Oryza sativa Japonica Group vs Actinidia chinensis LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Actinidia chinensis (Actinidia chinensis var. chinensis, Red5_PS1_1.69.0) 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: 110,167

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

Uncovered: 341,375,015 out of 375,049,285
Covered: 33,674,270 out of 375,049,285

Uncovered: 13,448,555 out of 34,349,962
Matches: 13,677,719 out of 34,349,962
Mismatches: 6,719,686 out of 34,349,962
Insertions: 504,002 out of 34,349,962

Actinidia chinensis var. chinensis

Uncovered: 530,670,961 out of 553,842,477
Covered: 23,171,516 out of 553,842,477

Uncovered: 26,838,940 out of 42,227,027
Matches: 10,197,925 out of 42,227,027
Mismatches: 4,852,217 out of 42,227,027
Insertions: 337,945 out of 42,227,027

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 Actinidia chinensis
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}