Oryza glaberrima vs Oryza sativa Indica LastZ Results

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Oryza glaberrima (Oryza glaberrima, AGI1.1) and Oryza sativa Indica (Oryza sativa Indica Group, ASM465v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 75. Oryza glaberrima 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: 115,178

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

Uncovered: 52,566,308 out of 285,037,524
Covered: 232,471,216 out of 285,037,524

Uncovered: 376,804 out of 36,404,702
Matches: 35,140,574 out of 36,404,702
Mismatches: 738,798 out of 36,404,702
Insertions: 148,526 out of 36,404,702

Oryza sativa Indica Group

Uncovered: 155,876,839 out of 374,545,499
Covered: 218,668,660 out of 374,545,499

Uncovered: 9,113,504 out of 42,733,995
Matches: 33,049,144 out of 42,733,995
Mismatches: 468,457 out of 42,733,995
Insertions: 102,890 out of 42,733,995

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 glaberrima Oryza sativa Indica
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}