Oryza sativa Japonica Group vs Marchantia polymorpha LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Marchantia polymorpha (Marchantia polymorpha str. Tak-1, Marchanta_polymorpha_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Oryza sativa Japonica Group 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: 78,298

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

Uncovered: 357,794,314 out of 375,049,285
Covered: 17,254,971 out of 375,049,285

Uncovered: 22,357,423 out of 34,349,962
Matches: 7,645,836 out of 34,349,962
Mismatches: 4,083,108 out of 34,349,962
Insertions: 263,595 out of 34,349,962

Marchantia polymorpha str. Tak-1

Uncovered: 214,634,878 out of 225,760,816
Covered: 11,125,938 out of 225,760,816

Uncovered: 15,426,974 out of 23,498,831
Matches: 5,136,767 out of 23,498,831
Mismatches: 2,724,295 out of 23,498,831
Insertions: 210,795 out of 23,498,831

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

Oryza sativa Japonica Group Marchantia polymorpha
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}