FN2953-S Chr1 11390065 11390065 0 0 Insertion 1 upstream_gene_variant HET FN2953-S Chr1 13632947 13632948 0 0 Deletion 1 upstream_gene_variant HET FN2953-S Chr1 14291369 14291379 0 0 Deletion 10 3_prime_UTR_variant HET FN2953-S Chr1 15683389 15683389 0 0 Insertion 98 intron_variant HET FN2953-S Chr1 16939636 16939645 0 0 Deletion 9 disruptive_inframe_deletion HET LOC_Os01g30990 transposon protein, putative, unclassified FN2953-S Chr1 18744728 C-T 0 0 Single Base Substitution 0 INTERGENIC HET FN2953-S Chr1 19809425 19809447 0 0 Deletion 22 upstream_gene_variant HET FN2953-S Chr1 27436600 27436601 0 0 Deletion 1 upstream_gene_variant HET FN2953-S Chr1 35974726 35974726 0 0 Insertion 5 upstream_gene_variant HET FN2953-S Chr1 40969287 G-T 0 0 Single Base Substitution 0 INTRON HET FN2953-S Chr1 43264101 43264108 0 0 Deletion 7 downstream_gene_variant HET FN2953-S Chr1 4354068 T-C 0 0 Single Base Substitution 0 INTRON HET FN2953-S Chr1 9889000 C-A 0 0 Single Base Substitution 0 UTR_3_PRIME HOMO FN2953-S Chr10 11149694 Chr9 9850710 0 Translocation 0 FN2953-S Chr10 1255092 1255093 0 0 Deletion 1 upstream_gene_variant HET FN2953-S Chr10 15056605 15056605 0 0 Insertion 1 upstream_gene_variant HET FN2953-S Chr10 15151619 15151619 0 0 Insertion 23 frameshift_variant&stop_gained HET LOC_Os10g29090 retrotransposon protein, putative, unclassified, expressed FN2953-S Chr10 22045490 G-C 0 0 Single Base Substitution 0 INTERGENIC HOMO FN2953-S Chr10 3209977 3209977 0 0 Insertion 1 upstream_gene_variant HET FN2953-S Chr10 5525714 5525719 0 0 Deletion 5 upstream_gene_variant HET FN2953-S Chr10 5527876 5527877 0 0 Deletion 1 upstream_gene_variant HET FN2953-S Chr10 7047390 Chr1 36582409 0 Translocation 0 FN2953-S Chr10 749754 749754 0 0 Insertion 1 frameshift_variant HET LOC_Os10g02180 retrotransposon protein, putative, unclassified FN2953-S Chr10 7669829 7669829 0 0 Insertion 47 upstream_gene_variant HET FN2953-S Chr10 8724646 8724646 0 0 Insertion 1 upstream_gene_variant HET FN2953-S Chr11 12004248 Chr10 2306195 0 Translocation 0 FN2953-S Chr11 14447008 14447009 0 0 Deletion 1 downstream_gene_variant HET FN2953-S Chr11 16724643 16724644 0 0 Deletion 1 upstream_gene_variant HET FN2953-S Chr11 18148243 Chr6 6320469 0 Translocation 0 FN2953-S Chr11 18250795 Chr1 26330533 0 Translocation 0 FN2953-S Chr11 19662770 G-T 0 0 Single Base Substitution 0 NON_SYNONYMOUS_CODING HET LOC_Os11g33260 retrotransposon protein, putative, unclassified, expressed FN2953-S Chr11 19662771 C-T 0 0 Single Base Substitution 0 NON_SYNONYMOUS_CODING HET LOC_Os11g33260 retrotransposon protein, putative, unclassified, expressed FN2953-S Chr11 20281824 Chr2 13966343 0 Translocation 0 LOC_Os02g24100 expressed protein FN2953-S Chr11 20473362 A-G 0 0 Single Base Substitution 0 INTERGENIC HET FN2953-S Chr11 20479001 20582000 0 0 Deletion 102999 LOC_Os11g34960 expressed protein FN2953-S Chr11 20479001 20582000 0 0 Deletion 102999 LOC_Os11g34970 NB-ARC