BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472392.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 = 19,888,098 number of mapped reads = 19,710,991 (99.11%) number of supplementary alignments = 79,962 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,892,453 number of mapped paired reads (second in pair) = 9,818,538 number of mapped paired reads (both in pair) = 19,595,698 number of mapped paired reads (singletons) = 115,293 number of mapped bases = 1,936,701,222 bp number of sequenced bases = 1,936,467,400 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,294,988 duplication rate = 46.17% >>>>>>> Insert size mean insert size = 21,262.5974 std insert size = 1,447,500.569 median insert size = 223 >>>>>>> Mapping quality mean mapping quality = 54.7787 >>>>>>> ACTG content number of A's = 527,164,686 bp (27.22%) number of C's = 442,860,493 bp (22.87%) number of T's = 527,705,793 bp (27.25%) number of G's = 438,504,221 bp (22.64%) number of N's = 232,207 bp (0.01%) GC percentage = 45.51% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 10,976,433 number of insertions = 112,923 mapped reads with insertion percentage = 0.57% number of deletions = 100,193 mapped reads with deletion percentage = 0.5% homopolymer indels = 46.57% >>>>>>> Coverage mean coverageData = 0.6256X std coverageData = 19.3757X There is a 5.68% of reference with a coverageData >= 1X There is a 2.32% of reference with a coverageData >= 2X There is a 0.97% of reference with a coverageData >= 3X There is a 0.71% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.49% of reference with a coverageData >= 6X There is a 0.45% of reference with a coverageData >= 7X There is a 0.43% of reference with a coverageData >= 8X There is a 0.41% of reference with a coverageData >= 9X There is a 0.4% of reference with a coverageData >= 10X There is a 0.39% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.36% of reference with a coverageData >= 13X There is a 0.35% of reference with a coverageData >= 14X There is a 0.35% of reference with a coverageData >= 15X There is a 0.34% of reference with a coverageData >= 16X There is a 0.33% of reference with a coverageData >= 17X There is a 0.32% of reference with a coverageData >= 18X There is a 0.32% of reference with a coverageData >= 19X There is a 0.31% of reference with a coverageData >= 20X There is a 0.3% of reference with a coverageData >= 21X There is a 0.3% of reference with a coverageData >= 22X There is a 0.29% of reference with a coverageData >= 23X There is a 0.29% of reference with a coverageData >= 24X There is a 0.28% of reference with a coverageData >= 25X There is a 0.28% of reference with a coverageData >= 26X There is a 0.27% of reference with a coverageData >= 27X There is a 0.27% of reference with a coverageData >= 28X There is a 0.26% of reference with a coverageData >= 29X There is a 0.26% of reference with a coverageData >= 30X There is a 0.26% of reference with a coverageData >= 31X There is a 0.25% of reference with a coverageData >= 32X There is a 0.25% of reference with a coverageData >= 33X There is a 0.25% of reference with a coverageData >= 34X There is a 0.24% of reference with a coverageData >= 35X There is a 0.24% of reference with a coverageData >= 36X There is a 0.24% of reference with a coverageData >= 37X There is a 0.23% of reference with a coverageData >= 38X There is a 0.23% of reference with a coverageData >= 39X There is a 0.23% of reference with a coverageData >= 40X There is a 0.22% of reference with a coverageData >= 41X There is a 0.22% of reference with a coverageData >= 42X There is a 0.22% of reference with a coverageData >= 43X There is a 0.22% of reference with a coverageData >= 44X There is a 0.21% of reference with a coverageData >= 45X There is a 0.21% of reference with a coverageData >= 46X There is a 0.21% of reference with a coverageData >= 47X There is a 0.21% of reference with a coverageData >= 48X There is a 0.2% of reference with a coverageData >= 49X There is a 0.2% of reference with a coverageData >= 50X There is a 0.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 165451680 0.6637964605111255 16.235214875160477 chr2 243199373 154035390 0.6333708352118161 18.331744721403926 chr3 198022430 135256222 0.6830348562029059 16.737578845382508 chr4 191154276 50734320 0.26541033275133225 9.779127773453327 chr5 180915260 63375604 0.3503054634528895 10.626409732053327 chr6 171115067 155630008 0.9095049940868153 25.569235296478638 chr7 159138663 148184387 0.9311652128182075 23.49569067557129 chr8 146364022 96377139 0.6584756122648775 18.03141193971976 chr9 141213431 53167940 0.3765076708602881 10.080080844678488 chr10 135534747 55753580 0.4113600477669391 11.483127159054346 chr11 135006516 73461332 0.5441317513889478 22.493810462590545 chr12 133851895 79567380 0.5944434331691755 18.343360944452044 chr13 115169878 82117898 0.7130154118944191 30.882253431020025 chr14 107349540 37575308 0.3500276573146005 17.11817336882974 chr15 102531392 62965283 0.6141073652837953 23.404537112672624 chr16 90354753 108854607 1.2047468825464003 32.49413548085578 chr17 81195210 96741551 1.1914686962445198 23.097618669877832 chr18 78077248 27005696 0.34588432215233816 20.55898532291821 chr19 59128983 55404241 0.9370064930763311 22.631711777565265 chr20 63025520 70297566 1.115382562492146 27.613758513308774 chr21 48129895 15760956 0.32746707633581995 16.883393216095172 chr22 51304566 20432001 0.3982491733776678 14.166525547254018 chrMT 16571 46709 2.818719449640939 2.537351418114997 chrX 155270560 127921131 0.8238595326763811 18.969832382851706 chrY 59373566 583293 0.00982411937325779 1.0197643937306085