~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~ Genome update of Brassica rapa ~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scaffold ----------------------------------------------------------------------30/08/2010 update from the original scaffolds assembled in BGI, scaffold000088 was split into two new scaffolds scaffold040552 and Scaffold040553 version 1.1 -------------------------------------------------------------------2010 scaffolds are anchored to the chromosomes with the lingkage maps version 1.2 -------------------------------------------------------------------20/11/2011 154 redundent gene IDs are rmoved from the total predicted gene set As listed below: #################################### # Bra000770 Bra000771 (removed) # # Bra001040 Bra001041 (removed) # # Bra001441 Bra001442 (removed) # # Bra001989 Bra001990 (removed) # # Bra002705 Bra002706 (removed) # # Bra003151 Bra003152 (removed) # # Bra003982 Bra003983 (removed) # # Bra004635 Bra004636 (removed) # # Bra004813 Bra004814 (removed) # # Bra004975 Bra004976 (removed) # # Bra005320 Bra005321 (removed) # # Bra006131 Bra006132 (removed) # # Bra006532 Bra006533 (removed) # # Bra006532 Bra006534 (removed) # # Bra006903 Bra006904 (removed) # # Bra007428 Bra007429 (removed) # # Bra007532 Bra007533 (removed) # # Bra008091 Bra008092 (removed) # # Bra008133 Bra008134 (removed) # # Bra009810 Bra009811 (removed) # # Bra010019 Bra010020 (removed) # # Bra010300 Bra010301 (removed) # # Bra010707 Bra010708 (removed) # # Bra010707 Bra010709 (removed) # # Bra010707 Bra010710 (removed) # # Bra010938 Bra010939 (removed) # # Bra011471 Bra011472 (removed) # # Bra011496 Bra011497 (removed) # # Bra011498 Bra011499 (removed) # # Bra011891 Bra011892 (removed) # # Bra012000 Bra012001 (removed) # # Bra012159 Bra012160 (removed) # # Bra013986 Bra013987 (removed) # # Bra013986 Bra013988 (removed) # # Bra014063 Bra014064 (removed) # # Bra014146 Bra014147 (removed) # # Bra014202 Bra014204 (removed) # # Bra014217 Bra014218 (removed) # # Bra014268 Bra014269 (removed) # # Bra014376 Bra014377 (removed) # # Bra014641 Bra014642 (removed) # # Bra014769 Bra014770 (removed) # # Bra014804 Bra014805 (removed) # # Bra014804 Bra014806 (removed) # # Bra014918 Bra014919 (removed) # # Bra015213 Bra015214 (removed) # # Bra015565 Bra015566 (removed) # # Bra015601 Bra015602 (removed) # # Bra015701 Bra015702 (removed) # # Bra015759 Bra015760 (removed) # # Bra016904 Bra016905 (removed) # # Bra016998 Bra016999 (removed) # # Bra017036 Bra017037 (removed) # # Bra017575 Bra017576 (removed) # # Bra017649 Bra017650 (removed) # # Bra017694 Bra017695 (removed) # # Bra017694 Bra017696 (removed) # # Bra017820 Bra017821 (removed) # # Bra017833 Bra017834 (removed) # # Bra018154 Bra018155 (removed) # # Bra018229 Bra018230 (removed) # # Bra018229 Bra018231 (removed) # # Bra018646 Bra018647 (removed) # # Bra018648 Bra018649 (removed) # # Bra020421 Bra020422 (removed) # # Bra020942 Bra020943 (removed) # # Bra020942 Bra020944 (removed) # # Bra021704 Bra021705 (removed) # # Bra022084 Bra022085 (removed) # # Bra022456 Bra022457 (removed) # # Bra022626 Bra022627 (removed) # # Bra022628 Bra022629 (removed) # # Bra022955 Bra022956 (removed) # # Bra023303 Bra023304 (removed) # # Bra023355 Bra023356 (removed) # # Bra023744 Bra023745 (removed) # # Bra024460 Bra024461 (removed) # # Bra024763 Bra024764 (removed) # # Bra025581 Bra025582 (removed) # # Bra025679 Bra025680 (removed) # # Bra025810 Bra025811 (removed) # # Bra026479 Bra026480 (removed) # # Bra027112 Bra027113 (removed) # # Bra027614 Bra027615 (removed) # # Bra027786 Bra027787 (removed) # # Bra027991 Bra027992 (removed) # # Bra028816 Bra028817 (removed) # # Bra029077 Bra029078 (removed) # # Bra029568 Bra029569 (removed) # # Bra029708 Bra029709 (removed) # # Bra029736 Bra029737 (removed) # # Bra030775 Bra030776 (removed) # # Bra031098 Bra031099 (removed) # # Bra031098 Bra031100 (removed) # # Bra031155 Bra031156 (removed) # # Bra031341 Bra031342 (removed) # # Bra031395 Bra031396 (removed) # # Bra031414 Bra031415 (removed) # # Bra031509 Bra031510 (removed) # # Bra031565 Bra031566 (removed) # # Bra031729 Bra031730 (removed) # # Bra031791 Bra031792 (removed) # # Bra032126 Bra032127 (removed) # # Bra032593 Bra032594 (removed) # # Bra033041 Bra033042 (removed) # # Bra033233 Bra033234 (removed) # # Bra033405 Bra033406 (removed) # # Bra033447 Bra033448 (removed) # # Bra033607 Bra033608 (removed) # # Bra033607 Bra033609 (removed) # # Bra033688 Bra033689 (removed) # # Bra033728 Bra033729 (removed) # # Bra033780 Bra033781 (removed) # # Bra034028 Bra034029 (removed) # # Bra034508 Bra034509 (removed) # # Bra034563 Bra034564 (removed) # # Bra034788 Bra034789 (removed) # # Bra034997 Bra034998 (removed) # # Bra035196 Bra035197 (removed) # # Bra035266 Bra035267 (removed) # # Bra035403 Bra035404 (removed) # # Bra036062 Bra036064 (removed) # # Bra036062 Bra036065 (removed) # # Bra036062 Bra036066 (removed) # # Bra036062 Bra036067 (removed) # # Bra036187 Bra036188 (removed) # # Bra036189 Bra036190 (removed) # # Bra036483 Bra036484 (removed) # # Bra036483 Bra036485 (removed) # # Bra036486 Bra036487 (removed) # # Bra036643 Bra036644 (removed) # # Bra037024 Bra037025 (removed) # # Bra037317 Bra037318 (removed) # # Bra037546 Bra037547 (removed) # # Bra037839 Bra037840 (removed) # # Bra038138 Bra038139 (removed) # # Bra038243 Bra038244 (removed) # # Bra038596 Bra038597 (removed) # # Bra038730 Bra038731 (removed) # # Bra038730 Bra038732 (removed) # # Bra038751 Bra038752 (removed) # # Bra038927 Bra038928 (removed) # # Bra039079 Bra039080 (removed) # # Bra039257 Bra039258 (removed) # # Bra039536 Bra039537 (removed) # # Bra039785 Bra039786 (removed) # # Bra039824 Bra039825 (removed) # # Bra040035 Bra040036 (removed) # # Bra040082 Bra040083 (removed) # # Bra040082 Bra040084 (removed) # # Bra040125 Bra040126 (removed) # # Bra040664 Bra040665 (removed) # # Bra041087 Bra041088 (removed) # # Bra041156 Bra041157 (removed) # #################################### version 1.5 -------------------------------------------------------------------28/5/2013 B. rapa genome V1.5 update 17 Scaffolds were split in V1.5, and some Scaffolds were resorted. Below is the new order of Scaffolds in 10 chromosomes of B. rapa: ******************B. rapa genome V1.5******************** Chr V1.5 Scaf ID BGI old ID Start Stop Orientation A01 Scaffold000011 Scaffold000011 1 4370687 R A01 Scaffold000190 Scaffold000190 1 178629 F A01 Scaffold000014 Scaffold000014 1 4138946 F A01 Scaffold000176 Scaffold000176 1 250372 * A01 Scaffold040554 Scaffold000051 1 1402290 R A01 Scaffold000188 