domain containing protein, expressed FN2953-S Chr11 20479001 20582000 0 0 Deletion 102999 LOC_Os11g34980 expressed protein FN2953-S Chr11 20479001 20582000 0 0 Deletion 102999 LOC_Os11g34990 DEFL79 - Defensin and Defensin-like DEFL family FN2953-S Chr11 20479001 20582000 0 0 Deletion 102999 LOC_Os11g35000 expressed protein FN2953-S Chr11 20479001 20582000 0 0 Deletion 102999 LOC_Os11g35020 yippee zinc-binding protein, putative, expressed FN2953-S Chr11 20479001 20582000 0 0 Deletion 102999 LOC_Os11g35030 growth regulating factor protein, putative, expressed FN2953-S Chr11 20479001 20582000 0 0 Deletion 102999 LOC_Os11g35040 aminotransferase, classes I and II, domain containing protein, expressed FN2953-S Chr11 20479001 20582000 0 0 Deletion 102999 LOC_Os11g35050 expressed protein FN2953-S Chr11 20479001 20582000 0 0 Deletion 102999 LOC_Os11g35060 agenet domain containing protein, expressed FN2953-S Chr11 20479001 20582000 0 0 Deletion 102999 LOC_Os11g35070 expressed protein FN2953-S Chr11 20479001 20582000 0 0 Deletion 102999 LOC_Os11g35080 expressed protein FN2953-S Chr11 20479001 20582000 0 0 Deletion 102999 LOC_Os11g35090 kinesin motor domain containing protein, putative, expressed FN2953-S Chr11 20479001 20582000 0 0 Deletion 102999 LOC_Os11g35100 conserved hypothetical protein FN2953-S Chr11 20479001 20582000 0 0 Deletion 102999 LOC_Os11g35520 transposon protein, putative, CACTA, En/Spm sub-class, expressed FN2953-S Chr11 20481894 20813279 0 0 Inversion 331385 FN2953-S Chr11 21228297 21228297 0 0 Insertion 1 downstream_gene_variant HET FN2953-S Chr11 21578809 C-A 0 0 Single Base Substitution 0 INTERGENIC HET FN2953-S Chr11 22525106 22525107 0 0 Deletion 1 intron_variant HET FN2953-S Chr11 24445386 Chr4 29686988 0 Translocation 0 LOC_Os04g49790 retrotransposon protein, putative, Ty1-copia subclass, expressed FN2953-S Chr11 24445386 Chr4 29686988 0 Translocation 0 LOC_Os11g40860 retrotransposon protein, putative, unclassified, expressed FN2953-S Chr11 27293985 27293986 0 0 Deletion 1 downstream_gene_variant HET FN2953-S Chr11 8360747 G-A 0 0 Single Base Substitution 0 INTERGENIC HET FN2953-S Chr11 8717928 T-A 0 0 Single Base Substitution 0 INTERGENIC HET FN2953-S Chr11 9268246 9268250 0 0 Deletion 4 downstream_gene_variant HET FN2953-S Chr12 11216461 C-T 0 0 Single Base Substitution 0 INTERGENIC HET FN2953-S Chr12 11421780 Chr1 42198377 0 Translocation 0 FN2953-S Chr12 11422019 Chr1 42198373 0 Translocation 0 FN2953-S Chr12 11840819 11840819 0 0 Insertion 46 upstream_gene_variant HET FN2953-S Chr12 12333270 12333273 0 0 Deletion 3 upstream_gene_variant HET FN2953-S Chr12 14426298 14426298 0 0 Insertion 2 upstream_gene_variant HET FN2953-S Chr12 14852262 14852281 0 0 Deletion 19 upstream_gene_variant HET FN2953-S Chr12 15598351 15598365 0 0 Deletion 14 upstream_gene_variant HET FN2953-S Chr12 16231854 16231854 0 0 Insertion 1 upstream_gene_variant HET FN2953-S Chr12 17996187 17996188 0 0 Deletion 1 