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Oryza sativa Japonica Group vs Pistacia vera LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Pistacia vera (Pistacia vera, PisVer_v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. 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 GroupPistacia vera
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 187,447 alignment blocks

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

Uncovered: 341,560,420 out of 375,049,285
Covered: 33,488,865 out of 375,049,285

Uncovered: 14,207,898 out of 34,424,450
Matches: 13,075,476 out of 34,424,450
Mismatches: 6,669,729 out of 34,424,450
Insertions: 471,347 out of 34,424,450
Identity over aligned base-pairs: 64.7%

Pistacia vera

Uncovered: 622,610,880 out of 671,152,441
Covered: 48,541,561 out of 671,152,441

Uncovered: 13,164,188 out of 38,113,229
Matches: 16,230,001 out of 38,113,229
Mismatches: 8,215,257 out of 38,113,229
Insertions: 503,783 out of 38,113,229
Identity over aligned base-pairs: 65.1%

Block size distribution

Size range All 187,447 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,336
6.6 kb
10 bp - 100 bp
29,020
2.0 Mb
7,677
556.0 kb
100 bp - 1 kb
146,563
47.8 Mb
47,691
18.7 Mb
1 kb - 10 kb
10,525
15.5 Mb
22,304
45.4 Mb
10 kb - 100 kb
3
36.4 kb
54
700.2 kb