Table 3.
Pairwise whole genome comparison of Pusa Ruby against Heinz1706, Fla1, and M82 computed by DNAdiff tool [50]. Pusa Ruby was the query while Heinz1706, Fla.8924, and M82 were the references in the NUCmer alignment and DNAdiff tool. Seqs: Sequences; Avg: average; SNPs: Single Nucleotide Polymorphisms; GSNPs: Single Nucleotide Polymorphisms(SNPs) bound by 20 exact base pair matches on either side; Indel: Insertion/deletions; GInDels: Insertions/deletions bound by exact match of 20 base pairs on either side; PR: Pusa Ruby.
| Heinz1706 | PR | Fla.8924 | PR | M82 | PR | |
|---|---|---|---|---|---|---|
| Sequences | ||||||
| Total Seqs | 13 | 13 | 13 | 13 | 13 | 13 |
| Aligned Seqs | 13 (100.00%) | 13 (100.00%) | 13 (100.00%) | 13 (100.00%) | 13 (100.00%) | 13 (100.00%) |
| Unaligned Seqs | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) | 0 (0.00%) |
| Bases | ||||||
| Total Bases | 782,520,033 | 718,639,073 | 796,004,315 | 718,639,073 | 792,934,937 | 718,639,073 |
| Aligned Bases | 726,051,384 (92.78%) | 690,758,192 (96.12%) | 715,955,700 (89.9437%) | 679,673,622 (94.58%) | 717,409,934 (90.48%) | 681,068,925 (94.77%) |
| Unaligned Bases | 56,468,649 (7.22%) | 27,880,881 (3.88%) | 80,048,615 (10.0563) | 38,965,451 (5.42%) | 75,525,003 (9.52%) | 37,570,148 (5.23%) |
| Alignments | ||||||
| one-to-one | 232,149 | 216,975 | 224,643 | |||
| Total Length (one-to-one) | 681,763,285 | 681,795,255 | 663,171,553 | 664,463,584 | 665,697,245 | 665,915,093 |
| Avg Length (one-to-one) | 2936.75 | 2936.89 | 3056.725 | 3062.67705 | 2964.6299 | 2902.57 |
| Avg Identity (one-to-one) | 99.84 | 99.5656 | 99.5777 | |||
| M-to-M | 399,293 | 393,605 | 401,181 | |||
| Total Length (M-to-M) | 771,135,016 | 771,128,110 | 781,072,565 | 783,869,191 | 774,217,622 | 774,798,581 |
| Avg Length (M-to-M) | 1931.25 | 1931.23 | 1985.6105 | 1992.7126 | 1930.32895 | 1931.7748 |
| Avg Identity (M-to-M) | 99.15 | 98.5888 | 98.66545 | |||
| Feature Estimates | ||||||
| Breakpoints | 798,577 | 798,553 | 787,208 | 787,189 | 802,352 | 802,339 |
| Relocations | 26,309 | 17,453 | 28,508 | 27,573 | 28,697 | 27,028 |
| Translocations | 7328 | 7221 | 16,357 | 14,667 | 12,041 | 11,130 |
| Inversions | 714 | 718 | 3173 | 2644 | 2422 | 2112 |
| Insertions | 242,155 | 319,388 | 235,641 | 323,561 | 247,574 | 323,754 |
| Insertion Sum | 130,014,304 | 49,843,243 | 162,162,183 | 80,350,739 | 156,691,957 | 70,683,091 |
| Insertion Avg | 536.91 | 156.06 | 688.5165 | 248.3442 | 633.373 | 218.5611 |
| Tandem Ins | 321 | 42 | 374 | 61 | 400 | 110 |
| Sum of Tandem Ins | 92,910 | 2859 | 59,361 | 4491 | 76,900 | 9232 |
| Tandem Ins Avg | 289.44 | 68.07 | 157.92195 | 72.5741 | 192.08725 | 83.38 |
| SNPs | ||||||
| Total SNPs | 335,439 | 786,423 | 1,452,890 | |||
| Total GSNPs | 167,484 | 266,642 | 734,607 | |||
| Total InDels | 356,419 | 1,572,447 | 880,972 | |||
| Total GInDels | 94,663 | 54,287 | 56,923 | |||