frameshift_variant HET LOC_Os12g30050 transposon protein, putative, unclassified, expressed FN2953-S Chr12 20240099 20240100 0 0 Deletion 1 downstream_gene_variant HET FN2953-S Chr12 2117055 2117056 0 0 Deletion 1 frameshift_variant HET LOC_Os12g04920 GRF zinc finger family protein FN2953-S Chr12 22111606 22111609 0 0 Deletion 3 intergenic_region HET FN2953-S Chr12 22805945 22805962 0 0 Deletion 17 upstream_gene_variant HET FN2953-S Chr12 23764592 23764592 0 0 Insertion 93 upstream_gene_variant HET FN2953-S Chr12 4584502 4584502 0 0 Insertion 6 intergenic_region HET FN2953-S Chr12 5156788 5156788 0 0 Insertion 2 intron_variant HET FN2953-S Chr2 11908506 11908506 0 0 Insertion 1 upstream_gene_variant HET FN2953-S Chr2 13728134 13728134 0 0 Insertion 1 intergenic_region HET FN2953-S Chr2 14519494 14519495 0 0 Deletion 1 intron_variant HET FN2953-S Chr2 15666557 15666558 0 0 Deletion 1 upstream_gene_variant HET FN2953-S Chr2 22168813 C-T 0 0 Single Base Substitution 0 INTERGENIC HOMO FN2953-S Chr2 22383688 T-C 0 0 Single Base Substitution 0 NON_SYNONYMOUS_CODING HOMO LOC_Os02g37050 phosphatidylinositolglycan class N family protein, expressed FN2953-S Chr2 22614136 22614148 0 0 Deletion 12 upstream_gene_variant HET FN2953-S Chr2 30370446 C-T 0 0 Single Base Substitution 0 INTERGENIC HOMO FN2953-S Chr2 32042403 A-T 0 0 Single Base Substitution 0 INTRON HOMO FN2953-S Chr2 354839 354840 0 0 Deletion 1 upstream_gene_variant HET FN2953-S Chr2 7642001 7829000 0 0 Deletion 186999 LOC_Os02g14020 expressed protein FN2953-S Chr2 7642001 7829000 0 0 Deletion 186999 LOC_Os02g14030 hypothetical protein FN2953-S Chr2 7642001 7829000 0 0 Deletion 186999 LOC_Os02g14040 retrotransposon protein, putative, unclassified FN2953-S Chr2 7642001 7829000 0 0 Deletion 186999 LOC_Os02g14059 ribosomal protein L5, putative, expressed FN2953-S Chr2 7642001 7829000 0 0 Deletion 186999 LOC_Os02g14080 expressed protein FN2953-S Chr2 7642001 7829000 0 0 Deletion 186999 LOC_Os02g14090 berberine and berberine like domain containing protein, expressed FN2953-S Chr2 7642001 7829000 0 0 Deletion 186999 LOC_Os02g14100 retrotransposon protein, putative, unclassified, expressed FN2953-S Chr2 7642001 7829000 0 0 Deletion 186999 LOC_Os02g14110 aminotransferase, classes I and II, domain containing protein, expressed FN2953-S Chr2 7642001 7829000 0 0 Deletion 186999 LOC_Os02g14120 BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 precursor, putative, expressed FN2953-S Chr2 7642001 7829000 0 0 Deletion 186999 LOC_Os02g14130 CGMC_GSK.4 - CGMC includes CDA, MAPK, GSK3, and CLKC kinases, expressed FN2953-S Chr2 7642001 7829000 0 0 Deletion 186999 LOC_Os02g14140 cytokinin inducible protein, putative, expressed FN2953-S Chr2 7642001 7829000 0 0 Deletion 186999 LOC_Os02g14150 transposon protein, putative, unclassified, expressed FN2953-S Chr2 7642001 7829000 0 0 Deletion 186999 LOC_Os02g14160 peroxidase precursor, putative, expressed FN2953-S Chr2 