Scaffold000188 1 191904 R A01 Scaffold000147 Scaffold000147 1 416879 R A01 Scaffold040553 Scaffold000088 574261 1083232 R A01 Scaffold000168 Scaffold000168 1 293885 F A01 Scaffold000236 Scaffold000236 1 62591 F A01 Scaffold000122 Scaffold000122 1 555495 R A01 Scaffold000131 Scaffold000131 1 529647 F A01 Scaffold000090 Scaffold000090 1 1025155 R A01 Scaffold000068 Scaffold000068 1 1334944 F A01 Scaffold000154 Scaffold000154 1 381115 F A01 Scaffold000105 Scaffold000105 1 763845 R A01 Scaffold000076 Scaffold000076 1 1263621 R A01 Scaffold040557 Scaffold000061 703009 1398616 R A01 Scaffold000042 Scaffold000042 1 1942182 F A01 Scaffold000142 Scaffold000142 1 435940 R A01 Scaffold000130 Scaffold000130 1 529974 F A01 Scaffold000033 Scaffold000033 1 2057823 R A01 Scaffold040564 Scaffold000034 1311619 2057289 R A01 Scaffold000151 Scaffold000151 1 401826 R A01 Scaffold040565 Scaffold000093 1 656133 R A01 Scaffold000186 Scaffold000186 1 201898 R A01 Scaffold000200 Scaffold000200 1 116650 R A01 Scaffold000195 Scaffold000195 1 142335 R A01 Scaffold000192 Scaffold000192 1 161858 F A01 Scaffold000189 Scaffold000189 1 179792 F A01 Scaffold040585 Scaffold000117 1 173523 F A01 Scaffold040559 Scaffold000034 717121 888333 F A01 Scaffold040561 Scaffold000034 984524 1101594 F A01 Scaffold040563 Scaffold000034 1174806 1311518 F A01 Scaffold000214 Scaffold000214 1 85841 F A02 Scaffold000063 Scaffold000063 1 1382322 R A02 Scaffold040568 Scaffold000062 1042408 1383848 R A02 Scaffold000041 Scaffold000041 1 1959666 F A02 Scaffold000030 Scaffold000030 1 2201279 F A02 Scaffold000107 Scaffold000107 1 716987 R A02 Scaffold000038 Scaffold000038 1 1975999 R A02 Scaffold000175 Scaffold000175 1 252121 F A02 Scaffold000226 Scaffold000226 1 71051 R A02 Scaffold000092 Scaffold000092 1 999131 R A02 Scaffold000144 Scaffold000144 1 431563 R A02 Scaffold000007 Scaffold000007 1 5225363 F A02 Scaffold040576 Scaffold000025 1823277 2470021 R A02 Scaffold000086 Scaffold000086 1 1135645 * A02 Scaffold000036 Scaffold000036 1 1987479 * A02 Scaffold000052 Scaffold000052 1 1608252 R A02 Scaffold000115 Scaffold000115 1 604939 R A02 Scaffold000085 Scaffold000085 1 1141961 F A02 Scaffold040569 Scaffold000031 1 1917249 R A02 Scaffold000065 Scaffold000065 1 1376758 R A02 Scaffold040571 Scaffold000078 1 868875 R A03 Scaffold000005 Scaffold000005 1 5419876 F A03 Scaffold000064 Scaffold000064 1 1378998 F A03 Scaffold000039 Scaffold000039 1 1971137 F A03 Scaffold001086 Scaffold001086 1 1248 * A03 Scaffold000001 Scaffold000001 1 10813983 F A03 Scaffold000013 Scaffold000013 1 4326260 R A03 Scaffold000152 Scaffold000152 1 401379 R A03 Scaffold000027 Scaffold000027 1 2416075 R A03 Scaffold000043 Scaffold000043 1 1939692 R A03 Scaffold000124 Scaffold000124 1 553162 R A03 Scaffold000023 Scaffold000023 1 2493878 F A04 Scaffold000205 Scaffold000205 1 106693 R A04 Scaffold000204 Scaffold000204 1 107120 R A04 Scaffold000016 Scaffold000016 1 3486918 F A04 Scaffold000177 Scaffold000177 1 250113 R A04 Scaffold000235 Scaffold000235 1 63582 R A04 Scaffold040579 Scaffold000029 1 314969 F A04 Scaffold040552 Scaffold000088 1 573412 F A04 Scaffold000083 Scaffold000083 1 1155924 R A04 Scaffold000060 Scaffold000060 1 1407754 F A04 Scaffold000048 Scaffold000048 1 1689678 R A04 Scaffold000070 Scaffold000070 1 1324702 R A04 