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Oryza glaberrima vs Oryza glumipatula LastZ results

Oryza glaberrima (Oryza glaberrima, Oryza_glaberrima_V1) and Oryza glumipatula (Oryza glumipatula, Oryza_glumaepatula_v1.5) 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 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 glaberrimaOryza glumipatula
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 114,024 alignment blocks

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

Uncovered: 56,973,044 out of 285,037,524
Covered: 228,064,480 out of 285,037,524

Uncovered: 382,818 out of 36,404,702
Matches: 35,145,711 out of 36,404,702
Mismatches: 726,014 out of 36,404,702
Insertions: 150,159 out of 36,404,702
Identity over aligned base-pairs: 97.6%

Oryza glumipatula

Uncovered: 159,830,465 out of 372,860,283
Covered: 213,029,818 out of 372,860,283

Uncovered: 7,068,348 out of 41,162,840
Matches: 33,531,579 out of 41,162,840
Mismatches: 453,639 out of 41,162,840
Insertions: 109,274 out of 41,162,840
Identity over aligned base-pairs: 98.3%