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Oryza sativa Indica Group vs Oryza glumipatula LastZ results

Oryza sativa Indica Group (Oryza sativa Indica Group, ASM465v1) and Oryza glumipatula (Oryza glumipatula, Oryza_glumaepatula_v1.5) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 75. Oryza sativa Indica Group 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 sativa Indica GroupOryza glumipatula
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 179,181 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Indica Group

Uncovered: 96,385,035 out of 374,545,499
Covered: 278,160,464 out of 374,545,499

Uncovered: 579,433 out of 42,733,995
Matches: 40,903,405 out of 42,733,995
Mismatches: 1,042,708 out of 42,733,995
Insertions: 208,449 out of 42,733,995
Identity over aligned base-pairs: 97.0%

Oryza glumipatula

Uncovered: 131,263,828 out of 372,860,283
Covered: 241,596,455 out of 372,860,283

Uncovered: 2,537,030 out of 41,162,840
Matches: 37,917,076 out of 41,162,840
Mismatches: 566,200 out of 41,162,840
Insertions: 142,534 out of 41,162,840
Identity over aligned base-pairs: 98.2%