7642001 7829000 0 0 Deletion 186999 LOC_Os02g14170 peroxidase precursor, putative, expressed FN2953-S Chr2 7642001 7829000 0 0 Deletion 186999 LOC_Os02g14180 peroxidase precursor, putative, expressed FN2953-S Chr2 7642001 7829000 0 0 Deletion 186999 LOC_Os02g14190 spermidine synthase, putative, expressed FN2953-S Chr2 7642001 7829000 0 0 Deletion 186999 LOC_Os02g14210 retrotransposon protein, putative, unclassified, expressed FN2953-S Chr2 7642001 7829000 0 0 Deletion 186999 LOC_Os02g14220 retrotransposon protein, putative, unclassified, expressed FN2953-S Chr2 7642001 7829000 0 0 Deletion 186999 LOC_Os02g14230 expressed protein FN2953-S Chr2 7642001 7829000 0 0 Deletion 186999 LOC_Os02g14240 hypothetical protein FN2953-S Chr2 7642001 7829000 0 0 Deletion 186999 LOC_Os02g14250 transposon protein, putative, unclassified, expressed FN2953-S Chr2 7642001 7829000 0 0 Deletion 186999 LOC_Os02g14260 retrotransposon protein, putative, unclassified, expressed FN2953-S Chr2 7642001 7829000 0 0 Deletion 186999 LOC_Os02g15100 zinc finger, C3HC4 type domain containing protein, expressed FN2953-S Chr3 13532182 13532182 0 0 Insertion 1 downstream_gene_variant HET FN2953-S Chr3 15859712 15859714 0 0 Deletion 2 upstream_gene_variant HET FN2953-S Chr3 21462544 21462545 0 0 Deletion 1 upstream_gene_variant HET FN2953-S Chr3 24089602 24089602 0 0 Insertion 2 upstream_gene_variant HET FN2953-S Chr3 24152622 A-T 0 0 Single Base Substitution 0 INTERGENIC HET FN2953-S Chr3 29958279 T-C 0 0 Single Base Substitution 0 NON_SYNONYMOUS_CODING HET LOC_Os03g52180 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, putative, expressed FN2953-S Chr3 32039583 Chr2 5535368 0 Translocation 0 FN2953-S Chr3 34749902 34749904 0 0 Deletion 2 upstream_gene_variant HET FN2953-S Chr3 7071576 7071577 0 0 Deletion 1 INTERGENIC HOMO FN2953-S Chr4 10481899 10481900 0 0 Deletion 1 intron_variant HET FN2953-S Chr4 13620641 G-T 0 0 Single Base Substitution 0 INTRON HET FN2953-S Chr4 13744715 13744727 0 0 Deletion 12 disruptive_inframe_deletion HET LOC_Os04g24060 retrotransposon protein, putative, Ty3-gypsy subclass, expressed FN2953-S Chr4 19682000 A-T 0 0 Single Base Substitution 0 UTR_3_PRIME HET FN2953-S Chr4 24450085 24450085 0 0 Insertion 1 intergenic_region HET FN2953-S Chr4 25905146 C-T 0 0 Single Base Substitution 0 INTERGENIC HET FN2953-S Chr4 26164892 26164892 0 0 Insertion 2 upstream_gene_variant HET FN2953-S Chr4 26413536 26413537 0 0 Deletion 1 downstream_gene_variant HET FN2953-S Chr4 2857915 2857916 0 0 Deletion 1 upstream_gene_variant HET FN2953-S Chr4 28947850 28947856 0 0 Deletion 6 upstream_gene_variant HET FN2953-S Chr4 3248445 3248446 0 0 Deletion 1 intergenic_region HET FN2953-S Chr4 3332318 3332318 0 0 Insertion 2 downstream_gene_variant HET FN2953-S Chr4 33350031 33350031 0 0 Insertion 1 upstream_gene_variant HET FN2953-S Chr4 5510393 5510411 0 0 Deletion 18 disruptive_inframe_deletion HET LOC_Os04g10190 retrotransposon