Oryza sativa Japonica Group vs Prunus_dulcis LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Prunus_dulcis (Prunus dulcis, ALMONDv2) 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: 134,518

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

Uncovered: 341,648,411 out of 375,049,285
Covered: 33,400,874 out of 375,049,285

Uncovered: 13,918,704 out of 34,424,450
Matches: 13,356,891 out of 34,424,450
Mismatches: 6,667,352 out of 34,424,450
Insertions: 481,503 out of 34,424,450

Prunus dulcis

Uncovered: 196,516,095 out of 227,498,357
Covered: 30,982,262 out of 227,498,357

Uncovered: 13,593,267 out of 33,980,404
Matches: 13,318,905 out of 33,980,404
Mismatches: 6,599,498 out of 33,980,404
Insertions: 468,734 out of 33,980,404

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 Prunus_dulcis
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options