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Oryza sativa Japonica Group vs Glycine max LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Glycine max (Glycine max, Glycine_max_v2.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 95. 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 GroupGlycine max
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 260,019 alignment blocks

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

Uncovered: 339,623,033 out of 375,049,285
Covered: 35,426,252 out of 375,049,285

Uncovered: 13,642,586 out of 34,403,043
Matches: 13,377,404 out of 34,403,043
Mismatches: 6,813,313 out of 34,403,043
Insertions: 569,740 out of 34,403,043
Identity over aligned base-pairs: 64.4%

Glycine max

Uncovered: 912,753,380 out of 978,491,270
Covered: 65,737,890 out of 978,491,270

Uncovered: 24,373,540 out of 65,618,132
Matches: 27,114,539 out of 65,618,132
Mismatches: 13,256,759 out of 65,618,132
Insertions: 873,294 out of 65,618,132
Identity over aligned base-pairs: 65.7%

Block size distribution

Size range All 260,019 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,020
9.8 kb
10 bp - 100 bp
42,306
3.0 Mb
10,263
748.6 kb
100 bp - 1 kb
203,884
63.7 Mb
64,914
24.4 Mb
1 kb - 10 kb
11,802
17.4 Mb
27,710
58.0 Mb
10 kb - 100 kb
7
76.7 kb
75
908.7 kb