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Table 2 Hypervariable regions on different chromosome of Brassica juncea

From: ddRAD sequencing-based identification of inter-genepool SNPs and association analysis in Brassica juncea

Chromosome Hyper-variable region No. of SNPs Frequency of SNPs (per bp) Predicted Protein Protein Accession ID BlastX e-value
A01 12,089,878 to 12,089,908 4 7.50 SMAX1-LIKE 2 [Brassica rapa] XP_009127888.1 1.00E-148
13,064,396 to13064410 6 2.33 Heptahelical transmembrane protein 2 [Brassica napus] XP_013730768.1 2.00E-040
23,525,876 to 23,525,886 4 2.50 Farnesyl transferase/ geranylgeranyl transferase type-1 subunit alpha
[Brassica rapa]
XP_009147222.1 2.00E-029
37,133,315 to 37,133,336 5 4.20 Uncharacterized protein LOC106335203
[Brassica oleracea]
XP_013629110.1 1.00E-042
38,650,911 to 38,650,931 4 5.00 Calcium-binding EF-hand family protein
(Arabidopsis thaliana)
NP_001332476.1 6.00E-056
A02 2,398,121 to 2398162 6 6.83 No significant hit   
14,416,494 to 14,416,505 5 2.20 Uncharacterized protein RQM01316.1 3.00E-030
A03 25,641,944 to 25,641,977 7 4.71 Hypothetical protein DY000_00001393 [Brassica cretica] RQL75529.1 1.00E-009
42,576,172 to 43,014,367 9 21.66 Uncharacterized protein LOC106363406 [Brassica napus] XP_013658605.1 3.00E-079
A04 8,377,252 to 8,377,288 10 3.60 Uncharacterized protein LOC106360747 [Brassica napus] XP_013655857.1 3.00E-113
14,731,032 to 14,908,156 4 31.00 Transcription factor MYC2 [Brassica rapa) XP_009151447.1 8.00E-166
A05 1,588,930 to 1,588,970 5 8.00 Polygalacturonase-like [Brassica oleracea] XP_013633855.1 4.00E-084
19,985,702 to 19,985,780 5 15.60 BnaC08g47040D [Brassica napus] CDY43697.1 8.00E-054
21,938,359 to 21,938,393 6 5.66 Probable LRR receptor-like serine/threonine-protein kinase At4g36180 [Brassica napus] XP_013716480.1 5.00E-166
27,265,183 to 27,265,231 5 9.60 Hypothetical protein BRARA_K01418 [Brassica rapa] RIA04352.1 1.00E-019
35,529,249 to 35,529,274 5 5.00 Cis-phytoenedesaturase, chloroplastic/chromoplastic [Brassica napus] XP_013750375.2 9.00E-065
A06 11,405,649 to 11,405,684 5 7.00 BnaA06g16240D [Brassica napus] CDY08102.1 4.00E-077
31,624,120 to 31,624,155 6 5.83 Hypothetical protein
RQL85806.1
RQL85806.1 2.00E-097
36,377,825 to 36,377,860 5 7.00 Uncharacterized protein LOC106401547 [Brassica napus] XP_022543736.1 5.00E-084
A07 13,947,963 to 13,948,008 5 9.00 Unnamed protein product (Brassica rapa) VDC98355.1 2.00E-072
16,375,261 to 16,375,275 5 2.80 Uncharacterized protein LOC103829921 [Brassica rapa] XP_009103854.1 6.00E-034
B01 24,425,289 to 24,425,343 10 5.40 Uncharacterized abhydrolase domain-containing protein DDB_G0269086-like [Brassica rapa]   4.00E-090
33,418,235 to 33,418,261 5 5.20 Unnamed protein product [Brassica rapa] VDC90843.1 2.00E-094
51,944,663 to 51944714 6 8.50 Uncharacterized protein LOC106308810 [Brassica oleracea] XP_013601383.1 4.00E-098
53,225,827 to 53,225,840 5 2.60 Homocysteine S-methyltransferase 2 [Brassica napus] XP_013712093.1 1.00E-040
53,650,933 to 53,650,972 5 7.80 Hypothetical protein DY000_00003913 [Brassica cretica] RQL77992.1 4.00E-076
B02 6,040,643 to 6,040,712 11 6.27 Unnamed protein product [Brassica rapa] VDD17261.1 4.00E-004
14,431,647 to 14,431,685 5 7.60 No significant hit   
B04 18,482,342 to 18,482,397 4 13.75 Uncharacterized protein At3g60930, chloroplastic-like [Brassica napus] XP_022567433.1 7.00E-009
29,636,717 to 29,636,764 8 5.87 BnaA02g16800D [Brassica napus] CDY49126.1 8.00E-035
46,447,876 to 46,447,889 6 2.16 hypothetical protein DY000_00030648 [Brassica cretica] RQM04119.1 4.00E-034
52,254,291 to 52,254,327 5 7.20 ras-related protein RABD2c isoform X1 [Brassica rapa] XP_009130704.1 1.00E-154
53,387,066 to 53,387,117 5 10.20 uncharacterized mitochondrial protein AtMg00810-like [Brassica oleracea var. oleracea] XP_013601341.1 2.00E-138
B05 12,937,005 to 12,937,060 5 10.00 hypothetical protein MANES_08G079400 [Manihot esculenta] OAY43565.1 3.00E-014
68,021,640 to 68,021,664 7 3.42 caffeic acid 3-O-methyltransferase-like [Raphanus sativus] XP_018461242.1 4.00E-058
80,717,492 to 80,717,516 7 3.43 glutathione S-transferase T3-like [Brassica oleracea var. oleracea] XP_013639324.1 3.00E-107
B06 1,593,067 to 1,593,109 11 3.82 BnaC04g03580D [Brassica napus] CDY17861.1 8.00E-011
2,770,283 to 2,770,305 5 4.40 uncharacterized acetyltransferase At3g50280 [Raphanus sativus] XP_018434505.1 0
B07 23,121,758 to 23121773 5 3.00 uncharacterized protein LOC108830363 [Raphanus sativus] XP_018459472.1 1.00E-150
B08 15,772,508 to 15,772,583 10 7.50 probable LRR receptor-like serine/threonine-protein kinase At4g36180 isoform X1 [Raphanus sativus] XP_018460684.1 2.00E-074
B09 29,343,310 to 29,343,368 8 7.25 No significant hit NA NA
32,306,181 to 32,306,211 6 5.00 U-box domain-containing protein 9-like [Brassica napus] XP_013684649.1 4.00E-055
B10 63,679,073 to 63,679,088 6 2.50 uncharacterized protein LOC106424516 [Brassica napus] XP_013720737.1 1.00E-107
69,805,021 to 69,805,080 7 8.42 uncharacterized protein LOC106361641 [Brassica napus] XP_022549137.1 0