BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779285.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 = 10,465,932 number of mapped reads = 10,116,366 (96.66%) number of supplementary alignments = 25,127 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,093,351 number of mapped paired reads (second in pair) = 5,023,015 number of mapped paired reads (both in pair) = 10,030,976 number of mapped paired reads (singletons) = 85,390 number of mapped bases = 805,155,614 bp number of sequenced bases = 805,000,509 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 219,982 duplication rate = 2% >>>>>>> Insert size mean insert size = 47,913.0146 std insert size = 2,095,287.5731 median insert size = 194 >>>>>>> Mapping quality mean mapping quality = 53.0054 >>>>>>> ACTG content number of A's = 248,064,948 bp (30.82%) number of C's = 153,921,752 bp (19.12%) number of T's = 245,932,385 bp (30.55%) number of G's = 156,927,997 bp (19.49%) number of N's = 153,427 bp (0.02%) GC percentage = 38.61% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 2,984,661 number of insertions = 58,648 mapped reads with insertion percentage = 0.57% number of deletions = 74,885 mapped reads with deletion percentage = 0.73% homopolymer indels = 46.46% >>>>>>> Coverage mean coverageData = 0.2601X std coverageData = 1.0441X There is a 13.04% of reference with a coverageData >= 1X There is a 5.52% of reference with a coverageData >= 2X There is a 2.76% of reference with a coverageData >= 3X There is a 1.55% of reference with a coverageData >= 4X There is a 0.94% of reference with a coverageData >= 5X There is a 0.6% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.27% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% 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 0.02% of reference with a coverageData >= 18X There is a 0.02% 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 0.01% 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 63937473 0.25651881124099585 1.292423575554746 chr2 243199373 72345153 0.297472613138686 1.0396256967430628 chr3 198022430 54289452 0.274158094110854 0.9698257519601683 chr4 191154276 63339473 0.331352634769206 1.0434746138471125 chr5 180915260 60476237 0.3342793581923382 1.0587848197555283 chr6 171115067 60082815 0.35112521681097786 1.135823758763797 chr7 159138663 75026235 0.4714519626195427 1.8434767584376364 chr8 146364022 52493625 0.35865115130547587 1.0722387588312519 chr9 141213431 34219745 0.2423264186534778 0.8716914930887664 chr10 135534747 19160699 0.14137112013054481 1.1579306305806096 chr11 135006516 30298115 0.22441964949306595 0.8945678555955976 chr12 133851895 40966263 0.306056653138904 1.069623231173009 chr13 115169878 20171657 0.17514698591588332 0.6926149607401505 chr14 107349540 14458098 0.1346824401855844 0.6161683950751878 chr15 102531392 15147327 0.14773355461710694 0.729141093945672 chr16 90354753 13681618 0.15142112114456224 0.6792648202598249 chr17 81195210 10192177 0.1255268260282842 0.6464574332584726 chr18 78077248 22459272 0.28765450339643117 0.9316356452661138 chr19 59128983 6473526 0.109481436540182 0.7854165300317835 chr20 63025520 15328211 0.24320641860630424 0.8505365165759566 chr21 48129895 9154482 0.19020365616837517 0.7191853746395727 chr22 51304566 3064548 0.05973246123941483 0.3651281279527599 chrMT 16571 959 0.05787218634964697 0.26926979054624756 chrX 155270560 47872741 0.30831820919561315 1.0779598439724116 chrY 59373566 515713 0.008685902409836728 0.13971432718153973