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Oryza glumipatula vs Oryza brachyantha LastZ results

Oryza glumipatula (Oryza glumipatula, Oryza_glumaepatula_v1.5) and Oryza brachyantha (Oryza brachyantha, Oryza_brachyantha.v1.4b) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 75. Oryza glumipatula was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

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

Chunking parameters

ParameterOryza glumipatulaOryza brachyantha
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 256,987 alignment blocks

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

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
Identity over aligned base-pairs: 85.1%

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
Identity over aligned base-pairs: 88.8%