Oryza sativa Japonica Group vs Malus domestica Golden LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Malus domestica Golden (Malus domestica, ASM211411v1) 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: 210,027

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

Uncovered: 338,970,391 out of 375,049,285
Covered: 36,078,894 out of 375,049,285

Uncovered: 13,175,238 out of 34,424,450
Matches: 13,747,440 out of 34,424,450
Mismatches: 6,943,482 out of 34,424,450
Insertions: 558,290 out of 34,424,450

Malus domestica

Uncovered: 651,446,021 out of 702,961,352
Covered: 51,515,331 out of 702,961,352

Uncovered: 16,589,007 out of 47,560,911
Matches: 20,347,716 out of 47,560,911
Mismatches: 9,913,239 out of 47,560,911
Insertions: 710,949 out of 47,560,911

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 Malus domestica Golden
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 10,100,000 10,100,000
Masking options