Oryza glumaepatula vs Leersia perrieri LastZ Results

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Oryza glumaepatula (Oryza glumaepatula, ALNU02000000) and Leersia perrieri (Leersia perrieri, Lperr_V1.4) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 75. Oryza glumaepatula 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: 237,821

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

Uncovered: 236,891,337 out of 372,860,283
Covered: 135,968,946 out of 372,860,283

Uncovered: 3,217,412 out of 41,162,840
Matches: 32,123,345 out of 41,162,840
Mismatches: 4,880,182 out of 41,162,840
Insertions: 941,901 out of 41,162,840

Leersia perrieri

Uncovered: 151,712,603 out of 266,687,832
Covered: 114,975,229 out of 266,687,832

Uncovered: 5,030,510 out of 36,899,367
Matches: 27,734,273 out of 36,899,367
Mismatches: 3,571,084 out of 36,899,367
Insertions: 563,500 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 glumaepatula 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}