Arabidopsis thaliana vs Panicum hallii FIL2 LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Panicum hallii FIL2 (Panicum hallii str. FIL2, PHallii_v3.1) 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 FIL2
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 77,499 alignment blocks

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

Uncovered: 93,830,182 out of 119,667,750
Covered: 25,837,568 out of 119,667,750

Uncovered: 14,382,632 out of 33,775,569
Matches: 12,625,456 out of 33,775,569
Mismatches: 6,402,125 out of 33,775,569
Insertions: 365,356 out of 33,775,569
Identity over aligned base-pairs: 65.1%

Panicum hallii FIL2

Uncovered: 517,261,402 out of 535,889,049
Covered: 18,627,647 out of 535,889,049

Uncovered: 25,220,505 out of 38,415,885
Matches: 8,560,310 out of 38,415,885
Mismatches: 4,330,664 out of 38,415,885
Insertions: 304,406 out of 38,415,885
Identity over aligned base-pairs: 64.9%

Block size distribution

Size range All 77,499 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
573
3.0 kb
10 bp - 100 bp
12,158
835.3 kb
1,856
131.1 kb
100 bp - 1 kb
60,113
20.0 Mb
13,074
5.6 Mb
1 kb - 10 kb
4,655
6.8 Mb
10,201
21.6 Mb
10 kb - 100 kb
29
364.1 kb