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Oryza glaberrima vs Leersia perrieri LastZ results

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 76. 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 glaberrimaLeersia perrieri
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 211,120 alignment blocks

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
Identity over aligned base-pairs: 84.7%

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
Identity over aligned base-pairs: 86.8%