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Oryza sativa Japonica Group vs Citrus clementina LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Citrus clementina (Citrus clementina, Citrus_clementina_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 99. 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 GroupCitrus clementina
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 133,591 alignment blocks

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

Uncovered: 342,230,704 out of 375,049,285
Covered: 32,818,581 out of 375,049,285

Uncovered: 14,366,389 out of 34,424,450
Matches: 13,012,599 out of 34,424,450
Mismatches: 6,593,369 out of 34,424,450
Insertions: 452,093 out of 34,424,450
Identity over aligned base-pairs: 64.9%

Citrus clementina

Uncovered: 269,979,727 out of 301,364,702
Covered: 31,384,975 out of 301,364,702

Uncovered: 10,917,890 out of 30,721,724
Matches: 12,851,149 out of 30,721,724
Mismatches: 6,510,874 out of 30,721,724
Insertions: 441,811 out of 30,721,724
Identity over aligned base-pairs: 64.9%

Block size distribution

Size range All 133,591 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
911
4.4 kb
10 bp - 100 bp
20,646
1.4 Mb
4,494
323.6 kb
100 bp - 1 kb
104,188
33.9 Mb
28,311
11.3 Mb
1 kb - 10 kb
7,844
11.7 Mb
16,276
34.8 Mb
10 kb - 100 kb
2
25.0 kb
55
705.2 kb