protein, putative, Ty3-gypsy subclass, expressed FN2953-S Chr4 7551233 7551233 0 0 Insertion 103 downstream_gene_variant HET FN2953-S Chr4 8027137 8027137 0 0 Insertion 1 upstream_gene_variant HET FN2953-S Chr4 8576183 8576183 0 0 Insertion 3 upstream_gene_variant HET FN2953-S Chr4 8745059 8745059 0 0 Insertion 6 upstream_gene_variant HET FN2953-S Chr4 9253948 9253949 0 0 Deletion 1 upstream_gene_variant HET FN2953-S Chr4 9840807 9840807 0 0 Insertion 1 upstream_gene_variant HET FN2953-S Chr5 11556600 11556600 0 0 Insertion 1 upstream_gene_variant HET FN2953-S Chr5 20358272 20358273 0 0 Deletion 1 upstream_gene_variant HET FN2953-S Chr5 24373217 24373239 0 0 Deletion 22 INTRON HET FN2953-S Chr5 27014414 27014414 0 0 Insertion 1 upstream_gene_variant HET FN2953-S Chr5 29411363 29411363 0 0 Insertion 42 upstream_gene_variant HET FN2953-S Chr5 29536988 29536988 0 0 Insertion 3 upstream_gene_variant HET FN2953-S Chr5 29849533 29849887 0 0 Deletion 354 intergenic_region HET FN2953-S Chr5 4919066 4919066 0 0 Insertion 1 intron_variant HET FN2953-S Chr5 9930890 9930890 0 0 Insertion 2 upstream_gene_variant HET FN2953-S Chr6 15173825 C-T 0 0 Single Base Substitution 0 INTERGENIC HET FN2953-S Chr6 19641970 19641971 0 0 Deletion 1 splice_region_variant&intron_variant HET FN2953-S Chr6 22187968 22187968 0 0 Insertion 1 upstream_gene_variant HET FN2953-S Chr6 22679281 22679281 0 0 Insertion 93 downstream_gene_variant HET FN2953-S Chr6 23392560 Chr2 20261349 0 Translocation 0 FN2953-S Chr6 311478 311489 0 0 Deletion 11 upstream_gene_variant HET FN2953-S Chr6 9104038 9104040 0 0 Deletion 2 downstream_gene_variant HET FN2953-S Chr7 12249760 12249761 0 0 Deletion 1 intergenic_region HET FN2953-S Chr7 12494071 T-C 0 0 Single Base Substitution 0 INTERGENIC HOMO FN2953-S Chr7 13577283 13577283 0 0 Insertion 1 downstream_gene_variant HET FN2953-S Chr7 19147967 19888647 0 0 Inversion 740680 FN2953-S Chr7 19888661 Chr6 1555753 0 Translocation 0 FN2953-S Chr7 19888811 Chr6 1555752 0 Translocation 0 FN2953-S Chr7 20707332 Chr6 518657 0 Translocation 0 FN2953-S Chr7 27613461 27613461 0 0 Insertion 2 upstream_gene_variant HET FN2953-S Chr8 12971336 G-C 0 0 Single Base Substitution 0 INTRON HOMO FN2953-S Chr8 1441919 1441920 0 0 Deletion 1 frameshift_variant&stop_lost&splice_region_variant HET LOC_Os08g03140 retrotransposon protein, putative, Ty3-gypsy subclass FN2953-S Chr8 15302134 15302138 0 0 Deletion 4 upstream_gene_variant HET FN2953-S Chr8 15935206 Chr7 6242593 0 Translocation 0 FN2953-S Chr8 16867262 16867262 0 0 Insertion 1 upstream_gene_variant HET FN2953-S Chr8 17046460 17046461 0 0 Deletion 1 upstream_gene_variant HET FN2953-S Chr8 18970871 18970895 0 0 Deletion 24 disruptive_inframe_deletion HET LOC_Os08g30750 transposon protein, putative, CACTA, En/Spm sub-class, expressed FN2953-S Chr8 24581001 24647000 0 0 Deletion 65999 LOC_Os08g38900 caffeoyl-CoA O-methyltransferase, putative, expressed FN2953-S Chr8 24581001 