• Alignment Docs

This page documents the mapping summary of markers db dna sequences to genome sequences.

1. complete mapping: For genomes with new or updated assembly, need to map all the desired sequences in the markers db including those mapped before to an older version of the genome assembly
2. incremental mapping: For genomes whose assemblies stay unchanged from last build, need to do incremental mapping, ie, only mapping those new sequenced added to markers db since last release.

The following is the mapping statistics for each build

• Gramene34

• Glycine max (Glyma1.0): new genome



sequence set	total sequence Count	mapped sequence Count	mapping percentage
glycine mrna	13831	13791	99.71
other mrna	593687	221057	37.23
glycine est cluster	126396	124317	98.36
other est cluster	4483038	1666321	37.17
glycine est	1441966	1411772	97.91



• Oryza glaberrima: assembly updated to AGI1.1



sequence set	total sequence Count	mapped sequence Count	mapping percentage
oryza mrna	119100	105280	88.40
other mrna	488418	186891	38.26
oryza est cluster	414264	326764	78.88
other est cluster	4195170	1405502	33.05
oryza est	1343927	1168125	86.92
oryza gss	51225	38273	74.72
oryza microarray probe	142508	116798	81.96
oryza rflp	4298	3790	88.18
oryza overgo	461	369	80.04



• Chlamydomonas reinhardtii (ENA1): new genome



sequence set	total sequence Count	mapped sequence Count	mapping percentage
Chlamydomonas mrna	3643	3601	98.85
other mrna	603875	42322	7.01
Chlamydomonas est cluster	12862	10964	85.24
other est cluster	4596572	259046	5.64
Chlamydomonas est	52233	48544	92.94



• Selaginella moellendorffii (ENA1): new genome



sequence set	total sequence Count	mapped sequence Count	mapping percentage
Selaginella mrna	96	61	63.54
other mrna	607422	90122	14.84
Selaginella est cluster	237	237	100.00
other est cluster	4609197	567205	12.31
Selaginella est	97498	92429	94.80



• Oryza minutaBB (BAC.Sanger.1.1): assembly updated



sequence set	total sequence Count	mapped sequence Count	mapping percentage
oryza mrna	119100	7958	6.68
other mrna	488418	38141	7.81
oryza est cluster	414264	24208	5.84
other est cluster	4195170	302085	7.20
oryza est	1343927	97345	7.24
oryza gss	51225	1888	3.69
oryza microarray probe	142508	5833	4.09
oryza rflp	4298	286	6.65
oryza overgo	461	30	6.51



• Oryza minutaCC ((BAC.Sanger.1.1): assembly updated



sequence set	total sequence Count	mapped sequence Count	mapping percentage
oryza mrna	119100	7889	6.62
other mrna	488418	42900	8.78
oryza est cluster	414264	24767	5.98
other est cluster	4195170	333935	7.96
oryza est	1343927	103685	7.72
oryza gss	51225	1810	3.53
oryza microarray probe	142508	5866	4.12
oryza rflp	4298	312	7.26
oryza overgo	461	28	6.07



• Oryza officinalis ((BAC.Sanger.1.1) : assembly updated



sequence set	total sequence Count	mapped sequence Count	mapping percentage
oryza mrna	119100	8399	7.05
other mrna	488418	44373	9.09
oryza est cluster	414264	25967	6.27
other est cluster	4195170	346780	8.27
oryza est	1343927	105431	7.84
oryza gss	51225	1980	3.87
oryza microarray probe	142508	6252	4.39
oryza rflp	4298	296	6.89
oryza overgo	461	29	6.29



• Oryza punctata (BAC.Sanger.1.1): assembly updated



sequence set	total sequence Count	mapped sequence Count	mapping percentage
oryza mrna	119100	8966	7.53
other mrna	488418	45490	9.31
oryza est cluster	414264	27516	6.64
other est cluster	4195170	347537	8.28
oryza est	1343927	110130	8.19
oryza gss	51225	2088	4.08
oryza microarray probe	142508	6499	4.56
oryza rflp	4298	328	7.63
oryza overgo	461	32	6.94

