BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174063.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 6,623,498 number of mapped reads = 6,444,296 (97.29%) number of supplementary alignments = 651,464 (9.84%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,229,816 number of mapped paired reads (second in pair) = 3,214,480 number of mapped paired reads (both in pair) = 6,326,626 number of mapped paired reads (singletons) = 117,670 number of mapped bases = 761,191,817 bp number of sequenced bases = 760,764,880 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,117,981 duplication rate = 66.07% >>>>>>> Insert size mean insert size = 946,216.9514 std insert size = 8,719,315.2291 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 52.7331 >>>>>>> ACTG content number of A's = 229,213,968 bp (30.13%) number of C's = 148,949,401 bp (19.58%) number of T's = 228,343,476 bp (30.01%) number of G's = 154,248,918 bp (20.28%) number of N's = 9,117 bp (0%) GC percentage = 39.85% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 7,743,349 number of insertions = 78,836 mapped reads with insertion percentage = 1.18% number of deletions = 172,661 mapped reads with deletion percentage = 2.61% homopolymer indels = 42.83% >>>>>>> Coverage mean coverageData = 0.2459X std coverageData = 3.4897X There is a 4.75% of reference with a coverageData >= 1X There is a 3.84% of reference with a coverageData >= 2X There is a 3.04% of reference with a coverageData >= 3X There is a 2.54% of reference with a coverageData >= 4X There is a 1.99% of reference with a coverageData >= 5X There is a 1.63% of reference with a coverageData >= 6X There is a 1.24% of reference with a coverageData >= 7X There is a 1.01% of reference with a coverageData >= 8X There is a 0.76% of reference with a coverageData >= 9X There is a 0.64% of reference with a coverageData >= 10X There is a 0.48% of reference with a coverageData >= 11X There is a 0.41% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.2% of reference with a coverageData >= 15X There is a 0.18% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% 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 70903754 0.2844677125197614 2.0215137100568814 chr2 243199373 55088238 0.22651472049642168 10.296122830068077 chr3 198022430 46188873 0.23325071306316159 1.4371275966168662 chr4 191154276 43868377 0.22949199943609946 1.7561074239614822 chr5 180915260 40755775 0.22527549638432934 1.3950627422032635 chr6 171115067 37424039 0.21870685998679473 1.44778781484665 chr7 159138663 68877988 0.43281743544621837 3.7150874201888335 chr8 146364022 82394946 0.5629453527862196 2.728197019757386 chr9 141213431 27833211 0.19710030981401477 1.6411994042856026 chr10 135534747 29416363 0.21703927333114068 3.9562104182913083 chr11 135006516 28585564 0.21173469879039022 1.4115016959286788 chr12 133851895 29081136 0.21726353594022707 1.3779873273383858 chr13 115169878 18772894 0.16300177030664215 1.199116709103602 chr14 107349540 26821422 0.2498512988504655 1.484866912446322 chr15 102531392 18844439 0.18379189663200907 1.2502574284244723 chr16 90354753 17562664 0.19437454496721385 1.7573438124506693 chr17 81195210 20228616 0.24913558324438104 1.6427464480362688 chr18 78077248 12930163 0.1656073098273136 2.0871698702880317 chr19 59128983 11327979 0.1915808191728919 1.6238397602572812 chr20 63025520 18857098 0.2991978170112678 1.6325908527700743 chr21 48129895 8913229 0.18519111666460109 1.3785915970830185 chr22 51304566 8442122 0.16454913584104774 1.1575060657143452 chrMT 16571 2555555 154.21851427192084 113.87288137387428 chrX 155270560 33984855 0.21887507200334694 1.4030527487577902 chrY 59373566 1532517 0.025811436018513694 0.942871872580861