BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013165.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 = 2,353,975 number of mapped reads = 1,876,009 (79.7%) number of supplementary alignments = 18,527 (0.79%) number of secondary alignments = 0 number of mapped bases = 116,052,082 bp number of sequenced bases = 115,948,511 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 370,277 duplication rate = 14.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.333 >>>>>>> ACTG content number of A's = 31,450,708 bp (27.12%) number of C's = 21,231,500 bp (18.31%) number of T's = 36,703,429 bp (31.65%) number of G's = 26,392,894 bp (22.76%) number of N's = 169,980 bp (0.15%) GC percentage = 41.07% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 1,246,880 number of insertions = 7,754 mapped reads with insertion percentage = 0.41% number of deletions = 59,810 mapped reads with deletion percentage = 3.12% homopolymer indels = 41.52% >>>>>>> Coverage mean coverageData = 0.0375X std coverageData = 0.4325X There is a 1.76% of reference with a coverageData >= 1X There is a 0.81% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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% 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 5820126 0.023350497489833737 0.501044331955538 chr2 243199373 10116546 0.04159774704682318 0.5842936577847466 chr3 198022430 4246489 0.02144448484951932 0.2736192015986754 chr4 191154276 5527587 0.028916889099566887 0.341587301797913 chr5 180915260 2771970 0.01532192475084744 0.22587564774306942 chr6 171115067 8506535 0.0497123669419479 0.4930573429513908 chr7 159138663 3789957 0.02381543823828657 0.33503147433475367 chr8 146364022 11422848 0.07804409747635932 0.589405021689047 chr9 141213431 6499469 0.04602585571339882 0.4614976050345832 chr10 135534747 6888082 0.050821521067213854 0.5296643907749295 chr11 135006516 4829704 0.03577385850028157 0.3600382713615841 chr12 133851895 6684563 0.04993999524623839 0.4261269346256974 chr13 115169878 2530760 0.02197414848351233 0.2751869785936931 chr14 107349540 1475656 0.013746272224361651 0.24072067471378644 chr15 102531392 5075779 0.04950463366380513 0.4265168041165812 chr16 90354753 4817317 0.05331559038183636 0.45286899170802186 chr17 81195210 1584360 0.01951297373330274 0.2841299652369006 chr18 78077248 4826538 0.06181747082069286 0.600040243210546 chr19 59128983 2986201 0.050503168640664765 0.5524111010785444 chr20 63025520 4405455 0.06989954228065076 0.5127087512558471 chr21 48129895 2369697 0.04923544919431052 0.44009735566354247 chr22 51304566 585398 0.011410251477422107 0.19723394423238122 chrMT 16571 13690 0.8261420553979845 1.3946494798675626 chrX 155270560 7871057 0.050692526645102584 0.44215306239606555 chrY 59373566 406298 0.00684307895537216 0.21300448408662123