Scaffold000079 Scaffold000079 1 1216605 R A04 Scaffold000094 Scaffold000094 1 991801 F A04 Scaffold040573 Scaffold000108 1 419196 R A04 Scaffold000184 Scaffold000184 1 213376 * A04 Scaffold000035 Scaffold000035 1 2033593 F A04 Scaffold000021 Scaffold000021 1 2574763 R A04 Scaffold000132 Scaffold000132 1 513311 R A04 Scaffold000197 Scaffold000197 1 131826 R A04 Scaffold000163 Scaffold000163 1 323206 R A04 Scaffold000210 Scaffold000210 1 92046 R A04 Scaffold040560 Scaffold000034 888434 984423 F A04 Scaffold040562 Scaffold000034 1101695 1174705 F A05 Scaffold000004 Scaffold000004 1 6818689 F A05 Scaffold040575 Scaffold000025 1 1823176 F A05 Scaffold000166 Scaffold000166 1 308587 F A05 Scaffold000125 Scaffold000125 1 550705 F A05 Scaffold040558 Scaffold000034 1 717020 F A05 Scaffold000139 Scaffold000139 1 452656 R A05 Scaffold000071 Scaffold000071 1 1301422 F A05 Scaffold000080 Scaffold000080 1 1216075 R A05 Scaffold000231 Scaffold000231 1 67379 * A05 Scaffold000202 Scaffold000202 1 115232 * A05 Scaffold000095 Scaffold000095 1 970325 F A05 Scaffold040584 Scaffold000009 3837991 4668752 R A05 Scaffold000091 Scaffold000091 1 1022021 F A05 Scaffold000275 Scaffold000275 1 38604 F A05 Scaffold000183 Scaffold000183 1 214468 R A05 Scaffold040577 Scaffold000075 1 1005126 R A05 Scaffold000109 Scaffold000109 1 666149 F A05 Scaffold000037 Scaffold000037 1 1983962 R A05 Scaffold000055 Scaffold000055 1 1457941 F A05 Scaffold000098 Scaffold000098 1 914953 F A05 Scaffold000067 Scaffold000067 1 1362032 R A05 Scaffold040570 Scaffold000031 1917350 2152628 F A05 Scaffold000165 Scaffold000165 1 313349 F A05 Scaffold040572 Scaffold000078 868976 1239337 F A05 Scaffold000222 Scaffold000222 1 75581 R A05 Scaffold000160 Scaffold000160 1 346677 R A06 Scaffold000137 Scaffold000137 1 460541 R A06 Scaffold000173 Scaffold000173 1 276235 R A06 Scaffold000026 Scaffold000026 1 2456282 R A06 Scaffold040580 Scaffold000029 315070 2294431 R A06 Scaffold000050 Scaffold000050 1 1640734 R A06 Scaffold000049 Scaffold000049 1 1643662 F A06 Scaffold000024 Scaffold000024 1 2486518 F A06 Scaffold000143 Scaffold000143 1 434198 F A06 Scaffold000028 Scaffold000028 1 2369083 F A06 Scaffold040582 Scaffold000009 2428632 3301456 F A06 Scaffold000150 Scaffold000150 1 403470 F A06 Scaffold000044 Scaffold000044 1 1904067 F A06 Scaffold040581 Scaffold000009 1 2428288 F A06 Scaffold040583 Scaffold000009 3301557 3837890 F A06 Scaffold000129 Scaffold000129 1 537490 F A06 Scaffold000047 Scaffold000047 1 1806105 R A06 Scaffold000046 Scaffold000046 1 1846652 F A06 Scaffold000089 Scaffold000089 1 1043522 R A07 Scaffold040586 Scaffold000117 173624 596576 R A07 Scaffold000158 Scaffold000158 1 359785 R A07 Scaffold000153 Scaffold000153 1 385962 R A07 Scaffold040597 Scaffold000059 1282189 1410856 F A07 Scaffold000171 Scaffold000171 1 281901 F A07 Scaffold000181 Scaffold000181 1 220824 R A07 Scaffold040591 Scaffold000002 1 1340624 R A07 Scaffold040589 Scaffold000018 1 877291 R A07 Scaffold000116 Scaffold000116 1 604765 * A07 Scaffold000017 Scaffold000017 1 3316254 R A07 Scaffold000069 Scaffold000069 1 1324989 R A07 Scaffold000012 Scaffold000012 1 4360253 R A07 Scaffold040567 Scaffold000062 1 1041412 F A07 Scaffold000003 Scaffold000003 1 7053424 F A07 Scaffold000019 Scaffold000019 1 3205366 R A07 Scaffold000101 