Table 8. Thirteen large-fragment InDels in candidate genes related to ripening.
| Annotated proteina | Gene & protein IDb | Gene ID &Chromosomec | Change-SBCd | Change-SBBMe |
|---|---|---|---|---|
| — | — | — | NS | NS/Sv |
| Chalcone synthase | sp|P51090|CHSY_VITVI | GSVIVT01032968001 in chr14 | 24,673,846 T AA | 24,673,846 T AA |
| halcone synthase | sp|P51090|CHSY_VITVI | GSVIVT01032968001 in chr14 | 24,673,881 A CC | 24,673,881A CC |
| Chalcone synthase | sp|P51090|CHSY_VITVI | GSVIVT01032968001 in chr14 | 24,673,978 C TT | 24,673,978 C TT |
| Chalcone synthase | sp|P51090|CHSY_VITVI | GSVIVT01032968001 in chr14 | 24,674,524 T CC | 24,674,194 T CY |
| Chalcone synthase | sp|P51090|CHSY_VITVI | GSVIVT01032968001 in chr14 | — | 24,674,524 T CC |
| Chalcone synthase | sp|P51090|CHSY_VITVI | GSVIVT01032968001 in chr14 | — | 24,675,008 C TT |
| Chalcone synthase | sp|P51090|CHSY_VITVI | GSVIVT01032968001 in chr14 | — | DEL: 13,541 from 24,674,193 to 24,687,822 |
| — | — | — | NS/Sv/F | NS |
| Myb-family transcription factor | sp|Q700D9|MYF _ARATH | GSVIVT01032776001 in chr13 | 838,415 C GG | 838,867 C GG |
| Myb-family transcription factor | sp|Q700D9|MYF _ARATH | GSVIVT01032776001 in chr13 | 838,558 C AM | 838,900 T AW |
| Myb-family transcription factor | sp|Q700D9|MYF _ARATH | GSVIVT01032776001 in chr13 | 838,867 C GG | 839,256 T CC |
| Myb-family transcription factor | sp|Q700D9|MYF _ARATH | GSVIVT01032776001 in chr13 | 838,900 T AW | 839,647 T CY |
| Myb-family transcription factor | sp|Q700D9|MYF _ARATH | GSVIVT01032776001 in chr13 | 839,256 T CC | 844,828 T CC |
| Myb-family transcription factor | sp|Q700D9|MYF _ARATH | GSVIVT01032776001 in chr13 | 839,647 T CY | 844,891T CY |
| Myb-family transcription factor | sp|Q700D9|MYF _ARATH | GSVIVT01032776001 in chr13 | 839,929 G AR | — |
| Myb-family transcription factor | sp|Q700D9|MYF _ARATH | GSVIVT01032776001 in chr13 | 840,005 C TY | — |
| Myb-family transcription factor | sp|Q700D9|MYF _ARATH | GSVIVT01032776001 in chr13 | 840,080 C AM | — |
| Myb-family transcription factor | sp|Q700D9|MYF _ARATH | GSVIVT01032776001 in chr13 | 844,891T CY | — |
| Myb-family transcription factor | sp|Q700D9|MYF _ARATH | GSVIVT01032776001 in chr13 | DEL4: from 838,413 to 838,420 | — |
| Myb-family transcription factor | sp|Q700D9|MYF _ARATH | GSVIVT01032776001 in chr13 | INS 2: from 84,0284to84,0286 | — |
| Myb-family transcription factor | sp|Q700D9|MYF _ARATH | GSVIVT01032776001 in chr13 | INS 1: from 84,4790to 84,4799 | — |
| — | — | — | NS | NS/Sv |
| Malonyl-coenzyme A | sp|Q8GSN8|3MAT_DAHPI | GSVIVT01000461001 in chr12 | 8,202,818 A TT | 8,202,818 A TT |
| Malonyl-coenzyme A | sp|Q8GSN8|3MAT_DAHPI | GSVIVT01000461001 in chr12 | 8,202,844 T CY | 8,203,022 G AA |
| Malonyl-coenzyme A | sp|Q8GSN8|3MAT_DAHPI | GSVIVT01000461001 in chr12 | 8,203,022 G AA | 8,203,027 A CM |
| Malonyl-coenzyme A | sp|Q8GSN8|3MAT_DAHPI | GSVIVT01000461001 in chr12 | 8,203,027 A CM | 8,203,486 C TT |
| Malonyl-coenzyme A | sp|Q8GSN8|3MAT_DAHPI | GSVIVT01000461001 in chr12 | 8,203,207 A TW | 8,210,389 G CS |
| Malonyl-coenzyme A | sp|Q8GSN8|3MAT_DAHPI | GSVIVT01000461001 in chr12 | 8,203,216 A TW | 8,210,633 A GR |
