Sorghum bicolor vs Hordeum vulgare LastZ results

Sorghum bicolor (Sorghum bicolor, Sorghum_bicolor_NCBIv3) and Hordeum vulgare (Hordeum vulgare subsp. vulgare, IBSC_v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 91. Sorghum bicolor 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

ParameterSorghum bicolorHordeum vulgare
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 377,368 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Sorghum bicolor

Uncovered: 620,667,269 out of 708,735,318
Covered: 88,068,049 out of 708,735,318

Uncovered: 5,005,645 out of 39,785,927
Matches: 25,327,212 out of 39,785,927
Mismatches: 8,446,153 out of 39,785,927
Insertions: 1,006,917 out of 39,785,927
Identity over aligned base-pairs: 72.8%

Hordeum vulgare

Uncovered: 4,688,235,563 out of 4,833,907,081
Covered: 145,671,518 out of 4,833,907,081

Uncovered: 6,142,469 out of 44,392,268
Matches: 28,893,146 out of 44,392,268
Mismatches: 8,381,292 out of 44,392,268
Insertions: 975,361 out of 44,392,268
Identity over aligned base-pairs: 75.5%

Block size distribution

Size range All 377,368 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,872
10.6 kb
10 bp - 100 bp
56,122
3.7 Mb
31,468
2.2 Mb
100 bp - 1 kb
277,347
97.8 Mb
157,684
54.4 Mb
1 kb - 10 kb
41,593
74.8 Mb
45,520
110.3 Mb
10 kb - 100 kb
426
10.4 Mb
977
18.4 Mb
100 kb - 1 Mb
8
930.0 kb
19
2.5 Mb