Medicago truncatula vs Glycine soja (Wild soybean) LastZ results
Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Glycine soja (Wild soybean) (Glycine soja, ASM419377v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 112. Medicago truncatula 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
Parameter | Value |
---|---|
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
Parameter | Medicago truncatula | Glycine soja (Wild soybean) |
---|---|---|
Chunk size | 10,000,000 | 10,100,000 |
Overlap | 0 | 100,000 |
Group set size | 10,100,000 | 10,100,000 |
Masking options |
Statistics over 514,897 alignment blocks
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Medicago truncatula |
Uncovered: 317,784,444 out of 429,196,467 |
Uncovered: 6,769,350 out of 45,081,035 |
Glycine soja (Wild soybean) |
Uncovered: 847,978,721 out of 1,013,766,566 |
Uncovered: 12,407,507 out of 61,659,035 |
Block size distribution
Size range | All 514,897 alignment blocks | Blocks grouped in nets | |||
---|---|---|---|---|---|
# blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
1 bp - 10 bp | 9,855 |
55.9 kb |
|||
10 bp - 100 bp | 102,939 |
5.7 Mb |
22,084 |
1.6 Mb |
|
100 bp - 1 kb | 353,997 |
131.6 Mb |
110,878 |
38.2 Mb |
|
1 kb - 10 kb | 48,086 |
76.8 Mb |
26,891 |
63.9 Mb |
|
10 kb - 100 kb | 20 |
369.2 kb |
827 |
19.2 Mb |
|
100 kb - 1 Mb | 118 |
36.6 Mb |
|||
1 Mb - 10 Mb | 31 |
55.2 Mb |