BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068090.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 = 3,739,484 number of mapped reads = 2,586,038 (69.15%) number of supplementary alignments = 23,673 (0.63%) number of secondary alignments = 0 number of mapped bases = 162,621,917 bp number of sequenced bases = 162,543,611 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 974,735 duplication rate = 20.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2764 >>>>>>> ACTG content number of A's = 41,140,487 bp (25.31%) number of C's = 28,980,498 bp (17.83%) number of T's = 53,618,879 bp (32.99%) number of G's = 38,786,492 bp (23.86%) number of N's = 17,255 bp (0.01%) GC percentage = 41.69% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 975,506 number of insertions = 10,825 mapped reads with insertion percentage = 0.41% number of deletions = 44,701 mapped reads with deletion percentage = 1.71% homopolymer indels = 44.93% >>>>>>> Coverage mean coverageData = 0.0525X std coverageData = 0.7995X There is a 1.49% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.65% of reference with a coverageData >= 3X There is a 0.49% of reference with a coverageData >= 4X There is a 0.37% of reference with a coverageData >= 5X There is a 0.28% of reference with a coverageData >= 6X There is a 0.22% of reference with a coverageData >= 7X There is a 0.17% of reference with a coverageData >= 8X There is a 0.13% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 14749640 0.05917594082945133 1.0043024319095937 chr2 243199373 14332835 0.058934506381313735 1.4759263520434664 chr3 198022430 8865338 0.044769362743402354 0.5902276448709366 chr4 191154276 9749903 0.05100541407716142 0.5991146729275962 chr5 180915260 5931577 0.03278649352188422 0.5009793912287688 chr6 171115067 13658741 0.07982196564841365 0.8827169470441639 chr7 159138663 12724368 0.07995774100477393 0.8300013605791591 chr8 146364022 4466528 0.030516570527147718 0.6245107084247844 chr9 141213431 4962656 0.03514294614086673 0.5565633144249631 chr10 135534747 6608222 0.048756663116064254 0.6629318852504794 chr11 135006516 11634701 0.08617881080643544 0.8551554328119373 chr12 133851895 4980110 0.03720612248336118 0.547140737197572 chr13 115169878 3212203 0.027890999415663184 0.48706233590086806 chr14 107349540 2246379 0.020925837222963414 0.4001487728294828 chr15 102531392 3518299 0.034314359059906256 0.5107057863845021 chr16 90354753 3048124 0.033735070915417144 0.521785057401612 chr17 81195210 4563201 0.056200371918491254 0.6628203723137891 chr18 78077248 6505929 0.08332682268719308 1.2855670220585047 chr19 59128983 3468165 0.058654230531920364 0.8150455240367223 chr20 63025520 3621194 0.05745599560305095 0.6470659760734205 chr21 48129895 3990682 0.08291482871508446 0.7626401007823838 chr22 51304566 1858986 0.03623431879337991 0.5231758561229924 chrMT 16571 113722 6.862711966688794 8.577166905464647 chrX 155270560 13240694 0.08527498065312575 0.7862752131470971 chrY 59373566 569720 0.009595515957387502 0.28009027568937295