Oryza glumaepatula vs Oryza brachyantha LastZ Results

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Oryza glumaepatula (Oryza glumaepatula, ALNU02000000) and Oryza brachyantha (Oryza brachyantha, Oryza_brachyantha.v1.4b) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 75. Oryza glumaepatula 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: 256,987

Genome coverage (bp) Coding exon coverage (bp)
Oryza glumaepatula

Uncovered: 243,186,783 out of 372,860,283
Covered: 129,673,500 out of 372,860,283

Uncovered: 4,685,435 out of 41,162,840
Matches: 31,033,088 out of 41,162,840
Mismatches: 4,601,533 out of 41,162,840
Insertions: 842,784 out of 41,162,840

Oryza brachyantha

Uncovered: 143,449,191 out of 250,927,218
Covered: 107,478,027 out of 250,927,218

Uncovered: 2,442,750 out of 30,210,943
Matches: 24,648,916 out of 30,210,943
Mismatches: 2,702,427 out of 30,210,943
Insertions: 416,850 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 glumaepatula 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}