BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1778460.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 256,823,158 number of mapped reads = 234,444,435 (91.29%) number of supplementary alignments = 232,865 (0.09%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 118,550,238 number of mapped paired reads (second in pair) = 115,894,197 number of mapped paired reads (both in pair) = 230,629,984 number of mapped paired reads (singletons) = 3,814,451 number of mapped bases = 16,228,969,176 bp number of sequenced bases = 16,227,507,821 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 157,233,537 duplication rate = 50.5% >>>>>>> Insert size mean insert size = 22,643.9418 std insert size = 1,474,471.2848 median insert size = 102 >>>>>>> Mapping quality mean mapping quality = 51.8501 >>>>>>> ACTG content number of A's = 4,106,998,423 bp (25.31%) number of C's = 4,023,598,851 bp (24.79%) number of T's = 4,098,142,039 bp (25.25%) number of G's = 3,996,839,322 bp (24.63%) number of N's = 1,929,186 bp (0.01%) GC percentage = 49.42% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 82,046,964 number of insertions = 500,441 mapped reads with insertion percentage = 0.21% number of deletions = 685,817 mapped reads with deletion percentage = 0.29% homopolymer indels = 37.05% >>>>>>> Coverage mean coverageData = 5.2424X std coverageData = 59.8045X There is a 36.23% of reference with a coverageData >= 1X There is a 24.85% of reference with a coverageData >= 2X There is a 15.66% of reference with a coverageData >= 3X There is a 12.24% of reference with a coverageData >= 4X There is a 8.71% of reference with a coverageData >= 5X There is a 7.18% of reference with a coverageData >= 6X There is a 5.61% of reference with a coverageData >= 7X There is a 4.84% of reference with a coverageData >= 8X There is a 4.1% of reference with a coverageData >= 9X There is a 3.69% of reference with a coverageData >= 10X There is a 3.31% of reference with a coverageData >= 11X There is a 3.08% of reference with a coverageData >= 12X There is a 2.87% of reference with a coverageData >= 13X There is a 2.73% of reference with a coverageData >= 14X There is a 2.6% of reference with a coverageData >= 15X There is a 2.51% of reference with a coverageData >= 16X There is a 2.43% of reference with a coverageData >= 17X There is a 2.36% of reference with a coverageData >= 18X There is a 2.3% of reference with a coverageData >= 19X There is a 2.25% of reference with a coverageData >= 20X There is a 2.21% of reference with a coverageData >= 21X There is a 2.16% of reference with a coverageData >= 22X There is a 2.13% of reference with a coverageData >= 23X There is a 2.09% of reference with a coverageData >= 24X There is a 2.06% of reference with a coverageData >= 25X There is a 2.03% of reference with a coverageData >= 26X There is a 2.01% of reference with a coverageData >= 27X There is a 1.98% of reference with a coverageData >= 28X There is a 1.96% of reference with a coverageData >= 29X There is a 1.93% of reference with a coverageData >= 30X There is a 1.91% of reference with a coverageData >= 31X There is a 1.89% of reference with a coverageData >= 32X There is a 1.87% of reference with a coverageData >= 33X There is a 1.85% of reference with a coverageData >= 34X There is a 1.83% of reference with a coverageData >= 35X There is a 1.82% of reference with a coverageData >= 36X There is a 1.8% of reference with a coverageData >= 37X There is a 1.78% of reference with a coverageData >= 38X There is a 1.77% of reference with a coverageData >= 39X There is a 1.75% of reference with a coverageData >= 40X There is a 1.74% of reference with a coverageData >= 41X There is a 1.72% of reference with a coverageData >= 42X There is a 1.71% of reference with a coverageData >= 43X There is a 1.69% of reference with a coverageData >= 44X There is a 1.68% of reference with a coverageData >= 45X There is a 1.67% of reference with a coverageData >= 46X There is a 1.65% of reference with a coverageData >= 47X There is a 1.64% of reference with a coverageData >= 48X There is a 1.63% of reference with a coverageData >= 49X There is a 1.62% of reference with a coverageData >= 50X There is a 1.6% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1785979294 7.165395563848966 77.65308289694205 chr2 243199373 1157956974 4.761348517127962 46.47638757934593 chr3 198022430 873722239 4.41223874992343 48.20302208818158 chr4 191154276 659641950 3.4508354393285976 35.279016995286405 chr5 180915260 1036743026 5.730544930261825 50.78112011139591 chr6 171115067 662732502 3.873022484922383 45.49508241128451 chr7 159138663 1666809125 10.473941992336583 155.9658757398531 chr8 146364022 535808983 3.6607970707446125 32.59423072737331 chr9 141213431 642691111 4.55120385114076 45.69810197183167 chr10 135534747 439898052 3.2456477894926827 33.925700967926225 chr11 135006516 841675929 6.234335600512793 48.71542330021618 chr12 133851895 765991607 5.722680332616882 43.906486940864504 chr13 115169878 294261771 2.5550237276451746 26.340537578437317 chr14 107349540 481313398 4.48360931961143 40.947929514882276 chr15 102531392 456148140 4.448863232052872 37.878146260787695 chr16 90354753 599319745 6.632963127020003 48.491608511009964 chr17 81195210 893437177 11.003570001235294 98.75911268426732 chr18 78077248 254674412 3.2618261852671857 32.486027574193685 chr19 59128983 833015637 14.088110343450351 77.94370159417615 chr20 63025520 354231425 5.620444305735201 41.42458628268594 chr21 48129895 178225438 3.703009075752191 38.207389596523534 chr22 51304566 315778821 6.154984743463184 46.671663033808514 chrMT 16571 1646187 99.3414398648241 39.77702950854779 chrX 155270560 413276893 2.661656485298952 38.16852954925948 chrY 59373566 83989340 1.414591469880721 36.95049997384844