Gramene32

• Oryza sativa Japonica (MSU6): assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
oryza mrna	1	1	100.00
other mrna	16	7	43.75
oryza microarray probe	3725	500	13.42
oryza rflp	140	87	62.14



• Oryza sativa Indica: assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
oryza mrna	1	1	100.00
other mrna	16	8	50.00
oryza microarray probe	11165	0	0.00
oryza rflp	274	0	0.00



• Oryza barthii chr3s: assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
oryza est cluster	314264	27676	8.81
other est cluster	4953927	203975	4.12
oryza est	1316380	123059	9.35
oryza gss	55033	4275	7.77
oryza mrna	117653	14506	12.33
other mrna	204013	13661	6.70
oryza overgo	461	38	8.24
oryza microarray probe	142508	10873	7.63
oryza rflp	4298	373	8.68



• Oryza brachyantha chr3s: new assembly BAC Pool 2009, completel mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
oryza est cluster	414264	15122	3.65
other est cluster	5716460	200756	3.51
oryza est	1343927	69668	5.18
oryza gss	55033	425	0.77
oryza mrna	119100	5291	4.44
other mrna	531477	26206	4.93
oryza overgo	461	22	4.77
oryza microarray probe	142508	2683	1.88
oryza rflp	4298	204	4.75



• Oryza glaberrima: assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
other est cluster	50938	2623	5.15
oryza est	546	24	4.40
oryza gss	1395	28	2.01
oryza mrna	296	9	3.04
other mrna	28502	2394	8.40
oryza microarray probe	138273	984	0.71
oryza rflp	4144	35	0.84



• Oryza minuta: BAC Sanger 2009, complete mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
oryza est cluster	414264	21110	5.10
other est cluster	5716460	260835	4.56
oryza est	1343927	83271	6.20
oryza gss	55033	1729	3.14
oryza mrna	119100	7171	6.02
other mrna	531477	32266	6.07
oryza overgo	461	26	5.64
oryza microarray probe	142508	5080	3.56
oryza rflp	4298	242	5.63



• Oryza nivara chr3s: BAC pool 2009, complete mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
oryza est cluster	414264	35552	8.58
other est cluster	5716460	216104	3.78
oryza est	1343927	117236	8.72
oryza gss	55033	3853	7.00
oryza mrna	119100	12583	10.57
other mrna	531477	28090	5.29
oryza overgo	461	45	9.76
oryza microarray probe	142508	10255	7.20
oryza rflp	4298	360	8.38



• Oryza officinalis chr3s: assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
other est cluster	50938	1728	3.39
oryza est	546	6	1.10
oryza gss	1395	3	0.22
oryza mrna	296	14	4.73
other mrna	28502	1644	5.77
oryza microarray probe	141505	866	0.61
oryza rflp	4258	56	1.32




• Oryza punctata chr3s: assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
other est cluster	50938	1890	3.71
oryza est	546	20	3.66
oryza gss	1395	6	0.43
oryza mrna	296	8	2.70
other mrna	28502	1796	6.30
oryza microarray probe	141294	1129	0.80
oryza rflp	4241	65	1.53




• Oryza rufipogon chr3s: BAC pool 2009, complete mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
oryza est cluster	414264	32065	7.74
other est cluster	5716460	207809	3.64
oryza est	1343927	106715	7.94
oryza gss	55033	3567	6.48
oryza mrna	119100	11239	9.44
other mrna	531477	26490	4.98
oryza overgo	461	38	8.24
oryza microarray probe	142508	8789	6.17
oryza rflp	4298	338	7.86




• Sorghum bicolor: assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
other mrna	17	8	47.06
sorghum rflp	50	35	70.00




• Brachypodium: assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
other mrna	17	7	41.18




