BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354877.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 24,128,072 number of mapped reads = 24,011,507 (99.52%) number of supplementary alignments = 127,524 (0.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,015,009 number of mapped paired reads (second in pair) = 11,996,498 number of mapped paired reads (both in pair) = 23,958,412 number of mapped paired reads (singletons) = 53,095 number of mapped bases = 3,564,273,444 bp number of sequenced bases = 3,562,784,904 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,548,438 duplication rate = 20.91% >>>>>>> Insert size mean insert size = 39,477.5117 std insert size = 1,995,287.0267 median insert size = 302 >>>>>>> Mapping quality mean mapping quality = 54.5091 >>>>>>> ACTG content number of A's = 1,024,943,979 bp (28.77%) number of C's = 756,943,012 bp (21.25%) number of T's = 1,017,111,592 bp (28.55%) number of G's = 763,716,205 bp (21.44%) number of N's = 70,116 bp (0%) GC percentage = 42.68% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 21,288,331 number of insertions = 516,779 mapped reads with insertion percentage = 2.01% number of deletions = 529,220 mapped reads with deletion percentage = 2.11% homopolymer indels = 45.07% >>>>>>> Coverage mean coverageData = 1.1514X std coverageData = 13.8121X There is a 52.92% of reference with a coverageData >= 1X There is a 29.24% of reference with a coverageData >= 2X There is a 14.32% of reference with a coverageData >= 3X There is a 7.01% of reference with a coverageData >= 4X There is a 3.24% of reference with a coverageData >= 5X There is a 1.55% of reference with a coverageData >= 6X There is a 0.73% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.12% 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 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% 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 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 300699162 1.206412889940202 32.54333935827973 chr2 243199373 305121338 1.2546139993543486 10.752940016249116 chr3 198022430 229481600 1.1588667001005897 1.5892085722429339 chr4 191154276 223805548 1.1708110991982204 11.015199776818644 chr5 180915260 208459521 1.1522495172601803 1.7081205496951788 chr6 171115067 199477734 1.165752014111066 4.551168838848895 chr7 159138663 197050987 1.2382345263262642 16.19741212060868 chr8 146364022 175142125 1.196620061451987 6.947442951863783 chr9 141213431 157833413 1.1176940598518565 20.40907932078928 chr10 135534747 191354550 1.4118486530985297 27.332408314244912 chr11 135006516 167806101 1.2429481625909078 6.44026870694624 chr12 133851895 158894391 1.187091083021275 1.834148902738324 chr13 115169878 106636332 0.9259047057425901 1.4109053022411504 chr14 107349540 109212993 1.0173587422917696 1.6181070342388468 chr15 102531392 104668265 1.0208411585790234 1.4824727286790949 chr16 90354753 118071482 1.3067545212591085 5.240971284473243 chr17 81195210 113198123 1.394147795171661 7.955249136276219 chr18 78077248 97400985 1.2474951089464628 15.242327113306564 chr19 59128983 85788876 1.450876907522661 14.89320201474586 chr20 63025520 81036813 1.285777777002078 4.216116935971957 chr21 48129895 50268168 1.0444271278796682 5.4791952734470755 chr22 51304566 52054930 1.0146256767867405 3.0396137167289234 chrMT 16571 5617194 338.97737010439926 39.25744166104005 chrX 155270560 91535047 0.589519655239216 2.454458668474092 chrY 59373566 33657766 0.5668813289739073 13.089567237894562