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Arabidopsis thaliana vs Galdieria sulphuraria LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Galdieria sulphuraria (Galdieria sulphuraria, ASM34128v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. Arabidopsis thaliana 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

ParameterArabidopsis thalianaGaldieria sulphuraria
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 9,116 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 117,738,136 out of 119,667,750
Covered: 1,929,614 out of 119,667,750

Uncovered: 32,091,138 out of 33,775,569
Matches: 1,052,720 out of 33,775,569
Mismatches: 578,097 out of 33,775,569
Insertions: 53,614 out of 33,775,569
Identity over aligned base-pairs: 62.5%

Galdieria sulphuraria

Uncovered: 12,597,977 out of 13,712,004
Covered: 1,114,027 out of 13,712,004

Uncovered: 7,376,341 out of 8,395,974
Matches: 638,073 out of 8,395,974
Mismatches: 352,402 out of 8,395,974
Insertions: 29,158 out of 8,395,974
Identity over aligned base-pairs: 62.6%

Block size distribution

Size range All 9,116 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
51
265.0 bp
10 bp - 100 bp
2,489
181.0 kb
290
21.3 kb
100 bp - 1 kb
6,374
1.7 Mb
2,315
1.0 Mb
1 kb - 10 kb
201
266.7 kb
702
1.1 Mb
10 kb - 100 kb
1
17.0 kb
1
17.0 kb