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Arabidopsis thaliana vs Lupinus angustifolius LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Lupinus angustifolius (Lupinus angustifolius, LupAngTanjil_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 91. 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 thalianaLupinus angustifolius
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 189,232 alignment blocks

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

Uncovered: 84,080,460 out of 119,667,750
Covered: 35,587,290 out of 119,667,750

Uncovered: 8,944,179 out of 33,775,569
Matches: 16,740,800 out of 33,775,569
Mismatches: 7,514,231 out of 33,775,569
Insertions: 576,359 out of 33,775,569
Identity over aligned base-pairs: 67.4%

Lupinus angustifolius

Uncovered: 553,664,160 out of 609,203,021
Covered: 55,538,861 out of 609,203,021

Uncovered: 8,665,503 out of 42,631,353
Matches: 23,043,068 out of 42,631,353
Mismatches: 10,030,182 out of 42,631,353
Insertions: 892,600 out of 42,631,353
Identity over aligned base-pairs: 67.8%

Block size distribution

Size range All 189,232 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,062
11.1 kb
10 bp - 100 bp
29,950
2.0 Mb
6,842
474.0 kb
100 bp - 1 kb
144,990
49.0 Mb
33,885
13.1 Mb
1 kb - 10 kb
12,229
18.3 Mb
21,180
50.3 Mb
10 kb - 100 kb
1
10.0 kb
347
5.4 Mb