Skip to main content

Table 1 Basic characteristics of simulated BAC-libraries

From: LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes

Characteristic Lib RiceChr1 Lib MaizeChr1
Sequence length 45,064,769 bp 300,239,041 bp
NBinEnds/LBin 12,570/3,585.1 bp 110,910/2,707.1 bp
NBandEnds (LBandReal) 179,050 (251.7 bp) 1,392,692 (215.6 bp)
nMean/nMeanObs 113.0/112.7 136.8/129.0
LClone/LCloneObs 133.3 kbp/138.1 kbp 132.0 kbp/134.5 kbp
L BandObs 1,225.9 bp 1,042.4. bp
NClones/NClonesSimul 4,417/5,000 29,924/35,000
Coverage 13.5 13.4
NCh = Nch2 + Nch3 + Nch4 202 = 198 + 4 + 0 1,016 = 999 + 16 + 1
  1. Here NBinEnds is the number of restriction sites corresponding to enzyme HindIII chosen for clone-end simulation; LBin is the mean length of bin equal to distance between restriction sites corresponding to enzyme HindIII; NBandEnds is the number of restriction sites corresponding to the enzymes BamHI, EcoRI, XbaI, XhoI and HaeIII used for fingerprinting; LBandReal is the mean distance between restriction sites corresponding to these enzyme; nMean is the mean number of bands (with length from 50 to 500 and colored end) per clone; nMeanObs is the mean observed number of bands (bands with different end-colors are taken twice, but among bands with the same color and length only one delegate is observed). LCloneObs and LClone are mean lengths of clones (with and without chimerical clones respectively); LBandObs is the mean length of bands with length from 50 to 500 bp; LBandMap is the mean length of bands used for band map length calculation (equal to LCloneObs/nMeanObs); NClonesSimul is the number of simulated clones; NClones is the number of simulated clones with observed number of bands from 50 to 250; Nch2, Nch3, and Nch4 are resulted numbers of chimerical clones with number of bands from 50 to 250 and composed by union of 2, 3 and 4 parts, respectively.