BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779165.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 = 10,696 number of mapped reads = 8,170 (76.38%) number of supplementary alignments = 40 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,922 number of mapped paired reads (second in pair) = 3,248 number of mapped paired reads (both in pair) = 6,416 number of mapped paired reads (singletons) = 1,754 number of mapped bases = 812,985 bp number of sequenced bases = 812,803 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37 duplication rate = 0.45% >>>>>>> Insert size mean insert size = 236,378.9492 std insert size = 4,525,510.9168 median insert size = 218 >>>>>>> Mapping quality mean mapping quality = 51.7253 >>>>>>> ACTG content number of A's = 248,648 bp (30.59%) number of C's = 155,796 bp (19.17%) number of T's = 248,408 bp (30.56%) number of G's = 159,733 bp (19.65%) number of N's = 218 bp (0.03%) GC percentage = 38.82% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 3,978 number of insertions = 60 mapped reads with insertion percentage = 0.73% number of deletions = 83 mapped reads with deletion percentage = 0.99% homopolymer indels = 43.36% >>>>>>> Coverage mean coverageData = 0.0003X std coverageData = 0.0175X There is a 0.02% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% 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 55698 2.234618304120494E-4 0.016156133384301295 chr2 243199373 57244 2.3537889630990125E-4 0.016451021233067586 chr3 198022430 58235 2.9408284707949496E-4 0.018396212427903968 chr4 191154276 61163 3.199666849199858E-4 0.019263695882522677 chr5 180915260 48760 2.6951844747645943E-4 0.01757525903281108 chr6 171115067 46931 2.742657372188038E-4 0.01760307654355181 chr7 159138663 73006 4.58757153187846E-4 0.022892399521774215 chr8 146364022 69792 4.768384951870208E-4 0.02345113470943805 chr9 141213431 32475 2.2997104291021722E-4 0.016578393168590333 chr10 135534747 17144 1.264915483259802E-4 0.012169675769110473 chr11 135006516 36370 2.693944046374769E-4 0.017653491277754424 chr12 133851895 36615 2.735486113214908E-4 0.018026330580681035 chr13 115169878 27512 2.3888190625677314E-4 0.016786009508029297 chr14 107349540 23009 2.1433720163123197E-4 0.01583131411707027 chr15 102531392 24209 2.3611305306378753E-4 0.016756642522491674 chr16 90354753 15284 1.6915546213711635E-4 0.014166166154814433 chr17 81195210 16034 1.9747470324912023E-4 0.015165725936613146 chr18 78077248 15698 2.0105729136354807E-4 0.015279791837076654 chr19 59128983 9710 1.6421726719027113E-4 0.013612994460277358 chr20 63025520 17563 2.7866489637848286E-4 0.01785478173876372 chr21 48129895 8127 1.6885555225084118E-4 0.014141878563183207 chr22 51304566 3999 7.794627869963855E-5 0.009953337469703548 chrMT 16571 0 0.0 0.0 chrX 155270560 57860 3.7263986167113713E-4 0.020821847420276506 chrY 59373566 547 9.212854083920106E-6 0.0030352543892134868