BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234081.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 = 912,840 number of mapped reads = 614,655 (67.33%) number of supplementary alignments = 3,758 (0.41%) number of secondary alignments = 0 number of mapped bases = 39,879,475 bp number of sequenced bases = 39,858,888 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,154 duplication rate = 2.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4262 >>>>>>> ACTG content number of A's = 11,285,142 bp (28.31%) number of C's = 6,648,271 bp (16.68%) number of T's = 12,964,502 bp (32.53%) number of G's = 8,953,401 bp (22.46%) number of N's = 7,572 bp (0.02%) GC percentage = 39.14% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 375,646 number of insertions = 3,375 mapped reads with insertion percentage = 0.54% number of deletions = 11,974 mapped reads with deletion percentage = 1.92% homopolymer indels = 47.43% >>>>>>> Coverage mean coverageData = 0.0129X std coverageData = 0.1592X There is a 1.2% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% 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 3383951 0.01357649977530046 0.21129039070726607 chr2 243199373 2997132 0.012323765324839057 0.15537555898869967 chr3 198022430 3225392 0.016288013433629716 0.13508141631421736 chr4 191154276 2357551 0.012333237055079008 0.11978789921198135 chr5 180915260 2482929 0.013724265161490523 0.12370428313858653 chr6 171115067 2164999 0.012652299052075875 0.1274496324837501 chr7 159138663 2648416 0.01664219084208342 0.19011286576552172 chr8 146364022 2124996 0.014518567957909765 0.35638279078752644 chr9 141213431 1486967 0.010529926151287975 0.12848681099975365 chr10 135534747 1966464 0.01450892884316964 0.13839445856997112 chr11 135006516 1766024 0.01308102788164684 0.1382555868312754 chr12 133851895 1513270 0.011305555293034888 0.11338708379428623 chr13 115169878 1394244 0.012105977918983296 0.11679695293455292 chr14 107349540 1539005 0.014336391194596641 0.12771671956434655 chr15 102531392 1040329 0.010146443735007518 0.10764634105627822 chr16 90354753 779798 0.008630403759722525 0.10133849656634016 chr17 81195210 953179 0.011739350141467705 0.11750408326552865 chr18 78077248 1049497 0.013441777558553294 0.19852177031718768 chr19 59128983 817714 0.013829326305172541 0.15260328856632877 chr20 63025520 888065 0.014090562045342902 0.12633966602956032 chr21 48129895 844301 0.01754213259762981 0.14153680174157915 chr22 51304566 394566 0.007690660515479265 0.092463584211577 chrMT 16571 23579 1.422907488986784 1.398958996659165 chrX 155270560 1934187 0.012456881716662836 0.12148452537337474 chrY 59373566 102920 0.0017334313387880392 0.050992784812580794