Skip to main content

Table 2 Contig assembly with FPC and LTC programs

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

  Lib RiceChr1 Lib MaizeChr1
Statistic FPC LTC FPC LTC
NClonesCtg /NClones (%) 4,293/4,417 (97.2%) 4,231/4,417 (95.7%) 28,899/29,924 (96.6%) 28,994/29,924 (96.9%)
N Ctgs 42 25 257 190
N MeanClonesCtg 102.2 169.2 112.4 152.6
L MeanClonesCtg 1,045 kbp 1,731 kbp 1,128 kbp 1,532 kbp
NChCtg/NCh 183/202 (91%) 22/202 (11%) 946/1,016 (93%) 196/1,016 (19%)
NQNotCh/NQ 105/124 (85%) 106/186 (57%) 955/1,025 (93%) 110/930 (19%)
NCtgsNonLinear/NCtgs 8/42 (19%) - 23/257 (9%) -
NCtgCh/NCtgs 22/42 (52%) 0/25 108/257(42%) 0/190
n CtgParts 1.79 1.00 1.67 1.00
NCtgOrdWrong/(NCtgs-NCtgCh) 4/20 (20%) 1/25 (4%) 47/149 (32%) 4/190 (2%)
  1. Here NClonesCtg is the total number of clones in contigs with 6 clones and more (others were excluded from the analysis); NCtgs is the number of contigs with 6 clones and more; NMeanClonesCtg is the mean number of clones in the contigs with 6 clones and more; LMeanClonesCtg = LCloneObs NMeanClonesCtg/Covarege is estimated mean length of the contigs with 6 clones and more; NChCtg is the number of chimerical clones in the contigs with 6 clones and more (false negatives in the procedure of Q-clone detection); NQNotCh is the number of non-chimerical clones that were identified as Q-clones (false positives); NQ is the number of clones that were not included into contigs; NCtgsNonLinear is the number of contigs with non-linear topological structure; NCtgCh is the number of contigs containing clones (except chimerical ones) from non-overlapping parts; nCtgParts is the mean number of non-overlapping parts per contig; NCtgOrdWrong is the number of continuous contigs with errors in clone ordering.