BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085117.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,095,554 number of mapped reads = 842,737 (76.92%) number of supplementary alignments = 4,366 (0.4%) number of secondary alignments = 0 number of mapped bases = 58,342,294 bp number of sequenced bases = 58,326,309 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,011 duplication rate = 1.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.7653 >>>>>>> ACTG content number of A's = 18,237,861 bp (31.27%) number of C's = 10,516,015 bp (18.03%) number of T's = 16,919,175 bp (29.01%) number of G's = 12,651,776 bp (21.69%) number of N's = 1,482 bp (0%) GC percentage = 39.72% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 507,868 number of insertions = 3,703 mapped reads with insertion percentage = 0.44% number of deletions = 9,793 mapped reads with deletion percentage = 1.15% homopolymer indels = 46% >>>>>>> Coverage mean coverageData = 0.0188X std coverageData = 0.1665X There is a 1.81% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5295819 0.021246964114885795 0.2516617245246115 chr2 243199373 5560426 0.022863652695354605 0.1775956843050995 chr3 198022430 3618260 0.018271970503543462 0.13875574363515977 chr4 191154276 3720454 0.019463095871316005 0.14293580648394089 chr5 180915260 3033880 0.016769619102335535 0.13222501820427254 chr6 171115067 4037424 0.023594789580978277 0.18095512981413392 chr7 159138663 4997019 0.03140040833445987 0.19918668216539662 chr8 146364022 3421087 0.023373824750456774 0.21187559395831376 chr9 141213431 1866312 0.013216249947216423 0.13139360064948943 chr10 135534747 3861254 0.02848903388590086 0.2132217175918622 chr11 135006516 2588345 0.01917200055736569 0.16652998405356917 chr12 133851895 2422778 0.01810043854814308 0.13817690168855823 chr13 115169878 1296018 0.011253098661787243 0.10769979762620256 chr14 107349540 1913851 0.017828217987706327 0.13715232230167423 chr15 102531392 1034732 0.010091855575314924 0.10185731269772397 chr16 90354753 1469363 0.0162621550191167 0.13582641629056325 chr17 81195210 907222 0.011173343846268764 0.11351152679286067 chr18 78077248 1516614 0.01942453197120882 0.21615159441758208 chr19 59128983 799849 0.013527190210594354 0.1664994117137087 chr20 63025520 1302755 0.020670277690687834 0.14769221692490062 chr21 48129895 676026 0.014045864841383926 0.12415715953303313 chr22 51304566 367132 0.007155932280959164 0.0859307713769882 chrMT 16571 7402 0.446683965964637 0.6749721407099091 chrX 155270560 2528928 0.016287234360460864 0.13635688412069188 chrY 59373566 99344 0.0016732025157458119 0.048526985194003974