| Malonyl-coenzyme A | sp|Q8GSN8|3MAT_DAHPI | GSVIVT01000461001 in chr12 | 8,203,346 C TY | — |
| Malonyl-coenzyme A | sp|Q8GSN8|3MAT_DAHPI | GSVIVT01000461001 in chr12 | 8,203,486 C TT | — |
| Malonyl-coenzyme A | sp|Q8GSN8|3MAT_DAHPI | GSVIVT01000461001 in chr12 | 8,210,571 T CY | — |
| Malonyl-coenzyme A | sp|Q8GSN8|3MAT_DAHPI | GSVIVT01000461001 in chr12 | 8,210,633 A GR | — |
| Malonyl-coenzyme A | sp|Q8GSN8|3MAT_DAHPI | GSVIVT01000461001 in chr12 | — | DEL25,483: from 829,838 to 8,235,429 |
| — | — | — | NS | NS/Sv |
| Ethylene-responsive transcription factor | sp|Q40478|ERF5_TOBAC | GSVIVT01013934001 in chr16 | 7,012,358 G AR | 7,011,626 T CC |
| Ethylene-responsive transcription factor | sp|Q40478|ERF5_TOBAC | GSVIVT01013934001 in chr16 | 7,012,365 A GR | 7,012,358 G AR |
| Ethylene-responsive transcription factor | sp|Q40478|ERF5_TOBAC | GSVIVT01013934001 in chr16 | 7,012,405 T GK | 7,025,216 G CS |
| Ethylene-responsive transcription factor | sp|Q40478|ERF5_TOBAC | GSVIVT01013934001 in chr16 | 7,020,752 G CS | 7,025,318 C TT |
| Ethylene-responsive transcription factor | sp|Q40478|ERF5_TOBAC | GSVIVT01013934001 in chr16 | 7,025,275 G AA | 7,025,356 T CY |
| Ethylene-responsive transcription factor | sp|Q40478|ERF5_TOBAC | GSVIVT01013934001 in chr16 | 7,025,356 T CY | 7,025,450 C TY |
| Ethylene-responsive transcription factor | sp|Q40478|ERF5_TOBAC | GSVIVT01013934001 in chr16 | 7,025,751 C TY | 7,025,692 A GR |
| Ethylene-responsive transcription factor | sp|Q40478|ERF5_TOBAC | GSVIVT01013934001 in chr16 | 7,025,772 A CC | — |
| Ethylene-responsive transcription factor | sp|Q40478|ERF5_TOBAC | GSVIVT01013934001 in chr16 | 7,025,782 G CC | — |
| Ethylene-responsive transcription factor | sp|Q40478|ERF5_TOBAC | GSVIVT01013934001 in chr16 | — | DEL8,818: from 7,011,486 to 7,020,308 |
| — | — | — | — | Sv |
| Ethylene-responsive transcription factor | sp|Q94AW5|ERF03_ARATH | GSVIVT01026334001 in chr4 | — | DEL12,460: from 14,176,993 to 14,189,460 |
| — | — | — | Sv | |
| ABSCISIC ACID-INSENSITIVE 5-like protein | sp|Q9LES3|AI5L2_ARATH | GSVIVT01033216001 in chr4 | DEL7,576:from 9,840,430 to 9,847,952 | — |
| — | — | — | S | S/Sv/F |
| Developmental protein SEPALLATA 1 | sp|P29382|SEP1_ARATH | GSVIVT01008139001 in chr17 | — | DEL4: from 5,464,406 to 5,464,422 |
| — | — | — | NS | NS/Sv |
| Sugar carrier protein C | sp|Q41144|STC_RICCO | GSVIVT01036440001 in chr14 | 21,932,262 A GG | 21,932,208 C TY |
| Sugar carrier protein C | sp|Q41144|STC_RICCO | GSVIVT01036440001 in chr14 | 21,932,385 T CY | 21,932,226 G AR |
| Sugar carrier protein C | sp|Q41144|STC_RICCO | GSVIVT01036440001 in chr14 | 21,932,496 C TY | 21,932,253 A GR |
| Sugar carrier protein C | sp|Q41144|STC_RICCO | GSVIVT01036440001 in chr14 | 21,939,640 A GR | 21,932,262 A GG |
| Sugar carrier protein C | sp|Q41144|STC_RICCO | GSVIVT01036440001 in chr14 | 21,939,792 T GK | 21,932,389 A CM |
| Sugar carrier protein C | sp|Q41144|STC_RICCO | GSVIVT01036440001 in chr14 | 21,940,202 T GK | 21,932,496 C TY |
| Sugar carrier protein C | sp|Q41144|STC_RICCO | GSVIVT01036440001 in chr14 | 21,940,212 C AM | 21,933,149 C AA |
