Table 2.
Comparison of heterogeneity among the contigs of the six datasets.
| Segment 1 | Segment 2 | Segment 3 | Segment 4 | Segment 5 | Segment 6 | |
|---|---|---|---|---|---|---|
| Assembly length [bp] | 3,210,343 | 3,217,969 | 3,239,714 | 3,116,424 | 2,544,604 | 2,402,354 |
| CDS [bp] | 2,836,815 | 2,843,091 | 2,882,289 | 2,757,582 | 2,221,023 | 2,106,546 |
| nCDS [bp] | 373,528 | 374,878 | 357,425 | 358,842 | 323,581 | 295,808 |
| Coding region [%] | 88.36 | 88.35 | 88.97 | 88.49 | 87.28 | 87.69 |
| SEGMENT 1 | ||||||
| Total SNPs | 0 | 132 | 86 | 145 | 300 | 757 |
| SNPs/100 kbp | 0 | 4.10 | 2.65 | 4.65 | 11.79 | 31.51 |
| Total indels | 0 | 8 | 14 | 27 | 41 | 82 |
| Indels/100 kbp | 0 | 0.25 | 0.43 | 0.87 | 1.61 | 3.41 |
| Total SNPs in CDS | 0 | 91 | 66 | 124 | 136 | 316 |
| SNPs in CDS/100 kbp | 0 | 3.20 | 2.29 | 4.50 | 6.12 | 15.00 |
| SNPs in nCDS/100 kbp | 0 | 10.94 | 5.60 | 5.85 | 50.68 | 149.08 |
| Total indels in CDS | 0 | 3 | 0 | 8 | 12 | 15 |
| Indels in CDS/100 kbp | 0 | 0.12 | 0 | 0.34 | 0.63 | 0.82 |
| Indels in nCDS/100 kbp | 0 | 1.33 | 3.92 | 5.29 | 8.96 | 22.65 |
| SEGMENT 2 | ||||||
| Total SNPs | 151 | 0 | 132 | 135 | 302 | 682 |
| SNPs/100 kbp | 4.70 | 0 | 4.07 | 4.33 | 11.87 | 28.39 |
| Total indels | 16 | 0 | 15 | 17 | 44 | 64 |
| Indels/100 kbp | 0.50 | 0 | 0.46 | 0.55 | 1.73 | 2.66 |
| Total SNPs in CDS | 94 | 0 | 116 | 135 | 138 | 303 |
| SNPs in CDS/100 kbp | 3.31 | 0 | 4.02 | 4.90 | 6.21 | 14.38 |
| SNPs in nCDS/100 kbp | 15.26 | 0 | 4.48 | 0 | 50.68 | 128.12 |
| Total indels in CDS | 3 | 0 | 3 | 3 | 12 | 13 |
| Indels in CDS/100 kbp | 0.11 | 0 | 0.10 | 0.11 | 0.54 | 0.62 |
| Indels in nCDS/100 kbp | 3.48 | 0 | 3.36 | 3.90 | 9.89 | 17.24 |
| SEGMENT 3 | ||||||
| Total SNPs | 84 | 118 | 0 | 194 | 341 | 798 |
| SNPs/100 kbp | 2.62 | 3.67 | 0 | 6.23 | 13.40 | 33.22 |
| Total indels | 24 | 15 | 0 | 24 | 47 | 76 |
| Indels/100 kbp | 0.75 | 0.47 | 0 | 0.77 | 1.85 | 3.16 |
| Total SNPs in CDS | 84 | 101 | 0 | 118 | 140 | 325 |
| SNPs in CDS/100 kbp | 2.96 | 3.55 | 0 | 4.28 | 6.30 | 15.43 |
| SNPs in nCDS/100 kb | 0.00 | 4.53 | 0 | 21.18 | 62.12 | 159.90 |
| Total indels in CDS | 0 | 3 | 0 | 8 | 12 | 15 |
| Indels in CDS/100 kbp | 0 | 0.11 | 0 | 0.29 | 0.54 | 0.71 |
