Oryza glumipatula vs Leersia perrieri LastZ results

Oryza glumipatula (Oryza glumipatula, Oryza_glumaepatula_v1.5) and Leersia perrieri (Leersia perrieri, Lperr_V1.4) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza glumipatula was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

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

Chunking parameters

ParameterOryza glumipatulaLeersia perrieri
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 237,821 alignment blocks

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

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
Identity over aligned base-pairs: 84.7%

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
Identity over aligned base-pairs: 87.0%