24647000 0 0 Deletion 65999 LOC_Os08g38910 caffeoyl-CoA O-methyltransferase, putative, expressed FN2953-S Chr8 24581001 24647000 0 0 Deletion 65999 LOC_Os08g38920 caffeoyl-CoA O-methyltransferase, putative, expressed FN2953-S Chr8 24581001 24647000 0 0 Deletion 65999 LOC_Os08g38930 retrotransposon protein, putative, Ty3-gypsy subclass FN2953-S Chr8 24581001 24647000 0 0 Deletion 65999 LOC_Os08g38940 retrotransposon protein, putative, Ty3-gypsy subclass, expressed FN2953-S Chr8 24581001 24647000 0 0 Deletion 65999 LOC_Os08g38950 expressed protein FN2953-S Chr8 24581001 24647000 0 0 Deletion 65999 LOC_Os08g38960 expressed protein FN2953-S Chr8 24581001 24647000 0 0 Deletion 65999 LOC_Os08g38970 transmembrane receptor, putative, expressed FN2953-S Chr8 24581001 24647000 0 0 Deletion 65999 LOC_Os08g38980 chloride transporter, chloride channel family, putative, expressed FN2953-S Chr8 24581001 24647000 0 0 Deletion 65999 LOC_Os08g38990 WRKY30, expressed FN2953-S Chr8 24581001 24647000 0 0 Deletion 65999 LOC_Os08g39160 formyl transferase, putative, expressed FN2953-S Chr8 24645782 Chr7 19888832 0 Translocation 0 FN2953-S Chr8 27201448 27201456 0 0 Deletion 8 upstream_gene_variant HET FN2953-S Chr8 4009896 Chr6 23504877 0 Translocation 0 FN2953-S Chr8 5509500 5509500 0 0 Insertion 1 downstream_gene_variant HET FN2953-S Chr8 5871009 5871012 0 0 Deletion 3 inframe_deletion HET LOC_Os08g10120 retrotransposon protein, putative, Ty1-copia subclass, expressed FN2953-S Chr8 6378823 6378824 0 0 Deletion 1 upstream_gene_variant HET FN2953-S Chr8 6395379 6395380 0 0 Deletion 1 upstream_gene_variant HET FN2953-S Chr8 6459106 6459106 0 0 Insertion 90 upstream_gene_variant HET FN2953-S Chr8 6945198 6945198 0 0 Insertion 1 upstream_gene_variant HET FN2953-S Chr8 6973635 6973635 0 0 Insertion 2 downstream_gene_variant HET FN2953-S Chr8 6973838 6973839 0 0 Deletion 1 downstream_gene_variant HET FN2953-S Chr8 8439030 8439031 0 0 Deletion 1 intron_variant HET FN2953-S Chr8 8740457 8740460 0 0 Deletion 3 upstream_gene_variant HET FN2953-S Chr9 12053404 12053404 0 0 Insertion 1 upstream_gene_variant HET FN2953-S Chr9 12953844 12953844 0 0 Insertion 5 intron_variant HET FN2953-S Chr9 13620982 Chr4 7872859 0 Translocation 0 FN2953-S Chr9 16373266 16373269 0 0 Deletion 3 downstream_gene_variant HET FN2953-S Chr9 21444277 21444278 0 0 Deletion 1 upstream_gene_variant HET FN2953-S Chr9 2858400 2858405 0 0 Deletion 5 upstream_gene_variant HET FN2953-S Chr9 4514786 4514786 0 0 Insertion 84 disruptive_inframe_insertion HET LOC_Os09g08630 retrotransposon protein, putative, unclassified, expressed FN2953-S Chr9 5190823 Chr6 8717945 0 Translocation 0 FN2953-S Chr9 7860427 7860466 0 0 Deletion 39 upstream_gene_variant HET FN2953-S Chr9 8131888 C-T 0 0 Single Base Substitution 0 INTERGENIC HET FN2953-S Chr9 8220863 C-T 0 0 Single Base Substitution 0 INTERGENIC HOMO FN2953-S Chr9 9845550 9845550 0 0 Insertion 1 upstream_gene_variant HET