BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354881.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 = 19,157,704 number of mapped reads = 19,016,419 (99.26%) number of supplementary alignments = 419,167 (2.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,518,740 number of mapped paired reads (second in pair) = 9,497,679 number of mapped paired reads (both in pair) = 18,973,152 number of mapped paired reads (singletons) = 43,267 number of mapped bases = 2,535,006,571 bp number of sequenced bases = 2,533,566,451 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,689,542 duplication rate = 32.8% >>>>>>> Insert size mean insert size = 197,056.0403 std insert size = 5,065,630.9437 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 53.9832 >>>>>>> ACTG content number of A's = 719,883,151 bp (28.41%) number of C's = 535,576,290 bp (21.14%) number of T's = 727,986,159 bp (28.73%) number of G's = 550,109,069 bp (21.71%) number of N's = 11,782 bp (0%) GC percentage = 42.85% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 19,595,437 number of insertions = 487,070 mapped reads with insertion percentage = 2.38% number of deletions = 502,615 mapped reads with deletion percentage = 2.51% homopolymer indels = 43.66% >>>>>>> Coverage mean coverageData = 0.8189X std coverageData = 18.9448X There is a 35.04% of reference with a coverageData >= 1X There is a 21.71% of reference with a coverageData >= 2X There is a 9.11% of reference with a coverageData >= 3X There is a 5.59% of reference with a coverageData >= 4X There is a 2.35% of reference with a coverageData >= 5X There is a 1.43% of reference with a coverageData >= 6X There is a 0.62% of reference with a coverageData >= 7X There is a 0.39% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.13% 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 0.03% 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 0.02% of reference with a coverageData >= 21X There is a 0.02% 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 0.01% of reference with a coverageData >= 43X There is a 0.01% 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 207822250 0.8337882937511317 22.03171462699318 chr2 243199373 227172247 0.9340988185853588 54.46049085706623 chr3 198022430 164694507 0.8316962224935832 1.7984717776962125 chr4 191154276 171246753 0.8958562506862259 13.860370459952149 chr5 180915260 149611261 0.8269687200515866 1.4918717376639745 chr6 171115067 142680968 0.8338305357996324 3.257747074739775 chr7 159138663 136974827 0.8607262648675137 11.960736164587736 chr8 146364022 123678313 0.8450048810492513 3.2102317194604604 chr9 141213431 108589385 0.7689734909139061 12.034686669349282 chr10 135534747 142959690 1.054782579112351 30.86637249841144 chr11 135006516 115839228 0.8580269414551813 4.2711809679059165 chr12 133851895 110531154 0.8257720520131597 1.5002807297310377 chr13 115169878 77702133 0.6746740931687016 1.307590790923149 chr14 107349540 76471592 0.7123606864081579 3.065772025566047 chr15 102531392 71869765 0.7009537625315767 1.3276457754963422 chr16 90354753 80057038 0.8860301792867499 5.666018556589792 chr17 81195210 72269435 0.8900701777851181 4.9651213672703225 chr18 78077248 68371219 0.8756868454175024 10.408476900394062 chr19 59128983 52667519 0.8907225581742206 11.256842711678948 chr20 63025520 53863245 0.8546259515193211 4.429718524436038 chr21 48129895 35503814 0.7376665583833083 6.901608074312461 chr22 51304566 31608391 0.616093136817491 2.547656490202293 chrMT 16571 12443852 750.9415243497676 166.48041396278873 chrX 155270560 67249595 0.43311233629865187 1.7114716675461148 chrY 59373566 33128390 0.557965307322117 16.50158915305821