BamQC report ----------------------------------- >>>>>>> Input bam file = SRR23117305.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP418207/SRP418207.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 = 390,629 number of mapped reads = 370,298 (94.8%) number of supplementary alignments = 1,882 (0.48%) number of secondary alignments = 0 number of mapped bases = 82,639,563 bp number of sequenced bases = 82,453,207 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,056 duplication rate = 15.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 53.4636 >>>>>>> ACTG content number of A's = 23,978,795 bp (29.08%) number of C's = 17,249,006 bp (20.92%) number of T's = 23,997,041 bp (29.1%) number of G's = 17,228,365 bp (20.89%) number of N's = 0 bp (0%) GC percentage = 41.81% >>>>>>> Mismatches and indels general error rate = 0.0147 number of mismatches = 492,984 number of insertions = 658,398 mapped reads with insertion percentage = 67.3% number of deletions = 156,060 mapped reads with deletion percentage = 28.7% homopolymer indels = 25.99% >>>>>>> Coverage mean coverageData = 0.0267X std coverageData = 0.5362X There is a 2.04% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 7227090 0.028995273797131283 1.6289081896693611 chr2 243199373 7245876 0.02979397483890717 0.22051144276032275 chr3 198022430 5723325 0.028902407671696585 0.21246094229154777 chr4 191154276 5416060 0.02833344936526557 0.21802089385317655 chr5 180915260 5034197 0.02782627070817575 0.2077020687241846 chr6 171115067 4989610 0.029159384310675576 0.21383629961892203 chr7 159138663 4446197 0.027939137580915832 0.7854573615452832 chr8 146364022 4306689 0.02942450570263777 0.21896130149004858 chr9 141213431 3513920 0.024883752027808178 0.2036124888226978 chr10 135534747 3961982 0.029232223379588407 0.27057805549129516 chr11 135006516 3737906 0.027686856240331393 0.2106549498472299 chr12 133851895 3728230 0.02785339721936697 0.20934952515297375 chr13 115169878 2611772 0.022677561575605732 0.18740351914956171 chr14 107349540 2520741 0.023481619017650193 0.19283612406507522 chr15 102531392 2395264 0.02336127456457433 0.19284977230427128 chr16 90354753 2236658 0.024754181996380423 0.23096922418588386 chr17 81195210 1984156 0.024436860253209517 0.22507475555196121 chr18 78077248 2212416 0.028336244638130687 0.24753370079747883 chr19 59128983 1178715 0.01993464017468388 0.3783170930825414 chr20 63025520 1717485 0.027250627999578583 0.22049524701010767 chr21 48129895 1087831 0.022601981575068885 0.2209847747690045 chr22 51304566 854205 0.016649687671073953 0.1687831370189501 chrMT 16571 68757 4.149236618188401 10.407287488824851 chrX 155270560 4326384 0.027863517720294176 0.20843382642655733 chrY 59373566 114097 0.0019216800958190721 0.10533581219235386