Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing

BMC Genomics

Table 3 Assessment and quantification of reassembly of duplicate BAC sequences

Assembly number	Parameters	Total # contigs	# contigs (> 100)^a	% Coverage of old contigs^b	% Identity to old contigs^c	% Coverage +103e11^d	% Identity +103e11^d
1	standard	551	44	98.52%	99.07%	98.44%	97.39%
2	revise_greedy	2538	45	91.41%	99.08%	92.74%	98.43%
3	forcelevel 5	2140	40	96.13%	99.21%	95.56%	98.52%
4	minmatch 30	2184	50	94.77%^e	98.92%^e	95.51%	97.91%
5	forcelevel 3	2326	43	98.40%	98.60%	97.74%	97.96%
6	forcelevel 5 minmatch 30	1781	43	88.75%^e	99.18%^e	86.17%	98.04%
7	forcelevel 3 minmach30	1950	46	93.38%^f	99.18%^f

^a Total number of contigs that contain greater than 100 sequence traces
^b Total length of the resulting contigs (not including any overlapping regions) divided by the length of the originally assembled BAC
^c Percent identity as calculated from Vmatch
^d Recalculated percent coverage and percent identity to include contigs containing traces from gmw1-103e11; these contigs did not meet the 80% sequence identity cutoff for Vmatch
^e One contig from gmw1-103e11 met the cutoff criteria of 80% sequence identity for Vmatch and was included in this estimation. The second contig was included in the +103e11 calculations
^f This parameter set matches the parameter set that was determined to give the best reassembly of gmw1-103e11 as a single BAC reassembly. Both resulting contigs met the 80% sequence identity cutoff for Vmatch and are included in these averages.

ISSN: 1471-2164