Oryza sativa Indica vs Oryza rufipogon LastZ Results

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Oryza sativa Indica (Oryza sativa Indica Group, ASM465v1) and Oryza rufipogon (Oryza rufipogon, OR_W1943) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 75. Oryza sativa Indica 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: 146,284

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

Uncovered: 76,144,342 out of 374,545,499
Covered: 298,401,157 out of 374,545,499

Uncovered: 266,217 out of 42,733,995
Matches: 41,714,102 out of 42,733,995
Mismatches: 624,432 out of 42,733,995
Insertions: 129,244 out of 42,733,995

Oryza rufipogon

Uncovered: 70,255,676 out of 338,040,714
Covered: 267,785,038 out of 338,040,714

Uncovered: 2,387,324 out of 42,764,129
Matches: 39,918,141 out of 42,764,129
Mismatches: 365,536 out of 42,764,129
Insertions: 93,128 out of 42,764,129

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
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 Indica Oryza rufipogon
Chunk size 30,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1}