Oryza glaberrima vs Leersia perrieri LastZ Results

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Oryza glaberrima (Oryza glaberrima, Oryza_glaberrima_V1) and Leersia perrieri (Leersia perrieri, Lperr_V1.4) 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: 211,120

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

Uncovered: 164,334,368 out of 285,037,524
Covered: 120,703,156 out of 285,037,524

Uncovered: 2,863,400 out of 36,404,702
Matches: 28,402,914 out of 36,404,702
Mismatches: 4,317,740 out of 36,404,702
Insertions: 820,648 out of 36,404,702

Leersia perrieri

Uncovered: 165,494,403 out of 266,687,832
Covered: 101,193,429 out of 266,687,832

Uncovered: 8,625,957 out of 36,899,367
Matches: 24,547,181 out of 36,899,367
Mismatches: 3,221,074 out of 36,899,367
Insertions: 505,155 out of 36,899,367

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 Leersia perrieri
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}