| Sugar carrier protein C | sp|Q41144|STC_RICCO | GSVIVT01036440001 in chr14 | 21,940,573 T CY | 21,939,727 G AR |
| Sugar carrier protein C | sp|Q41144|STC_RICCO | GSVIVT01036440001 in chr14 | 21,940,659 A CC | 21,939,792 T GK |
| Sugar carrier protein C | sp|Q41144|STC_RICCO | GSVIVT01036440001 in chr14 | 21,940,702 G CS | 21,940,059 A CM |
| Sugar carrier protein C | sp|Q41144|STC_RICCO | GSVIVT01036440001 in chr14 | 21,941,645 C TY | 21,940,118 G TK |
| Sugar carrier protein C | sp|Q41144|STC_RICCO | GSVIVT01036440001 in chr14 | 21,941,697 C TY | 21,940,202 T GK |
| Sugar carrier protein C | sp|Q41144|STC_RICCO | GSVIVT01036440001 in chr14 | 21,941,924 A GR | 21,940,212 C AM |
| Sugar carrier protein C | sp|Q41144|STC_RICCO | GSVIVT01036440001 in chr14 | 21,941,948 A GR | 21,940,573 T CY |
| Sugar carrier protein C | sp|Q41144|STC_RICCO | GSVIVT01036440001 in chr14 | 21,942,036 C AM | 21,940,659 A CC |
| Sugar carrier protein C | sp|Q41144|STC_RICCO | GSVIVT01036440001 in chr14 | 21,942,092 A TW | 21,940,702 G CS |
| Sugar carrier protein C | sp|Q41144|STC_RICCO | GSVIVT01036440001 in chr14 | — | DEL3,328: from 21,935,542 to 21,938,876 |
| — | — | — | NS/Sv | NS |
| Sugar transporter | sp|Q3ECP7|ERDL5_ARATH | GSVIVT01022025001 in chr14 | 4,161,687 A GR | 4,161,760 G AR |
| Sugar transporter | sp|Q3ECP7|ERDL5_ARATH | GSVIVT01022025001 in chr14 | 4,161,760 G AR | 4,161,928 G CS |
| Sugar transporter | sp|Q3ECP7|ERDL5_ARATH | GSVIVT01022025001 in chr14 | 4,161,906 T CY | 4,161,979 C TT |
| Sugar transporter | sp|Q3ECP7|ERDL5_ARATH | GSVIVT01022025001 in chr14 | 4,161,928 G CS | 4,162,107 C TT |
| Sugar transporter | sp|Q3ECP7|ERDL5_ARATH | GSVIVT01022025001 in chr14 | 4,161,979 C TT | 4,164,395 C TT |
| Sugar transporter | sp|Q3ECP7|ERDL5_ARATH | GSVIVT01022025001 in chr14 | 4,162,107 C TT | 4,164,776 T GG |
| Sugar transporter | sp|Q3ECP7|ERDL5_ARATH | GSVIVT01022025001 in chr14 | — | 4,164,823 G AR |
| Sugar transporter | sp|Q3ECP7|ERDL5_ARATH | GSVIVT01022025001 in chr14 | — | 4,164,829 G CC |
| Sugar transporter | sp|Q3ECP7|ERDL5_ARATH | GSVIVT01022025001 in chr14 | DEL1,903: from 4,164,061 to 4,165,992 | — |
| — | — | — | NS | NS/Sv |
| sugar phosphate/phosphate translocator | sp|Q8H184|PT106_ARATH | GSVIVT01020780001 in chr12 | 2,066,209 A CM | 2,066,209 A CM |
| sugar phosphate/phosphate translocator | sp|Q8H184|PT106_ARATH | GSVIVT01020780001 in chr12 | 2,068,143 A TT | 2,066,236 C TY |
| sugar phosphate/phosphate translocator | sp|Q8H184|PT106_ARATH | GSVIVT01020780001 in chr12 | 2,068,152 C TY | 2,068,143 A TT |
| sugar phosphate/phosphate translocator | sp|Q8H184|PT106_ARATH | GSVIVT01020780001 in chr12 | 2,071,379 C TY | 2,068,152 C TY |
| sugar phosphate/phosphate translocator | sp|Q8H184|PT106_ARATH | GSVIVT01020780001 in chr12 | 2,071,382T CY | 2,071,379 C TY |
| sugar phosphate/phosphate translocator | sp|Q8H184|PT106_ARATH | GSVIVT01020780001 in chr12 | — | 2,071,382 T CY |
| sugar phosphate/phosphate translocator | sp|Q8H184|PT106_ARATH | GSVIVT01020780001 in chr12 | — | DEL17,541: from 2,095,192 to 2,112,841 |
| — | — | — | NS | NS/Sv |
