BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231749.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 = 4,493,873 number of mapped reads = 4,224,777 (94.01%) number of supplementary alignments = 22,904 (0.51%) number of secondary alignments = 0 number of mapped bases = 284,688,596 bp number of sequenced bases = 284,587,419 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 294,780 duplication rate = 3.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5048 >>>>>>> ACTG content number of A's = 74,604,807 bp (26.22%) number of C's = 56,345,854 bp (19.8%) number of T's = 80,752,589 bp (28.38%) number of G's = 72,822,488 bp (25.59%) number of N's = 61,681 bp (0.02%) GC percentage = 45.39% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 1,973,858 number of insertions = 20,751 mapped reads with insertion percentage = 0.49% number of deletions = 61,823 mapped reads with deletion percentage = 1.45% homopolymer indels = 45.32% >>>>>>> Coverage mean coverageData = 0.092X std coverageData = 14.8905X There is a 6.76% of reference with a coverageData >= 1X There is a 1.38% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% 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% 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 24679787 0.09901594989406265 1.121621690539999 chr2 243199373 29198991 0.12006195015971526 53.05772464001843 chr3 198022430 21492339 0.1085348715294525 0.42099795980937155 chr4 191154276 17377717 0.09090938148828018 0.40797558040704046 chr5 180915260 20790000 0.11491567930753879 0.44612591047452993 chr6 171115067 23739141 0.13873203228795744 0.9318379957454359 chr7 159138663 17626434 0.11076148101106015 1.594030588402782 chr8 146364022 16950443 0.11581017498958864 0.7341447655276107 chr9 141213431 9496073 0.06724624515355059 0.8761720582841785 chr10 135534747 8809103 0.06499516319604744 0.5343138849847855 chr11 135006516 10927112 0.08093766377913196 0.9666361606169664 chr12 133851895 9333620 0.06973095151174363 0.3539376028085962 chr13 115169878 8173964 0.07097310635338173 0.3299886157496282 chr14 107349540 8422401 0.07845772790456298 0.5993724258192489 chr15 102531392 4078414 0.039777222570039815 0.2569421434320346 chr16 90354753 8453618 0.0935603022455277 0.512040590665378 chr17 81195210 7357356 0.09061317779706463 0.6233209325505099 chr18 78077248 5733021 0.07342754959805961 1.5680034337843056 chr19 59128983 8083501 0.13670962343458537 0.9046528981935144 chr20 63025520 9330270 0.14803955604015642 0.54589612659078 chr21 48129895 4990178 0.1036814645035066 0.5030625120307723 chr22 51304566 2392087 0.0466252263005207 0.2721421127649809 chrMT 16571 8224 0.4962886971214773 0.9774006981532052 chrX 155270560 6721551 0.04328928162557023 0.4461953736406685 chrY 59373566 523251 0.008812861265567238 0.19523958596323504