BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083767.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 = 2,366,431 number of mapped reads = 1,614,169 (68.21%) number of supplementary alignments = 8,745 (0.37%) number of secondary alignments = 0 number of mapped bases = 101,898,119 bp number of sequenced bases = 101,864,741 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,612 duplication rate = 2.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8211 >>>>>>> ACTG content number of A's = 28,448,849 bp (27.93%) number of C's = 19,485,430 bp (19.13%) number of T's = 31,081,149 bp (30.51%) number of G's = 22,848,199 bp (22.43%) number of N's = 1,114 bp (0%) GC percentage = 41.56% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 818,407 number of insertions = 7,480 mapped reads with insertion percentage = 0.46% number of deletions = 20,996 mapped reads with deletion percentage = 1.29% homopolymer indels = 46.63% >>>>>>> Coverage mean coverageData = 0.0329X std coverageData = 0.2441X There is a 2.91% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 8182988 0.0328303615339839 0.3200864844628527 chr2 243199373 8487684 0.034900106424205296 0.3127352674535426 chr3 198022430 7071267 0.03570942443237365 0.2083098966758304 chr4 191154276 6502018 0.03401450459836954 0.20788792503356907 chr5 180915260 6305174 0.03485153214825549 0.2062823741570104 chr6 171115067 6169111 0.036052412614255645 0.23219103498432267 chr7 159138663 5544456 0.03484040832993551 0.2815379612760439 chr8 146364022 5120282 0.034983200994572285 0.25343807998737866 chr9 141213431 4276541 0.030284236915113266 0.23435950721483065 chr10 135534747 4610452 0.03401675291429142 0.24473232545030923 chr11 135006516 4804557 0.035587593416602205 0.23305909673823896 chr12 133851895 4409002 0.03293940664792232 0.20160699503034393 chr13 115169878 3244288 0.02816958788477661 0.1861169025890726 chr14 107349540 3075387 0.028648348190406778 0.19660052894851046 chr15 102531392 3053874 0.029784770697348965 0.19260519386309716 chr16 90354753 2670849 0.029559584983869083 0.20330765011205637 chr17 81195210 2856510 0.035180769900096324 0.22851774546063722 chr18 78077248 2886181 0.036965711189000924 0.3972470804746406 chr19 59128983 1955834 0.033077416535305534 0.2685512746035252 chr20 63025520 1969773 0.03125357791573953 0.1973750833722707 chr21 48129895 1338358 0.027807207973339645 0.18961757995875028 chr22 51304566 1151319 0.022440868128579435 0.16571836563305167 chrMT 16571 11242 0.6784140969162996 0.9656857430582495 chrX 155270560 5956517 0.03836217889598646 0.22792435669070304 chrY 59373566 244455 0.0041172362798623215 0.09120054912409035