BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472461.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 = 16,733,918 number of mapped reads = 16,618,749 (99.31%) number of supplementary alignments = 59,030 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,328,593 number of mapped paired reads (second in pair) = 8,290,156 number of mapped paired reads (both in pair) = 16,556,028 number of mapped paired reads (singletons) = 62,721 number of mapped bases = 1,625,049,967 bp number of sequenced bases = 1,624,848,967 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,950,656 duplication rate = 48.15% >>>>>>> Insert size mean insert size = 15,542.9597 std insert size = 1,242,821.0017 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 55.0614 >>>>>>> ACTG content number of A's = 432,346,799 bp (26.61%) number of C's = 380,801,357 bp (23.44%) number of T's = 433,891,679 bp (26.7%) number of G's = 377,606,627 bp (23.24%) number of N's = 202,505 bp (0.01%) GC percentage = 46.68% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 7,837,230 number of insertions = 99,074 mapped reads with insertion percentage = 0.59% number of deletions = 73,239 mapped reads with deletion percentage = 0.43% homopolymer indels = 46.26% >>>>>>> Coverage mean coverageData = 0.5249X std coverageData = 20.0151X There is a 4.2% of reference with a coverageData >= 1X There is a 2% of reference with a coverageData >= 2X There is a 0.85% of reference with a coverageData >= 3X There is a 0.63% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.41% 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 0.31% 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 178901976 0.7177593992835027 20.095085666338093 chr2 243199373 134828437 0.5543946735421887 22.02754032078327 chr3 198022430 151145375 0.7632740139589237 24.719559782258944 chr4 191154276 54224073 0.2836665448174437 11.889910932798358 chr5 180915260 64494716 0.3564912987439534 12.043222312841523 chr6 171115067 121499679 0.7100466436424328 21.653284976001252 chr7 159138663 69812272 0.43868831548496795 15.28957726107601 chr8 146364022 81956969 0.5599529712295006 18.048678588328503 chr9 141213431 83608394 0.5920711182210423 18.747664826893818 chr10 135534747 49734361 0.3669491558500493 19.489505083725433 chr11 135006516 47993764 0.35549220453922387 12.32668777435929 chr12 133851895 92160897 0.6885288923253571 36.986171397896534 chr13 115169878 34187107 0.29684069822493 14.438552108280035 chr14 107349540 52820308 0.49204037576686405 17.76358840304113 chr15 102531392 41165514 0.4014918084794947 16.357275786914776 chr16 90354753 70880519 0.7844691800551986 25.22736848315134 chr17 81195210 83777860 1.0318079108361196 29.523848584249293 chr18 78077248 25477659 0.3263134863564863 12.27816716393297 chr19 59128983 52831924 0.8935030051167969 30.634010173386955 chr20 63025520 54332991 0.862079218069125 32.23969864393797 chr21 48129895 7493919 0.1557019602889223 8.139577802893 chr22 51304566 12828747 0.25005078495352634 7.143608557288358 chrMT 16571 6492 0.3917687526401545 0.9306609590189613 chrX 155270560 55591714 0.3580312584690878 12.455862063354429 chrY 59373566 3294300 0.05548428740156857 4.065845438386806