Oryza sativa Japonica Group vs Pistacia vera LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Pistacia vera (Pistacia vera, PisVer_v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Oryza sativa Japonica Group 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: 187,447

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 341,560,420 out of 375,049,285
Covered: 33,488,865 out of 375,049,285

Uncovered: 14,207,898 out of 34,424,450
Matches: 13,075,476 out of 34,424,450
Mismatches: 6,669,729 out of 34,424,450
Insertions: 471,347 out of 34,424,450

Pistacia vera

Uncovered: 622,610,880 out of 671,152,441
Covered: 48,541,561 out of 671,152,441

Uncovered: 13,164,188 out of 38,113,229
Matches: 16,230,001 out of 38,113,229
Mismatches: 8,215,257 out of 38,113,229
Insertions: 503,783 out of 38,113,229

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
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)--ambiguous=iupac

Chunking parameters

Oryza sativa Japonica Group Pistacia vera
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options