a coverageData >= 6X There is a 0.34% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.27% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.25% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.23% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.21% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.2% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.19% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.17% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.17% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.16% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.15% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.14% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 195918221 0.7860290185595967 26.693884432373963 chr2 243199373 101762982 0.4184343929209061 16.5380491272167 chr3 198022430 139997707 0.7069790376777014 29.681996380000616 chr4 191154276 29182111 0.15266261163836062 7.322907278553658 chr5 180915260 52611728 0.29080868026279266 11.519841840949635 chr6 171115067 70936742 0.4145557912793267 12.944365654375893 chr7 159138663 91356721 0.5740699291912488 23.748531932273025 chr8 146364022 76732299 0.5242565621761883 17.454596410303115 chr9 141213431 106205415 0.7520914565130848 42.97165816902144 chr10 135534747 37065059 0.2734727427498721 13.915986875993589 chr11 135006516 41129035 0.3046448143288136 13.350636500924205 chr12 133851895 117665029 0.8790688320101856 48.16081285822522 chr13 115169878 36506740 0.3169816677239165 13.869005424428748 chr14 107349540 26804067 0.249689630714766 14.350868514970863 chr15 102531392 20559651 0.20052054886760926 8.404094766509663 chr16 90354753 64173916 0.7102439425627116 26.246548790580146 chr17 81195210 64043269 0.7887567382361595 33.16485162226923 chr18 78077248 14181659 0.18163625592951227 7.887082320465008 chr19 59128983 62489778 1.0568383697720625 65.11418864052668 chr20 63025520 45667659 0.7245899597496379 25.038877328323256 chr21 48129895 8373874 0.173984879875595 11.173996218747618 chr22 51304566 19769938 0.38534461045825824 38.64465327518287 chrMT 16571 9631 0.5811960654154849 1.0872188012862884 chrX 155270560 79153415 0.5097773525129297 23.700295273345642 chrY 59373566 1050069 0.017685799771568377 0.805221588362989