Vitis vinifera vs Brassica rapa LastZ Results

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Vitis vinifera (Vitis vinifera, IGGP_12x) and Brassica rapa (Brassica rapa subsp. pekinensis, IVFCAASv1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Vitis vinifera was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 170,116

Genome coverage (bp) Coding exon coverage (bp)
Vitis vinifera

Uncovered: 428,224,789 out of 486,265,422
Covered: 58,040,633 out of 486,265,422

Uncovered: 7,052,369 out of 32,794,161
Matches: 17,301,662 out of 32,794,161
Mismatches: 7,753,876 out of 32,794,161
Insertions: 686,254 out of 32,794,161

Brassica rapa subsp. pekinensis

Uncovered: 252,092,825 out of 283,822,783
Covered: 31,729,958 out of 283,822,783

Uncovered: 28,807,222 out of 48,055,850
Matches: 13,141,464 out of 48,055,850
Mismatches: 5,710,422 out of 48,055,850
Insertions: 396,742 out of 48,055,850

Configuration parameters

ParameterValue
Gap open penalty (O)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
Other parameters (other)