Oryza barthii vs Oryza brachyantha LastZ Results

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Oryza barthii (Oryza barthii, O.barthii_v1) and Oryza brachyantha (Oryza brachyantha, Oryza_brachyantha.v1.4b) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza barthii 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: 286,150

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

Uncovered: 170,602,059 out of 308,272,304
Covered: 137,670,245 out of 308,272,304

Uncovered: 4,405,020 out of 39,538,509
Matches: 26,143,957 out of 39,538,509
Mismatches: 8,154,651 out of 39,538,509
Insertions: 834,881 out of 39,538,509

Oryza brachyantha

Uncovered: 151,892,017 out of 260,838,168
Covered: 108,946,151 out of 260,838,168

Uncovered: 4,707,356 out of 33,473,466
Matches: 22,076,962 out of 33,473,466
Mismatches: 6,230,814 out of 33,473,466
Insertions: 458,334 out of 33,473,466

Configuration parameters

ParameterValue
Gap open penalty (O)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
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)