BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046432.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 6,444,450 number of mapped reads = 6,410,522 (99.47%) number of supplementary alignments = 53,177 (0.83%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,207,182 number of mapped paired reads (second in pair) = 3,203,340 number of mapped paired reads (both in pair) = 6,387,376 number of mapped paired reads (singletons) = 23,146 number of mapped bases = 615,402,104 bp number of sequenced bases = 615,256,270 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,073,824 duplication rate = 41.19% >>>>>>> Insert size mean insert size = 15,024.6378 std insert size = 1,200,169.0537 median insert size = 131 >>>>>>> Mapping quality mean mapping quality = 52.1939 >>>>>>> ACTG content number of A's = 181,801,351 bp (29.55%) number of C's = 126,284,502 bp (20.53%) number of T's = 181,607,840 bp (29.52%) number of G's = 125,506,793 bp (20.4%) number of N's = 55,784 bp (0.01%) GC percentage = 40.92% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 2,763,629 number of insertions = 56,548 mapped reads with insertion percentage = 0.87% number of deletions = 57,316 mapped reads with deletion percentage = 0.87% homopolymer indels = 46.38% >>>>>>> Coverage mean coverageData = 0.1988X std coverageData = 22.0979X There is a 1.61% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 105304201 0.4224832041642135 27.62016560098536 chr2 243199373 49010765 0.2015250466949189 21.10517206447829 chr3 198022430 18189448 0.09185549333982014 6.275844657601909 chr4 191154276 29578971 0.15473873574243246 20.79156731231283 chr5 180915260 39256134 0.21698630618555892 20.039025527094445 chr6 171115067 23104938 0.13502573680434582 11.869450371130116 chr7 159138663 28245414 0.17748932577119866 16.26184519391445 chr8 146364022 34339189 0.2346149588592202 22.977741668589132 chr9 141213431 6778293 0.048000342120431874 6.257010253290006 chr10 135534747 22958348 0.16939086476473816 15.985261174292539 chr11 135006516 19930161 0.14762369691845095 11.584767158589642 chr12 133851895 4665020 0.03485210276627014 1.4000088261922072 chr13 115169878 9397656 0.08159821094887328 7.464781666639732 chr14 107349540 62461001 0.5818469366519875 48.13175892384197 chr15 102531392 13479134 0.1314634838859888 13.063096946281513 chr16 90354753 57380725 0.6350603935578243 54.697725824771524 chr17 81195210 35686165 0.43951071744256837 31.805918228740016 chr18 78077248 6788842 0.08695032386387389 7.186800558061399 chr19 59128983 1558242 0.026353269089711893 1.6438091806071673 chr20 63025520 18432146 0.2924552784332442 37.88443652630553 chr21 48129895 7877808 0.16367806329101695 21.620916220218273 chr22 51304566 1056536 0.020593410730733012 1.687340342379673 chrMT 16571 186966 11.282722829038683 5.661090634336229 chrX 155270560 19654899 0.12658484003664314 26.087136959990694 chrY 59373566 81102 0.0013659614111774926 0.11180077250234374