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Arabidopsis thaliana vs Panicum hallii HAL2 LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Panicum hallii HAL2 (Panicum hallii var. hallii str. HAL2, PhalliiHAL_v2.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 96. 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 thalianaPanicum hallii HAL2
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 77,573 alignment blocks

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

Uncovered: 93,815,542 out of 119,667,750
Covered: 25,852,208 out of 119,667,750

Uncovered: 14,369,921 out of 33,775,569
Matches: 12,637,197 out of 33,775,569
Mismatches: 6,401,110 out of 33,775,569
Insertions: 367,341 out of 33,775,569
Identity over aligned base-pairs: 65.1%

Panicum hallii HAL2

Uncovered: 468,814,870 out of 487,473,734
Covered: 18,658,864 out of 487,473,734

Uncovered: 24,490,237 out of 37,739,336
Matches: 8,599,142 out of 37,739,336
Mismatches: 4,345,113 out of 37,739,336
Insertions: 304,844 out of 37,739,336
Identity over aligned base-pairs: 64.9%

Block size distribution

Size range All 77,573 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
620
3.2 kb
10 bp - 100 bp
12,112
835.1 kb
1,765
126.6 kb
100 bp - 1 kb
60,231
20.1 Mb
13,137
5.6 Mb
1 kb - 10 kb
4,610
6.8 Mb
10,173
21.6 Mb
10 kb - 100 kb
32
408.3 kb