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Oryza sativa Japonica Group vs Amborella trichopoda LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Amborella trichopoda (Amborella trichopoda, AMTR1.0) 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 GroupAmborella trichopoda
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 125,838 alignment blocks

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

Uncovered: 346,314,506 out of 375,049,285
Covered: 28,734,779 out of 375,049,285

Uncovered: 15,774,107 out of 34,403,043
Matches: 12,116,866 out of 34,403,043
Mismatches: 6,110,455 out of 34,403,043
Insertions: 401,615 out of 34,403,043
Identity over aligned base-pairs: 65.0%

Amborella trichopoda

Uncovered: 682,484,550 out of 706,332,640
Covered: 23,848,090 out of 706,332,640

Uncovered: 10,685,047 out of 25,807,211
Matches: 9,901,226 out of 25,807,211
Mismatches: 4,901,839 out of 25,807,211
Insertions: 319,099 out of 25,807,211
Identity over aligned base-pairs: 65.5%

Block size distribution

Size range All 125,838 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
824
4.0 kb
10 bp - 100 bp
20,515
1.5 Mb
5,572
412.0 kb
100 bp - 1 kb
99,886
29.4 Mb
36,760
13.5 Mb
1 kb - 10 kb
4,608
7.2 Mb
12,147
23.5 Mb
10 kb - 100 kb
5
79.7 kb
46
657.6 kb