BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231845.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 7,080,941 number of mapped reads = 5,422,371 (76.58%) number of supplementary alignments = 51,757 (0.73%) number of secondary alignments = 0 number of mapped bases = 354,104,946 bp number of sequenced bases = 353,954,586 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 415,517 duplication rate = 5.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.4882 >>>>>>> ACTG content number of A's = 103,808,023 bp (29.33%) number of C's = 67,705,550 bp (19.13%) number of T's = 106,231,134 bp (30.01%) number of G's = 76,183,884 bp (21.52%) number of N's = 25,995 bp (0.01%) GC percentage = 40.65% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 2,256,365 number of insertions = 26,792 mapped reads with insertion percentage = 0.49% number of deletions = 88,658 mapped reads with deletion percentage = 1.62% homopolymer indels = 45.39% >>>>>>> Coverage mean coverageData = 0.1144X std coverageData = 4.9371X There is a 8.13% of reference with a coverageData >= 1X There is a 2.06% of reference with a coverageData >= 2X There is a 0.57% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 34722236 0.13930651751515596 1.93088536660578 chr2 243199373 28487933 0.11713818439819744 17.252685827915432 chr3 198022430 21442339 0.10828237488046177 0.4240040775090724 chr4 191154276 6885279 0.036019487212517284 0.47787827388176823 chr5 180915260 34391259 0.1900959543158493 0.5684614932477199 chr6 171115067 24731702 0.14453257935492028 0.8752234757778101 chr7 159138663 19550466 0.12285176732947668 1.3925351910919845 chr8 146364022 18678978 0.12762001033286718 1.6266869160841155 chr9 141213431 17367488 0.12298750817831201 0.9639610289036571 chr10 135534747 22585039 0.16663652310503077 0.9162708047272015 chr11 135006516 23484171 0.17394842631151225 1.2475681844940283 chr12 133851895 8154495 0.06092177477203442 0.3492962685034055 chr13 115169878 15730118 0.1365818760353293 0.4770418959177798 chr14 107349540 24866538 0.23164084354716377 0.6760161802009564 chr15 102531392 2552812 0.024897857623936287 0.2242024292281952 chr16 90354753 4185499 0.046322953259581155 0.49561479809232106 chr17 81195210 2972567 0.036610127617134065 0.47925616442847735 chr18 78077248 12652781 0.16205464874991496 2.039789477741897 chr19 59128983 1765108 0.02985182410460197 1.2633296921030794 chr20 63025520 12434533 0.19729362010817206 0.6009525719748475 chr21 48129895 9318502 0.19361151733241885 0.6775770686876659 chr22 51304566 2851897 0.055587586492788964 0.30176892689432144 chrMT 16571 822723 49.648361595558505 27.182461253200355 chrX 155270560 2563587 0.01651045117632087 0.4917970295496254 chrY 59373566 906896 0.015274406795778444 0.44011387201337