BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819078.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 712,187 number of mapped reads = 649,632 (91.22%) number of supplementary alignments = 2,395 (0.34%) number of secondary alignments = 0 number of mapped bases = 37,714,244 bp number of sequenced bases = 37,702,906 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,422 duplication rate = 1.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5238 >>>>>>> ACTG content number of A's = 9,650,112 bp (25.6%) number of C's = 7,051,960 bp (18.7%) number of T's = 11,486,765 bp (30.47%) number of G's = 9,513,457 bp (25.23%) number of N's = 612 bp (0%) GC percentage = 43.94% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 192,965 number of insertions = 2,616 mapped reads with insertion percentage = 0.4% number of deletions = 6,852 mapped reads with deletion percentage = 1.05% homopolymer indels = 42.97% >>>>>>> Coverage mean coverageData = 0.0122X std coverageData = 0.1378X There is a 1.14% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.01% 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 3472992 0.013933734592380414 0.1872847787060715 chr2 243199373 2991145 0.012299147662687436 0.15674620908461265 chr3 198022430 2000842 0.01010411800319792 0.10550340347874902 chr4 191154276 2250714 0.011774332476873288 0.12129022641965154 chr5 180915260 2125338 0.011747698895051749 0.11318391025946277 chr6 171115067 1660231 0.00970242439258724 0.11035601592414808 chr7 159138663 1937582 0.012175432188970948 0.16708947823407355 chr8 146364022 3567924 0.024377056268650502 0.17716023931386152 chr9 141213431 1660302 0.011757394379858952 0.1272969686098961 chr10 135534747 1890597 0.013949168326554665 0.1552361298280027 chr11 135006516 1338489 0.009914254805301398 0.13651466907068208 chr12 133851895 1832633 0.013691498353459994 0.1227394342272424 chr13 115169878 883063 0.007667482290812186 0.09054558473256964 chr14 107349540 936464 0.008723502681054804 0.09927688604626833 chr15 102531392 849383 0.008284126289829363 0.09675619666923002 chr16 90354753 1178083 0.013038417580533921 0.12479710548206469 chr17 81195210 1137450 0.01400883130913757 0.12904678789512414 chr18 78077248 941131 0.012053844418286873 0.20211059652825242 chr19 59128983 712471 0.01204943775204116 0.15240053631684652 chr20 63025520 1125483 0.017857575788347322 0.13984912233485058 chr21 48129895 509711 0.010590320215741173 0.11245944560439008 chr22 51304566 208878 0.00407133353393926 0.06667119872220942 chrMT 16571 5873 0.35441433830185265 0.652699633805551 chrX 155270560 2367090 0.015244937610838784 0.1355538352192645 chrY 59373566 130375 0.0021958425067478684 0.07075785796022335