Oryza sativa Japonica Group vs Arabis alpina LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Arabis alpina (Arabis alpina, A_alpina_V4) 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: 125,739

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

Uncovered: 345,027,738 out of 375,049,285
Covered: 30,021,547 out of 375,049,285

Uncovered: 15,999,052 out of 34,424,450
Matches: 11,745,127 out of 34,424,450
Mismatches: 6,221,771 out of 34,424,450
Insertions: 458,500 out of 34,424,450

Arabis alpina

Uncovered: 279,008,413 out of 308,032,609
Covered: 29,024,196 out of 308,032,609

Uncovered: 11,470,366 out of 25,084,253
Matches: 8,800,847 out of 25,084,253
Mismatches: 4,560,710 out of 25,084,253
Insertions: 252,330 out of 25,084,253

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