Arabidopsis thaliana vs Leersia perrieri LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Leersia perrieri (Leersia perrieri, Lperr_V1.4) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Arabidopsis thaliana 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: 108,346

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 93,480,492 out of 119,667,750
Covered: 26,187,258 out of 119,667,750

Uncovered: 14,451,781 out of 33,775,569
Matches: 12,552,935 out of 33,775,569
Mismatches: 6,369,591 out of 33,775,569
Insertions: 401,262 out of 33,775,569

Leersia perrieri

Uncovered: 238,908,214 out of 266,687,832
Covered: 27,779,618 out of 266,687,832

Uncovered: 17,640,812 out of 36,898,596
Matches: 12,397,578 out of 36,898,596
Mismatches: 6,381,281 out of 36,898,596
Insertions: 478,925 out of 36,898,596

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
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
Other parameters (other)--ambiguous=iupac

Chunking parameters

Arabidopsis thaliana Leersia perrieri
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}