vs LastZ Results

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(, IRGSP-1.0) and (, TGACv1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 84. 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: 316,810

Genome coverage (bp) Coding exon coverage (bp)

Uncovered: 296,887,686 out of 374,424,240
Covered: 77,536,554 out of 374,424,240

Uncovered: 3,767,216 out of 34,124,807
Matches: 23,440,177 out of 34,124,807
Mismatches: 6,052,745 out of 34,124,807
Insertions: 864,669 out of 34,124,807

Uncovered: 4,266,137,399 out of 4,386,473,599
Covered: 120,336,200 out of 4,386,473,599

Uncovered: 5,497,166 out of 41,298,743
Matches: 27,532,797 out of 41,298,743
Mismatches: 7,393,791 out of 41,298,743
Insertions: 874,989 out of 41,298,743

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

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}