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Oryza meridionalis vs Oryza sativa Japonica Group LastZ Results

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Oryza meridionalis (Oryza meridionalis, Oryza_meridionalis_v1.3) and Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 79. Oryza meridionalis 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: 343,106

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

Uncovered: 97,874,978 out of 335,668,232
Covered: 237,793,254 out of 335,668,232

Uncovered: 420,569 out of 35,224,824
Matches: 33,566,367 out of 35,224,824
Mismatches: 995,076 out of 35,224,824
Insertions: 242,812 out of 35,224,824

Oryza sativa Japonica Group

Uncovered: 183,181,862 out of 374,424,240
Covered: 191,242,378 out of 374,424,240

Uncovered: 5,949,666 out of 34,124,807
Matches: 27,452,391 out of 34,124,807
Mismatches: 572,333 out of 34,124,807
Insertions: 150,417 out of 34,124,807

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 meridionalis Oryza sativa Japonica Group
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}