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Oryza sativa Japonica Group vs Galdieria sulphuraria LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Galdieria sulphuraria (Galdieria sulphuraria, ASM34128v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. Oryza sativa Japonica Group was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

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

Chunking parameters

ParameterOryza sativa Japonica GroupGaldieria sulphuraria
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 8,356 alignment blocks

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

Uncovered: 373,320,870 out of 375,049,285
Covered: 1,728,415 out of 375,049,285

Uncovered: 33,183,717 out of 34,403,043
Matches: 766,375 out of 34,403,043
Mismatches: 425,436 out of 34,403,043
Insertions: 27,515 out of 34,403,043
Identity over aligned base-pairs: 62.9%

Galdieria sulphuraria

Uncovered: 12,742,296 out of 13,712,004
Covered: 969,708 out of 13,712,004

Uncovered: 7,499,058 out of 8,395,974
Matches: 561,326 out of 8,395,974
Mismatches: 312,640 out of 8,395,974
Insertions: 22,950 out of 8,395,974
Identity over aligned base-pairs: 62.6%

Block size distribution

Size range All 8,356 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
35
180.0 bp
10 bp - 100 bp
2,366
173.2 kb
387
28.3 kb
100 bp - 1 kb
5,748
1.4 Mb
2,362
944.6 kb
1 kb - 10 kb
207
320.8 kb
569
933.0 kb
10 kb - 100 kb
1
11.8 kb