BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063565.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 = 1,983,897 number of mapped reads = 1,771,325 (89.29%) number of supplementary alignments = 15,435 (0.78%) number of secondary alignments = 0 number of mapped bases = 116,743,878 bp number of sequenced bases = 116,693,983 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,775 duplication rate = 3.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7661 >>>>>>> ACTG content number of A's = 32,260,847 bp (27.65%) number of C's = 21,286,668 bp (18.24%) number of T's = 37,334,503 bp (31.99%) number of G's = 25,809,651 bp (22.12%) number of N's = 2,314 bp (0%) GC percentage = 40.36% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 910,323 number of insertions = 9,142 mapped reads with insertion percentage = 0.51% number of deletions = 30,462 mapped reads with deletion percentage = 1.7% homopolymer indels = 46.92% >>>>>>> Coverage mean coverageData = 0.0377X std coverageData = 0.3857X There is a 3.14% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 14696857 0.058964174055157116 0.8204308570863955 chr2 243199373 12752384 0.05243592466005247 0.47066888453835287 chr3 198022430 8415900 0.0424997309648205 0.24167409056044095 chr4 191154276 6980122 0.03651564666018771 0.22989828710116347 chr5 180915260 5208636 0.028790473506767753 0.19960846171504268 chr6 171115067 4709196 0.027520639079666783 0.21286887723365852 chr7 159138663 6729239 0.04228538102019872 0.3199137076902432 chr8 146364022 3727005 0.025463942224818063 0.5200507464961678 chr9 141213431 5353180 0.03790843379479959 0.37824217697454043 chr10 135534747 4732524 0.034917422319753914 0.33674730930751023 chr11 135006516 3437996 0.025465407906682076 0.22028851742301359 chr12 133851895 4693343 0.035063702310677035 0.22721675305516464 chr13 115169878 3805037 0.033038473827331834 0.21062668994345557 chr14 107349540 1939802 0.018069960989120216 0.195190457281746 chr15 102531392 2768873 0.027005124440327506 0.19113324540183615 chr16 90354753 3421825 0.037871001650571716 0.24845786857855034 chr17 81195210 3782853 0.046589607933768505 0.255063945925901 chr18 78077248 3271805 0.04190471723593536 0.6311121992580143 chr19 59128983 3249240 0.05495173153916752 0.5805661486660892 chr20 63025520 2469699 0.03918569811086049 0.2364237248729094 chr21 48129895 1893885 0.03934945214403646 0.2457297633093505 chr22 51304566 1761076 0.034325911654724844 0.21397141806953335 chrMT 16571 22507 1.3582161607627783 1.4039640015861892 chrX 155270560 6625741 0.04267222968732772 0.2747852218454151 chrY 59373566 295153 0.004971117955084591 0.15619682373171537