Oryza sativa Japonica Group vs Eragrostis tef LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Eragrostis tef (Eragrostis tef, ASM97063v1) 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: 410,789

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

Uncovered: 265,075,038 out of 375,049,285
Covered: 109,974,247 out of 375,049,285

Uncovered: 2,976,006 out of 34,424,450
Matches: 21,144,238 out of 34,424,450
Mismatches: 9,421,913 out of 34,424,450
Insertions: 882,293 out of 34,424,450

Eragrostis tef

Uncovered: 421,416,292 out of 607,317,615
Covered: 185,901,323 out of 607,317,615

Uncovered: 3,966,328 out of 47,955,771
Matches: 34,942,617 out of 47,955,771
Mismatches: 8,360,345 out of 47,955,771
Insertions: 686,481 out of 47,955,771

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 Eragrostis tef
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}