• Zea mays: new assembly AGPv2, complete mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
zea est cluster	461295	330554	71.66
other est cluster	5669429	1522129	26.85
zea est	2023314	1735286	85.76
zea gss	1053547	341474	32.41
maize fpc markers	70958	50871	71.69
zea mrna	156259	144591	92.53
other mrna	494318	176143	35.63
zea overgo	11570	10046	86.83
zea microarray probe	17620	16363	92.87
zea rflp	2602	2520	96.85




• Physcomitrella patens: new assembly Phypa v1.1, complete mapping

i

sequence set	total sequence Count	mapped sequence Count	mapping percentage
physcomitrella est cluster	88344	79302	89.77
physcomitrella est	382584	371545	97.11
physcomitrella mrna	33299	33298	100.00
other mrna	617278	93607	15.16




• Arabidopsis thaliana: assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
other mrna	17	10	58.82
arabidopsis microarray probe	6	0	0.00




• Arabidopsis lyrata: assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
other mrna	17	7	41.18
arabidopsis microarray probe	14330	11696	81.62
arabidopsis rflp	21	20	95.24




• Vitis vinifera: assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
other mrna	17	12	70.59
vitis microarray probe	1810	934	51.60




• Poplar: assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
other mrna	17	10	58.82
populus microarray probe	10450	4456	42.64

Gramene31

• Oryza sativa Japonica (MSU6): assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
oryza est cluster	88838	1864	2.10
other est cluster	4388235	142019	3.24
oryza est	114613	10591	9.24
other est	14218826	765130	5.38
oryza gss	8038	1377	17.13
oryza mrna	4254	894	21.02
other mrna	366831	29883	8.15
oryza overgo	53	4	7.55
oryza microarray probe	4203	478	11.37
oryza rflp	144	4	2.78



• Oryza sativa Indica: assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
other est cluster	50938	28841	56.62
oryza est	546	518	94.87
other est	1064372	279511	26.26
oryza gss	5130	2644	51.54
oryza mrna	295	236	80.00
other mrna	28486	17360	60.94
oryza microarray probe	16014	4849	30.28
oryza rflp	303	29	9.57



• Sorghum bicolor: assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
other est cluster	50938	27333	53.66
sorghum mrna	50	50	100.00
other mrna	28731	17809	61.99
sorghum rflp	52	2	3.85



• Brachypodium distachyon: assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
other est cluster	50938	32703	64.20
other est	1064918	271899	25.53
brachypodium mrna	1	1	100.00
other mrna	28780	16667	57.91



• Arabidopsis thaliana (Tair9): assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
other est cluster	50938	4944	9.71
arabidopsis est	339	278	82.01
other est	1064579	275285	25.86
arabidopsis mrna	31	30	96.77
other mrna	28750	7366	25.62
arabidopsis microarray probe	6	0	0.00



• Arabidopsis lyrata: assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
other est cluster	50938	4477	8.79
arabidopsis est	339	197	58.11
other est	1064579	275451	25.87
arabidopsis mrna	31	12	38.71
other mrna	28750	7258	25.25
arabidopsis microarray probe	14333	3	0.02
arabidopsis rflp	22	1	4.55



• Vitis vinifera: updated assembly IGGP 12x, complete mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
vitis est cluster	117268	106582	90.89
other est cluster	6013456	1652326	27.48
vitis est	387979	364004	93.82
other est	20279796	5897028	29.08
vitis mrna	23886	23801	99.64
other mrna	626674	201687	32.18
vitis microarray probe	16436	14626	88.99



• Populus trichocarpa: assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
populus est cluster	305210	248806	81.52
other est cluster	5825514	1491744	25.61
populus est	420865	351221	83.45
other est	20246911	5546071	27.39
populus mrna	61495	54799	89.11
other mrna	589065	174198	29.57
populus overgo	1	1	100.00
populus microarray probe	61312	50862	82.96



