Oryza sativa Indica vs Oryza brachyantha LastZ Results

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Oryza sativa Indica (Oryza sativa Indica Group, ASM465v1) and Oryza brachyantha (Oryza brachyantha, Oryza_brachyantha.v1.4b) 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: 284,996

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

Uncovered: 236,548,872 out of 374,545,499
Covered: 137,996,627 out of 374,545,499

Uncovered: 4,998,586 out of 42,733,995
Matches: 32,006,964 out of 42,733,995
Mismatches: 4,877,055 out of 42,733,995
Insertions: 851,390 out of 42,733,995

Oryza brachyantha

Uncovered: 143,631,718 out of 250,927,218
Covered: 107,295,500 out of 250,927,218

Uncovered: 2,494,841 out of 30,210,943
Matches: 24,563,889 out of 30,210,943
Mismatches: 2,730,438 out of 30,210,943
Insertions: 421,775 out of 30,210,943

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 brachyantha
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}