BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230357.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 = 842,876 number of mapped reads = 763,483 (90.58%) number of supplementary alignments = 6,965 (0.83%) number of secondary alignments = 0 number of mapped bases = 51,619,808 bp number of sequenced bases = 51,593,909 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,974 duplication rate = 2.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4504 >>>>>>> ACTG content number of A's = 15,136,679 bp (29.34%) number of C's = 9,358,051 bp (18.14%) number of T's = 16,497,534 bp (31.98%) number of G's = 10,574,159 bp (20.49%) number of N's = 27,486 bp (0.05%) GC percentage = 38.63% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 454,004 number of insertions = 4,601 mapped reads with insertion percentage = 0.6% number of deletions = 15,447 mapped reads with deletion percentage = 2% homopolymer indels = 46.65% >>>>>>> Coverage mean coverageData = 0.0167X std coverageData = 0.185X There is a 1.5% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% 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 3556196 0.014267551213041912 0.27243462515427375 chr2 243199373 4659507 0.019159206467197595 0.18826370157483793 chr3 198022430 3432831 0.017335566481029446 0.1432718429212734 chr4 191154276 3306557 0.017297844804685405 0.1519786011794694 chr5 180915260 3497084 0.019329955914166665 0.15095984360949327 chr6 171115067 3249523 0.01899027979809633 0.16119611140606122 chr7 159138663 2554949 0.016054860282444374 0.18843045160653427 chr8 146364022 2775521 0.018963136992778185 0.3166862917387537 chr9 141213431 2293626 0.016242265227590143 0.17816308108991713 chr10 135534747 2353361 0.01736352523681621 0.1964254972153451 chr11 135006516 2247847 0.016649914882626852 0.16588743378485749 chr12 133851895 2329905 0.017406589574245474 0.14411122058708417 chr13 115169878 1746021 0.015160396366834738 0.1333556096258014 chr14 107349540 1648539 0.015356740233819353 0.13970300286088308 chr15 102531392 1312683 0.012802742403029112 0.12215229586040022 chr16 90354753 1446998 0.01601463068578141 0.14969399080942067 chr17 81195210 822736 0.010132814484992403 0.1126434607262808 chr18 78077248 1747972 0.022387725550982535 0.29782837972251935 chr19 59128983 780860 0.013206044825766748 0.1814567873244335 chr20 63025520 843714 0.013386862972332478 0.1269223150210591 chr21 48129895 725481 0.015073396690352223 0.14145918857724663 chr22 51304566 455804 0.00888427747347088 0.10148991167188826 chrMT 16571 1635 0.09866634481926256 0.35045876502565815 chrX 155270560 3690444 0.02376782823479222 0.17482235002050978 chrY 59373566 140014 0.0023581874802668917 0.07490858081627927