Table II. Summary of de novo assembly results of 454 sequence data using various programs.
| Parameter | Velvet | ABySS | MIRA | Newbler v2.3 | Newbler v2.5p1 | CLC | CAP3 | TGICL |
| Contigs (100 bp or greater) | 83,335 | 52,095 | 55,282 | 31,879 | 29,877 | 38,041 | 32,157 | 40,849 |
| Total size (Mb) | 30.71 | 22.14 | 51.78 | 38.25 | 28.54 | 36.54 | 32.03 | 40.14 |
| Large contigs (1,000 bp or greater) | 1,433 | 4,525 | 16,319 | 15,194 | 10,600 | 12,878 | 11,635 | 14,336 |
| Maximum length (bp) | 3,179 | 4,873 | 12,197 | 15,658 | 15,658 | 13,146 | 11,477 | 12,323 |
| Average length (bp) | 369 | 425 | 937 | 1,200 | 955 | 961 | 996 | 983 |
| N50 (bp) | 398 | 640 | 1,169 | 1,617 | 1,393 | 1,325 | 1,159 | 1,252 |
| Reads mapped (%) | 315,439 (16.3) | 442,895 (22.9) | 1,796,444 (93.0) | 1,643,234 (85.1) | 1,412,622 (73.2) | 1,731,780 (89.7) | 1,749,894 (90.6) | 1,836,847 (95.1) |
| Uniquely mapped reads (%) | 306,201 (15.9) | 442,889 (22.9) | 1,522,393 (78.8) | 1,251,637 (64.8) | 1,391,651 (72.1) | 1,646,375 (85.3) | 1,621,452 (84.0) | 1,702,241 (88.1) |
| Contigs with significant hits (%)a | 69,380 (83.3) | 38,540 (74.0) | 46,379 (83.9) | 26,977 (84.6) | 23,301 (78.0) | 28,006 (73.6) | 28,352 (88.2) | 33,166 (81.2) |
| Contigs with 80% or greater coverage (%)b | 1,008 (1.2) | 2,877 (5.5) | 11,952 (21.6) | 11,638 (36.5) | 9,066 (30.3) | 9,048 (23.8) | 8,010 (24.9) | 10,124 (24.8) |
| Soybean protein hits (%)c | 22,917 (49.4) | 20,545 (44.3) | 21,617 (46.6) | 16,663 (35.9) | 17,191 (37.1) | 19,480 (42.0) | 18,109 (39.0) | 20,453 (44.1) |
| Soybean proteins with 80% or greater coverage (%)d | 967 (2.1) | 2,831 (6.1) | 9,884 (21.3) | 7,447 (16.1) | 8,585 (18.5) | 8,566 (18.5) | 7,484 (16.1) | 9,414 (20.3) |
a
Contigs showing significant hits (E ≤ 1e-5) with soybean proteins.
b
Contigs showing 80% or greater coverage of soybean proteins.
c
Unique soybean proteins to which contigs show significant hits (E ≤ 1e-5).
d
Unique soybean proteins to which contigs show 80% or greater coverage.