BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524494.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 = 1,753,321 number of mapped reads = 1,597,061 (91.09%) number of supplementary alignments = 3,662 (0.21%) number of secondary alignments = 0 number of mapped bases = 93,199,545 bp number of sequenced bases = 93,170,064 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,612 duplication rate = 3.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3647 >>>>>>> ACTG content number of A's = 23,785,733 bp (25.53%) number of C's = 17,343,419 bp (18.61%) number of T's = 29,823,121 bp (32.01%) number of G's = 22,215,977 bp (23.84%) number of N's = 1,814 bp (0%) GC percentage = 42.46% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 436,231 number of insertions = 5,895 mapped reads with insertion percentage = 0.37% number of deletions = 17,166 mapped reads with deletion percentage = 1.07% homopolymer indels = 42.66% >>>>>>> Coverage mean coverageData = 0.0301X std coverageData = 0.2738X There is a 2.64% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 9184239 0.03684740669111512 0.47701579480382117 chr2 243199373 7317918 0.030090200931562436 0.3134731290281548 chr3 198022430 5068654 0.025596362997868473 0.17957333638909065 chr4 191154276 5248878 0.02745885736817104 0.20859639962640011 chr5 180915260 5161486 0.028529854253311743 0.18874444190705464 chr6 171115067 4037401 0.023594655168501323 0.21535152798569415 chr7 159138663 4701519 0.02954353713528434 0.372442158556838 chr8 146364022 8516613 0.05818788581800519 0.3080026177987497 chr9 141213431 3978780 0.028175648533035075 0.24405875016159512 chr10 135534747 4883717 0.036032951756644366 0.27320038496565663 chr11 135006516 3203164 0.02372599556602142 0.2672029046009934 chr12 133851895 4312985 0.03222206902636679 0.2000381836133096 chr13 115169878 2122882 0.018432614819649282 0.15324601773566845 chr14 107349540 2246217 0.02092432813405628 0.16612945610766874 chr15 102531392 2506167 0.0244429237827962 0.17906163691153007 chr16 90354753 2946317 0.03260832332749557 0.21341865842114296 chr17 81195210 3218575 0.03963996151989754 0.2349574549085344 chr18 78077248 2091479 0.026787304286134676 0.4046719106288839 chr19 59128983 1880835 0.03180901995219502 0.34380588738058765 chr20 63025520 2676787 0.042471478220251095 0.23266991524763048 chr21 48129895 1283057 0.026658213154215276 0.19397929126639935 chr22 51304566 754136 0.01469919850798465 0.134593858656448 chrMT 16571 8173 0.4932110313197755 0.8613338657636961 chrX 155270560 5564092 0.035834816336078136 0.23164655026177006 chrY 59373566 285474 0.0048080992810841106 0.12250318678440171