Oryza meridionalis vs Oryza sativa Indica LastZ Results

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Oryza meridionalis (Oryza meridionalis, Oryza_meridionalis_v1.3) and Oryza sativa Indica (Oryza sativa Indica Group, ASM465v1) 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: 304,044

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

Uncovered: 110,277,054 out of 335,668,232
Covered: 225,391,178 out of 335,668,232

Uncovered: 468,151 out of 35,224,824
Matches: 33,409,976 out of 35,224,824
Mismatches: 1,084,701 out of 35,224,824
Insertions: 261,996 out of 35,224,824

Oryza sativa Indica Group

Uncovered: 233,504,177 out of 427,004,890
Covered: 193,500,713 out of 427,004,890

Uncovered: 12,187,280 out of 45,465,969
Matches: 32,266,070 out of 45,465,969
Mismatches: 808,833 out of 45,465,969
Insertions: 203,786 out of 45,465,969

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 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}