| Indels in nCDS/100 kbp | 6.43 | 3.20 | 0 | 4.46 | 10.82 | 20.62 |
| SEGMENT 4 | ||||||
| Total SNPs | 126 | 153 | 146 | 0 | 358 | 568 |
| SNPs/100 kbp | 3.92 | 4.75 | 4.51 | 0 | 14.07 | 23.64 |
| Total indels | 24 | 13 | 24 | 0 | 43 | 64 |
| Indels/100 kbp | 0.75 | 0.40 | 0.74 | 0 | 1.69 | 2.66 |
| Total SNPs in CDS | 91 | 94 | 112 | 0 | 158 | 301 |
| SNPs in CDS/100 kbp | 3.21 | 3.31 | 3.89 | 0 | 7.11 | 14.29 |
| SNPs in nCDS/100 kbp | 9.37 | 15.74 | 9.51 | 0 | 61.81 | 90.26 |
| Total indels in CDS | 8 | 3 | 8 | 0 | 21 | 13 |
| Indels in CDS/100 kbp | 0.28 | 0.11 | 0.28 | 0 | 0.95 | 0.62 |
| Indels in nCDS 100 kbp | 4.28 | 2.67 | 4.48 | 0 | 6.80 | 17.24 |
| SEGMENT 5 | ||||||
| Total SNPs | 374 | 352 | 394 | 456 | 0 | 548 |
| SNPs/100 kbp | 11.65 | 10.94 | 12.16 | 14.63 | 0 | 22.81 |
| Total indels | 55 | 54 | 61 | 59 | 0 | 58 |
| Indels/100 kbp | 1.71 | 1.68 | 1.88 | 1.89 | 0 | 2.41 |
| Total SNPs in CDS | 192 | 162 | 153 | 209 | 0 | 201 |
| SNPs in CDS/100 kbp | 6.77 | 5.70 | 5.31 | 7.58 | 0 | 9.54 |
| SNPs in nCDS/100 kbp | 48.72 | 50.68 | 67.43 | 68.83 | 0 | 117.31 |
| Total indels in CDS | 17 | 17 | 17 | 26 | 0 | 16 |
| Indels in CDS/100 kbp | 0.60 | 0.60 | 0.59 | 0.94 | 0 | 0.76 |
| Indels in nCDS/100 kbp | 10.17 | 9.87 | 12.31 | 9.20 | 0 | 14.20 |
| SEGMENT 6 | ||||||
| Total SNPs | 663 | 624 | 712 | 649 | 587 | 0 |
| SNPs/100 kbp | 20.65 | 19.39 | 21.98 | 20.83 | 23.07 | 0 |
| Total indels | 80 | 75 | 76 | 77 | 65 | 0 |
| Indels/100 kbp | 2.49 | 2.33 | 2.35 | 2.47 | 2.55 | 0 |
| Total SNPs in CDS | 354 | 339 | 342 | 345 | 193 | 0 |
| SNPs in CDS/100 kbp | 12.48 | 11.92 | 11.87 | 12.51 | 8.69 | 0 |
| SNPs in nCDS/100 kbp | 82.72 | 76.02 | 103.52 | 84.72 | 121.76 | 0 |
| Total indels in CDS | 15 | 13 | 15 | 15 | 16 | 0 |
| Indels in CDS/100 kbp | 0.53 | 0.46 | 0.52 | 0.54 | 0.72 | 0 |
| Indels in nCDS/100 kbp | 17.40 | 16.54 | 17.07 | 17.28 | 15.14 | 0 |
As all datasets have a different length, total numbers of mismatches are also given as a ratio per 100 kb based on aligned regions. Single nucleotide polymorphisms (“SNPs”) represent a single exchange of a nucleotide; “indel” represents an insertion or deletion of a single nucleotide; CDS, coding DNA sequence; nCDS, non-coding DNA sequence.