BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779218.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 = 15,770,922 number of mapped reads = 15,352,678 (97.35%) number of supplementary alignments = 35,845 (0.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,724,442 number of mapped paired reads (second in pair) = 7,628,236 number of mapped paired reads (both in pair) = 15,231,426 number of mapped paired reads (singletons) = 121,252 number of mapped bases = 1,221,698,608 bp number of sequenced bases = 1,221,462,849 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 351,182 duplication rate = 2.05% >>>>>>> Insert size mean insert size = 38,793.8103 std insert size = 1,804,225.403 median insert size = 194 >>>>>>> Mapping quality mean mapping quality = 52.698 >>>>>>> ACTG content number of A's = 377,201,133 bp (30.88%) number of C's = 231,899,835 bp (18.99%) number of T's = 376,320,340 bp (30.81%) number of G's = 235,811,159 bp (19.31%) number of N's = 230,382 bp (0.02%) GC percentage = 38.29% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 4,569,836 number of insertions = 89,638 mapped reads with insertion percentage = 0.58% number of deletions = 114,046 mapped reads with deletion percentage = 0.73% homopolymer indels = 46.72% >>>>>>> Coverage mean coverageData = 0.3946X std coverageData = 1.3659X There is a 18.9% of reference with a coverageData >= 1X There is a 8.72% of reference with a coverageData >= 2X There is a 4.53% of reference with a coverageData >= 3X There is a 2.56% of reference with a coverageData >= 4X There is a 1.53% of reference with a coverageData >= 5X There is a 0.96% of reference with a coverageData >= 6X There is a 0.62% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.28% of reference with a coverageData >= 9X There is a 0.2% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% 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 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% 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 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 41463732 0.16635357550423113 1.7077992077331345 chr2 243199373 87693972 0.360584696079788 1.0686615495340914 chr3 198022430 90358046 0.4563020764869919 1.1833721853578394 chr4 191154276 129543693 0.6776918398623738 1.4741929385235724 chr5 180915260 99579163 0.5504188148639313 1.3245429799125443 chr6 171115067 57549967 0.33632320057473375 1.0387675059911443 chr7 159138663 112991985 0.7100222087450867 2.592919101770633 chr8 146364022 102162853 0.6980052310942917 1.523605546226029 chr9 141213431 37185600 0.2633290596841316 1.005781820331792 chr10 135534747 16024066 0.11822847169958564 1.640926364402475 chr11 135006516 51013035 0.37785609547912485 1.083272093946369 chr12 133851895 52839078 0.3947577880761419 1.1116113530493021 chr13 115169878 51988469 0.4514068253159042 1.199842106888361 chr14 107349540 46004456 0.42854823597753655 1.1726552923783713 chr15 102531392 18641988 0.18181736965006776 0.6749727388122047 chr16 90354753 18898712 0.20916123803691877 0.7478456963449059 chr17 81195210 17787887 0.21907557108356515 0.8777831632799329 chr18 78077248 58369552 0.7475872100410097 1.6236294177395063 chr19 59128983 9367192 0.1584196366103574 1.0890310354340424 chr20 63025520 21690350 0.3441518610239154 0.9793061539802719 chr21 48129895 6675587 0.13869938839467652 0.5950521150241909 chr22 51304566 3742697 0.07295056350345114 0.43453410965711636 chrMT 16571 775 0.04676845090821315 0.27232734417956006 chrX 155270560 89338189 0.5753710748515366 1.549668753555359 chrY 59373566 787564 0.01326455614944873 0.22059603165845992