Scaffold000101 1 876625 F A08 Scaffold000073 Scaffold000073 1 1297272 F A08 Scaffold000015 Scaffold000015 1 3682553 R A08 Scaffold000099 Scaffold000099 1 914790 R A08 Scaffold000198 Scaffold000198 1 122455 F A08 Scaffold000266 Scaffold000266 1 44249 F A08 Scaffold000179 Scaffold000179 1 240354 R A08 Scaffold000174 Scaffold000174 1 265934 R A08 Scaffold000138 Scaffold000138 1 457557 R A08 Scaffold000120 Scaffold000120 1 559574 R A08 Scaffold000106 Scaffold000106 1 739939 F A08 Scaffold000156 Scaffold000156 1 363423 F A08 Scaffold000146 Scaffold000146 1 427917 R A08 Scaffold000032 Scaffold000032 1 2073141 R A08 Scaffold000276 Scaffold000276 1 38480 * A08 Scaffold000097 Scaffold000097 1 936682 R A08 Scaffold000187 Scaffold000187 1 194640 R A08 Scaffold000010 Scaffold000010 1 4416462 F A08 Scaffold000020 Scaffold000020 1 2662187 F A08 Scaffold000072 Scaffold000072 1 1299336 R A09 Scaffold000128 Scaffold000128 1 540196 F A09 Scaffold000114 Scaffold000114 1 606580 R A09 Scaffold040566 Scaffold000093 656234 992749 F A09 Scaffold000159 Scaffold000159 1 357979 R A09 Scaffold000113 Scaffold000113 1 616177 R A09 Scaffold000118 Scaffold000118 1 594701 R A09 Scaffold040555 Scaffold000051 1402291 1633677 F A09 Scaffold000110 Scaffold000110 1 663065 R A09 Scaffold000133 Scaffold000133 1 503233 F A09 Scaffold000126 Scaffold000126 1 545451 F A09 Scaffold000127 Scaffold000127 1 544056 R A09 Scaffold040588 Scaffold000148 212145 409194 F A09 Scaffold000119 Scaffold000119 1 587715 R A09 Scaffold000481 Scaffold000481 1 9588 * A09 Scaffold000057 Scaffold000057 1 1431623 R A09 Scaffold000054 Scaffold000054 1 1517392 F A09 Scaffold000058 Scaffold000058 1 1417104 F A09 Scaffold000056 Scaffold000056 1 1452355 F A09 Scaffold000022 Scaffold000022 1 2561885 R A09 Scaffold000134 Scaffold000134 1 480632 F A09 Scaffold000145 Scaffold000145 1 430878 R A09 Scaffold000135 Scaffold000135 1 472823 F A09 Scaffold000102 Scaffold000102 1 857705 R A09 Scaffold000066 Scaffold000066 1 1372560 F A09 Scaffold040596 Scaffold000059 1 1282088 R A09 Scaffold000040 Scaffold000040 1 1960303 R A09 Scaffold000081 Scaffold000081 1 1190370 R A09 Scaffold000084 Scaffold000084 1 1148610 R A09 Scaffold000045 Scaffold000045 1 1881595 R A09 Scaffold040578 Scaffold000075 1005528 1273006 R A09 Scaffold000112 Scaffold000112 1 624823 F A09 Scaffold000393 Scaffold000393 1 15282 * A09 Scaffold000121 Scaffold000121 1 555930 R A09 Scaffold000006 Scaffold000006 1 5402024 F A09 Scaffold000161 Scaffold000161 1 346497 R A09 Scaffold000182 Scaffold000182 1 217179 R A09 Scaffold040587 Scaffold000148 1 212144 F A09 Scaffold000074 Scaffold000074 1 1278161 R A09 Scaffold000053 Scaffold000053 1 1546948 F A09 Scaffold000077 Scaffold000077 1 1257653 R A09 Scaffold000082 Scaffold000082 1 1169063 F A10 Scaffold040590 Scaffold000018 882155 3291834 R A10 Scaffold000087 Scaffold000087 1 1100015 R A10 Scaffold000136 Scaffold000136 1 472737 R A10 Scaffold040574 Scaffold000108 419197 708920 F A10 Scaffold040556 Scaffold000061 1 703008 F A10 Scaffold040592 Scaffold000002 1340826 7864415 R A10 Scaffold000227 Scaffold000227 1 70316 * A10 Scaffold040593 Scaffold000008 1 2385745 F A10 Scaffold040594 Scaffold000008 2389086 3687316 R A10 Scaffold040595 Scaffold000008 3688085 4795218 F ******************B. rapa genome V1.5********************