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Oryza sativa Japonica Group vs Chondrus crispus LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Chondrus crispus (Chondrus crispus, ASM35022v2) 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
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
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 GroupChondrus crispus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 9,239 alignment blocks

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

Uncovered: 373,084,160 out of 375,049,285
Covered: 1,965,125 out of 375,049,285

Uncovered: 33,228,548 out of 34,818,902
Matches: 998,422 out of 34,818,902
Mismatches: 546,461 out of 34,818,902
Insertions: 45,471 out of 34,818,902
Identity over aligned base-pairs: 62.8%

Chondrus crispus

Uncovered: 103,864,766 out of 104,980,420
Covered: 1,115,654 out of 104,980,420

Uncovered: 9,311,410 out of 10,311,317
Matches: 622,177 out of 10,311,317
Mismatches: 349,377 out of 10,311,317
Insertions: 28,353 out of 10,311,317
Identity over aligned base-pairs: 62.2%

Block size distribution

Size range All 9,239 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
37
201.0 bp
10 bp - 100 bp
2,486
182.0 kb
440
32.5 kb
100 bp - 1 kb
6,426
1.6 Mb
3,023
1.2 Mb
1 kb - 10 kb
290
417.9 kb
637
975.3 kb
10 kb - 100 kb
1
12.2 kb