Oryza meridionalis vs Oryza glaberrima LastZ Results

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Oryza meridionalis (Oryza meridionalis, Oryza_meridionalis_v1.3) and Oryza glaberrima (Oryza glaberrima, AGI1.1) 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: 263,514

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

Uncovered: 136,108,439 out of 335,668,232
Covered: 199,559,793 out of 335,668,232

Uncovered: 1,551,351 out of 35,224,824
Matches: 31,831,704 out of 35,224,824
Mismatches: 1,525,906 out of 35,224,824
Insertions: 315,863 out of 35,224,824

Oryza glaberrima

Uncovered: 144,427,094 out of 316,419,574
Covered: 171,992,480 out of 316,419,574

Uncovered: 7,497,953 out of 36,293,721
Matches: 27,937,921 out of 36,293,721
Mismatches: 690,976 out of 36,293,721
Insertions: 166,871 out of 36,293,721

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 glaberrima
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}