• Oryza glaberrima (3s): updated assembly BAC Pool 2009, completel mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
Rice FstTransposon	16335	562	3.44
Rice T DNA Insert	19279	1322	6.86
oryza est cluster	414264	12325	2.98
other est cluster	5665522	207892	3.67
oryza est	1339739	52888	3.95
other est	18255541	782283	4.29
Rice tos17 insert	18024	564	3.13
oryza mrna	118802	4474	3.77
other mrna	502446	22495	4.48
oryza overgo	461	23	4.99
oryza microarray probe	142508	4235	2.97
other microarray probe	118114	1052	0.89
oryza rflp	4298	154	3.58
other rflp	5561	392	7.05



• Oryza minuta (3s): new assembly BAC Pool 2009, completel mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
Rice FstTransposon	16335	198	1.21
Rice T DNA Insert	19279	521	2.70
oryza est cluster	414264	5101	1.23
other est cluster	5665522	192178	3.39
oryza est	1339739	26947	2.01
other est	18255541	682663	3.74
Rice tos17 insert	18024	459	2.55
oryza mrna	118802	2207	1.86
other mrna	502446	21563	4.29
oryza overgo	461	19	4.12
oryza microarray probe	142508	1829	1.28
other microarray probe	118114	1107	0.94
oryza rflp	4298	87	2.02
other rflp	5561	344	6.19



• Oryza officinalis (3s): new assembly BAC Pool 2009, completel mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
Rice FstTransposon	16335	110	0.67
Rice T DNA Insert	19279	340	1.76
oryza est cluster	414264	2780	0.67
other est cluster	5665522	147016	2.59
oryza est	1339739	13136	0.98
other est	18255541	516436	2.83
Rice tos17 insert	18024	212	1.18
oryza mrna	118802	1210	1.02
other mrna	502446	15367	3.06
oryza overgo	461	5	1.08
oryza microarray probe	142508	1003	0.70
other microarray probe	118114	638	0.54
oryza rflp	4298	40	0.93
other rflp	5561	244	4.39



• Oryza punctata (3s): new assembly BAC Pool 2009, completel mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
Rice FstTransposon	16335	218	1.33
Rice T DNA Insert	19279	399	2.07
oryza est cluster	414264	3169	0.76
other est cluster	5665522	149797	2.64
oryza est	1339739	15645	1.17
other est	18255541	503104	2.76
Rice tos17 insert	18024	245	1.36
oryza mrna	118802	1332	1.12
other mrna	502446	15546	3.09
oryza overgo	461	10	2.17
oryza microarray probe	142508	1214	0.85
other microarray probe	118114	738	0.62
oryza rflp	4298	57	1.33
other rflp	5561	201	3.61

Gramene30

• Oryza sativa Japonica (MSU6): New genome assembly, complete mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
Oryza mRNA	118802	114843	96.67
other mRNA	502446	164101	32.66
Oryza EST	1289739	1179683	91.47
other EST	18155540	5052707	27.83
Oryza EST_cluster	414264	325426	78.56
other EST_cluster	5315590	1188369	22.36
Oryza RFLP	4298	4158	96.65
other RFLP	5561	2973	50.69
Oryza Microarray probe	142508	138305	97.05
other Microarray probe	118114	13565	11.48
Oryza Overgo	461	408	88.50
Oryza tos17_insert	18024	17853	99.05
Oryza T_DNA_Insert	19279	17990	93.31
Oryza FstTransposon	16335	11152	68.27
OMAP BES	2508376	1132351	45.14



• Arabidopsis thaliana (Tair9): New genome assembly, complete mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
Arabidopsis mRNA	110770	109357	98.72
other mRNA	511009	111556	21.83
Arabidopsis EST	1530097	1310723	85.66
other EST	18119329	4498022	24.82
Arabidopsis EST_cluster	414088	292657	70.68
other EST_cluster	5665698	1199452	21.17
Arabidopsis RFLP	48	48	100
other RFLP	9811	1481	15.10
Arabidopsis Microarray probe	22746	22740	99.97
other Microarray probe	237876	9181	3.86
Arabidopsis Overgo	56	51	91.07



• Brachypodium distachyon: New genome assembly, complete mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
Brachypodium mRNA	4	3	75.00
other mRNA	621775	250295	40.25
Brachypodium EST	20596	19753	95.91
other EST	19482265	6130866	31.47
Brachypodium EST_cluster	12709	12007	94.48
other EST_cluster	6017095	1604982	26.67



