Oryza sativa Japonica Group vs Camelina sativa LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Camelina sativa (Camelina sativa, Cs) 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: 324,421

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

Uncovered: 333,644,070 out of 375,049,285
Covered: 41,405,215 out of 375,049,285

Uncovered: 14,422,756 out of 34,424,450
Matches: 12,115,361 out of 34,424,450
Mismatches: 7,357,692 out of 34,424,450
Insertions: 528,641 out of 34,424,450

Camelina sativa

Uncovered: 548,212,446 out of 641,356,059
Covered: 93,143,613 out of 641,356,059

Uncovered: 46,751,522 out of 107,028,261
Matches: 39,252,998 out of 107,028,261
Mismatches: 19,830,471 out of 107,028,261
Insertions: 1,193,270 out of 107,028,261

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