BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524472.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 992,912 number of mapped reads = 915,761 (92.23%) number of supplementary alignments = 1,881 (0.19%) number of secondary alignments = 0 number of mapped bases = 53,393,982 bp number of sequenced bases = 53,377,485 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,997 duplication rate = 2.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4198 >>>>>>> ACTG content number of A's = 13,311,882 bp (24.94%) number of C's = 9,445,585 bp (17.7%) number of T's = 16,713,444 bp (31.31%) number of G's = 13,905,400 bp (26.05%) number of N's = 1,174 bp (0%) GC percentage = 43.75% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 249,021 number of insertions = 3,324 mapped reads with insertion percentage = 0.36% number of deletions = 9,423 mapped reads with deletion percentage = 1.02% homopolymer indels = 42.75% >>>>>>> Coverage mean coverageData = 0.0172X std coverageData = 0.1847X There is a 1.57% of reference with a coverageData >= 1X There is a 0.11% 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 5300703 0.021266558850419073 0.31747944902986064 chr2 243199373 4159768 0.017104353307687187 0.19814025516834294 chr3 198022430 3065079 0.01547844352783672 0.1345795189172521 chr4 191154276 3045734 0.015933381474553046 0.14505504356468624 chr5 180915260 2948252 0.016296314639240493 0.13726234221781622 chr6 171115067 2274549 0.013292511523839102 0.1484544910956912 chr7 159138663 2631925 0.016538564233130448 0.2232719932038761 chr8 146364022 4936103 0.03372483847157466 0.2176908317450485 chr9 141213431 2190966 0.015515280554297984 0.16915021731654517 chr10 135534747 2811338 0.0207425627909277 0.1986636924031484 chr11 135006516 1842595 0.013648193099064936 0.1684896118993596 chr12 133851895 2480237 0.018529711514356968 0.14658001852816754 chr13 115169878 1217601 0.010572217502913392 0.11002848012804443 chr14 107349540 1260636 0.011743282737867344 0.11840051098694411 chr15 102531392 1398975 0.0136443578177501 0.1271959326927901 chr16 90354753 1657171 0.01834071750492196 0.1518009661355962 chr17 81195210 1800132 0.022170421136911894 0.16347400786032956 chr18 78077248 1281501 0.016413244995520333 0.26212476470902757 chr19 59128983 1093578 0.01849478791136996 0.22802658207999338 chr20 63025520 1513774 0.02401842936004336 0.16708281098606206 chr21 48129895 724299 0.01504883814934564 0.13860004391508626 chr22 51304566 436546 0.008508911273121382 0.09969966359713377 chrMT 16571 3856 0.23269567316396114 0.5905296027908841 chrX 155270560 3159502 0.020348364815583844 0.16539893501820385 chrY 59373566 159162 0.002680687900740205 0.07906853541136423