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Arabidopsis thaliana vs Solanum tuberosum LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Solanum tuberosum (Solanum tuberosum, SolTub_3.0) 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 thalianaSolanum tuberosum
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 153,848 alignment blocks

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

Uncovered: 85,513,927 out of 119,667,750
Covered: 34,153,823 out of 119,667,750

Uncovered: 9,465,582 out of 33,775,569
Matches: 16,047,342 out of 33,775,569
Mismatches: 7,720,356 out of 33,775,569
Insertions: 542,289 out of 33,775,569
Identity over aligned base-pairs: 66.0%

Solanum tuberosum

Uncovered: 767,951,720 out of 810,654,046
Covered: 42,702,326 out of 810,654,046

Uncovered: 15,245,210 out of 36,745,425
Matches: 14,282,098 out of 36,745,425
Mismatches: 6,651,675 out of 36,745,425
Insertions: 566,442 out of 36,745,425
Identity over aligned base-pairs: 66.4%

Block size distribution

Size range All 153,848 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,255
6.7 kb
10 bp - 100 bp
23,655
1.6 Mb
6,324
449.9 kb
100 bp - 1 kb
119,136
39.7 Mb
33,730
13.1 Mb
1 kb - 10 kb
9,781
14.5 Mb
18,013
39.8 Mb
10 kb - 100 kb
21
590.5 kb
180
3.1 Mb