BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173924.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 = 1,461,872 number of mapped reads = 1,427,275 (97.63%) number of supplementary alignments = 127,173 (8.7%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 711,079 number of mapped paired reads (second in pair) = 716,196 number of mapped paired reads (both in pair) = 1,403,554 number of mapped paired reads (singletons) = 23,721 number of mapped bases = 169,044,996 bp number of sequenced bases = 168,971,023 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,089,850 duplication rate = 65.56% >>>>>>> Insert size mean insert size = 670,623.4606 std insert size = 7,696,304.1934 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 52.998 >>>>>>> ACTG content number of A's = 50,339,959 bp (29.79%) number of C's = 33,707,390 bp (19.95%) number of T's = 50,225,785 bp (29.72%) number of G's = 34,695,922 bp (20.53%) number of N's = 1,967 bp (0%) GC percentage = 40.48% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 1,599,680 number of insertions = 16,869 mapped reads with insertion percentage = 1.15% number of deletions = 29,208 mapped reads with deletion percentage = 1.99% homopolymer indels = 45.27% >>>>>>> Coverage mean coverageData = 0.0546X std coverageData = 0.9791X There is a 1.17% of reference with a coverageData >= 1X There is a 0.93% of reference with a coverageData >= 2X There is a 0.71% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.36% of reference with a coverageData >= 6X There is a 0.26% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.08% 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 0.03% 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 12527794 0.05026183665957647 0.7168709725563827 chr2 243199373 15474872 0.06363039431026822 2.5624608864187652 chr3 198022430 14818540 0.07483263385869975 0.7864638164131091 chr4 191154276 8436865 0.04413641785339921 0.6085183595933079 chr5 180915260 10679760 0.05903183623095144 0.6973654472392564 chr6 171115067 8453787 0.049404106536100646 0.6570064570206332 chr7 159138663 8519458 0.05353480945105087 0.6842078509118753 chr8 146364022 8075735 0.05517568381661444 0.6850015102722721 chr9 141213431 6464338 0.045777076261251666 0.6373077705363087 chr10 135534747 9267958 0.06838067879375612 0.8018497828727286 chr11 135006516 5241056 0.03882076328819566 0.5609093276568133 chr12 133851895 8060703 0.0602210600006821 0.6952535060616077 chr13 115169878 4170502 0.03621174279615022 0.5482114711211382 chr14 107349540 5190758 0.04835379825567953 0.6165302251850282 chr15 102531392 4161651 0.04058904223206099 0.571790692623494 chr16 90354753 11641979 0.1288474442512172 1.0975331130506893 chr17 81195210 6749719 0.08312952204939184 0.8394511869769331 chr18 78077248 3036204 0.03888718003995223 0.6319095585220461 chr19 59128983 2099685 0.03551025053145257 0.5760576814156214 chr20 63025520 7316777 0.11609229086884171 0.9935274862975103 chr21 48129895 1952040 0.04055774482782479 0.5716379249451764 chr22 51304566 1188353 0.02316271421144075 0.410435483717948 chrMT 16571 567319 34.23565264618912 35.359276317672254 chrX 155270560 4778620 0.030776085305546652 0.4937036927067433 chrY 59373566 170523 0.0028720356799859384 0.14149563218347813