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Oryza sativa Indica Group vs Oryza brachyantha LastZ results

Oryza sativa Indica Group (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 67. Oryza sativa Indica Group 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 sativa Indica GroupOryza brachyantha
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 284,996 alignment blocks

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
Identity over aligned base-pairs: 84.8%

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
Identity over aligned base-pairs: 88.6%