| Auxin-induced protein | sp|P33080|AX10A_SOYBN | GSVIVT01023911001 in chr3 | 2,525,484 A TW | 2,525,618 C AM |
| Auxin-induced protein | sp|P33080|AX10A_SOYBN | GSVIVT01023911001 in chr3 | 2,525,502 T AW | 2,525,636 G TT |
| Auxin-induced protein | sp|P33080|AX10A_SOYBN | GSVIVT01023911001 in chr3 | 2,525,618 C AM | 2,525,670 T CC |
| Auxin-induced protein | sp|P33080|AX10A_SOYBN | GSVIVT01023911001 in chr3 | 2,525,636 G TT | 2,525,815 C GS |
| Auxin-induced protein | sp|P33080|AX10A_SOYBN | GSVIVT01023911001 in chr3 | 2,525,670 T CC | 2,525,831 T AW |
| Auxin-induced protein | sp|P33080|AX10A_SOYBN | GSVIVT01023911001 in chr3 | 2,525,815 C GS | 2,525,874 T CY |
| Auxin-induced protein | sp|P33080|AX10A_SOYBN | GSVIVT01023911001 in chr3 | 2,525,831 T AW | — |
| Auxin-induced protein | sp|P33080|AX10A_SOYBN | GSVIVT01023911001 in chr3 | 2,525,874 T CY | — |
| Auxin-induced protein | sp|P33080|AX10A_SOYBN | GSVIVT01023911001 in chr3 | — | DEL7,836: from 2,525,478 to 2,533,405 |
| — | — | — | NS | NS/Sv |
| .Auxin-induced protein | sp|P33082|AXX15_SOYBN | GSVIVT01024129001 in chr3 | 888,891 C TY | 888,891 C TY |
| Auxin-induced protein | p|P33082|AXX15_SOYBN | GSVIVT01024129001 in chr3 | 888,934 G TK | — |
| Auxin-induced protein | p|P33082|AXX15_SOYBN | GSVIVT01024129001 in chr3 | — | DEL9,447: from 886,035 to 895,516 |
| — | — | — | NS | NS/Sv |
| 9-cis-epoxycarotenoid dioxygenase | sp|Q9LRM7|NCED6_ARATH | GSVIVT01029057001 in chr5 | 11,589,359 G CC | 11,589,359 G CC |
| 9-cis-epoxycarotenoid dioxygenase | sp|Q9LRM7|NCED6_ARATH | GSVIVT01029057001 in chr5 | 11,589,455 T GK | 11,589,444 T GK |
| 9-cis-epoxycarotenoid dioxygenase | sp|Q9LRM7|NCED6_ARATH | GSVIVT01029057001 in chr5 | 11,589,539 T GG | 11,589,455 T GK |
| 9-cis-epoxycarotenoid dioxygenase | sp|Q9LRM7|NCED6_ARATH | GSVIVT01029057001 in chr5 | 11,589,680 C TT | 11,589,680 C TX |
| 9-cis-epoxycarotenoid dioxygenase | sp|Q9LRM7|NCED6_ARATH | GSVIVT01029057001 in chr5 | 11,589,818 T GG | 11,589,818 T GG |
| 9-cis-epoxycarotenoid dioxygenase | sp|Q9LRM7|NCED6_ARATH | GSVIVT01029057001 in chr5 | 11,589,955 T AA | 11,589,955 T AA |
| 9-cis-epoxycarotenoid dioxygenase | sp|Q9LRM7|NCED6_ARATH | GSVIVT01029057001 in chr5 | 11,589,956 T CY | 11,589,956 T CY |
| 9-cis-epoxycarotenoid dioxygenase | sp|Q9LRM7|NCED6_ARATH | GSVIVT01029057001 in chr5 | 11,590,009 G TK | 11,590,009 G TK |
| 9-cis-epoxycarotenoid dioxygenase | sp|Q9LRM7|NCED6_ARATH | GSVIVT01029057001 in chr5 | 11,590,035 C AM | 11,590,283 G AR |
| 9-cis-epoxycarotenoid dioxygenase | sp|Q9LRM7|NCED6_ARATH | GSVIVT01029057001 in chr5 | 11,590,697 C TY | 11,590,829 C TT |
| 9-cis-epoxycarotenoid dioxygenase | sp|Q9LRM7|NCED6_ARATH | GSVIVT01029057001 in chr5 | 11,590,698 G AR | — |
| 9-cis-epoxycarotenoid dioxygenase | sp|Q9LRM7|NCED6_ARATH | GSVIVT01029057001 in chr5 | 11,590,829 C TT | — |
| 9-cis-epoxycarotenoid dioxygenase | sp|Q9LRM7|NCED6_ARATH | GSVIVT01029057001 in chr5 | — | DEL15: from 11,591,007 to11,591,031 |
aThe functional annotation of genes.
bGenes and proteins ID.
cGene ID and chromosome position.
dChange occurred inSBC.
eChange occurred inSBBM. S/NS/Sv/F represents synonymous/non-synonymous/structure variation/frameshift variation.