• Arabidopsis lyrata: assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
Arabidopsis mRNA	35441	6930	19.55
other mRNA	293470	55555	18.93
Arabidopsis EST	187528	61037	32.55
other EST	4427676	1029500	23.25
Arabidopsis EST_cluster	28117	5273	18.75
other EST_cluster	784865	181050	23.07



• Oryza sativa Indica: assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
Oryza mRNA	1447	1035	71.53
other mRNA	327464	107689	32.89
Oryza EST	27547	22539	81.82
other EST	4587657	1083810	23.62
Oryza EST_cluster	50449	43481	86.19
other EST_cluster	712540	219948	30.87



• Sorghum bicolor: assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
Sorghum mRNA	18	17	94.44
other mRNA	328893	137717	41.87
Sorghum EST	658	577	87.69
other EST	4871494	1030735	21.16
Sorghum EST_cluster	24404	23151	94.87
other EST_cluster	749701	226082	30.16



• Vitis vinifera: assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
Vitis mRNA	23054	23050	99.98
other mRNA	305857	84660	27.68
Vitis EST	12109	7989	65.98
other EST	4707310	1454965	30.91
Vitis EST_cluster	25100	24328	96.92
other EST_cluster	811518	283955	34.99



• Populus trichocarpa: assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
Populus mRNA	46207	45104	97.61
other mRNA	282704	73573	26.02
Populus EST	19678	16383	83.26
other EST	4595526	1464385	31.87
Populus EST_cluster	54292	48458	89.25
other EST_cluster	758690	271460	35.78



• Oryza glaberrima (3s): assembly unchanged, incremental mapping



sequence set	total sequence Count	mapped sequence Count	mapping percentage
Oryza mRNA	1447	89	6.15
other mRNA	327464	24829	7.58
Oryza EST	27547	3526	12.80
other EST	4537657	191005	27.83
Oryza EST_cluster	50449	3428	6.79
other EST_cluster	762533	47493	6.23



• Oryza barthii (3s): new assembly, should be complete mapping, but used the incremental query sequences dumped for Oryza glaberrima, will map the rest in the next build



sequence set	total sequence Count	mapped sequence Count	mapping percentage
Oryza mRNA	1447	99	6.84
other mRNA	327464	18394	5.62
Oryza EST	27547	3483	4.21
other EST	4537657	191005	27.83
Oryza EST_cluster	50449	3543	7.02
other EST_cluster	762533	42185	5.53



• Oryza brachyantha (3s): new assembly, should be complete mapping, but used the incremental query sequences dumped for Oryza glaberrima, will map the rest in the next build



sequence set	total sequence Count	mapped sequence Count	mapping percentage
Oryza mRNA	1447	5	0.35
other mRNA	327464	4457	1.36
Oryza EST	27547	98	0.36
other EST	4537657	64973	1.42
Oryza EST_cluster	50449	77	0.15
other EST_cluster	762533	11592	1.52



• Oryza nivara (3s): new assembly, should be complete mapping, but used the incremental query sequences dumped for Oryza glaberrima, will map the rest in the next build



sequence set	total sequence Count	mapped sequence Count	mapping percentage
Oryza mRNA	1447	28	1.94
other mRNA	327464	7022	2.14
Oryza EST	27547	768	2.79
other EST	4537657	70446	1.54
Oryza EST_cluster	50449	1466	2.91
other EST_cluster	762533	16022	2.10



• Oryza rufipogon (3s): new assembly, should be complete mapping, but used the incremental query sequences dumped for Oryza glaberrima, will map the rest in the next build




sequence set	total sequence Count	mapped sequence Count	mapping percentage
Oryza mRNA	1447	93	6.43
other mRNA	327464	16885	5.16
Oryza EST	27547	2044	7.42
other EST	4537657	186205	4.06
Oryza EST_cluster	50449	3460	6.86
other EST_cluster	762533	38592	5.06

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