Supporting Table S1aCoverage of the reads from resequencing of the elite inbred parent 9001 Awith IlluminaGAIIxto the Nipponbare
genome.
Chromosome
a
Nipponbaregenome
(bp)a
Length of consensus
sequence aligned to
reference (bp)b
Coverage
(%)
Uniquely mapped reads
Total number
Sequencing
depth (fold)
bp
Chromosome 1
43261740
34574647
79.92
3926191
279898156
6.45
Chromosome 2
35954743
29269000
81.41
3462255
246824159
6.83
Chromosome 3
36192742
30801784
85.10
3501877
249648811
6.87
Chromosome 4
35498469
25829743
72.76
3027759
215848939
6.06
Chromosome 5
29737217
23839481
80.17
2750503
196083359
6.58
Chromosome 6
30731886
23364294
76.03
2680410
191086429
6.20
Chromosome 7
29644043
22047624
74.37
2473305
176321913
5.94
Chromosome 8
28434780
21491645
75.58
2442462
174123116
6.12
Chromosome 9
22696651
17067815
75.20
1963834
140001726
6.15
Chromosome 10
22685906
16927713
74.62
1974209
140741360
6.20
Chromosome 11
28386948
19468829
68.58
2180712
155462958
5.47
Chromosome 12
27566993
19533184
70.86
2339570
166787945
6.06
Total/ Averagec
370792118
284215759
76.22
32723087
2332828872
6.24
Nipponbare reference genome (Genbank accession - AACV000000000.1); bLength of the consensus sequence; cTotal number except for
the column of coverage ad sequencing depth, which are average values; dCoverage is calculated basedon consensus of 9001 A aligned
lengthto the Nipponbare reference. The value is slightly different from average coverage of respective chromosome.
Supporting Table S1bCoverage of the reads from resequencing of the elite inbred parent 9002 A with IlluminaGAIIx to the Nipponbare
genome.
Chromosome
a
Nipponbaregenome
(bp)a
Length of consensus
sequence aligned to
reference (bp)b
Coverage
(%)
Uniquely mapped reads
Total number
bp
Sequencing
depth (fold)
Chromosome 1
43261740
34813324
80.47
3970304
288005852
6.64
Chromosome 2
35954743
29396765
81.76
3403959
246923186
6.84
Chromosome 3
36192742
30759706
84.99
3459136
250925725
6.91
Chromosome 4
35498469
25536731
71.94
2885581
209320046
5.88
Chromosome 5
29737217
23826272
80.12
2676309
194139455
6.51
Chromosome 6
30731886
23619763
76.86
2664503
193283048
6.28
Chromosome 7
29644043
22154754
74.74
2440510
177034595
5.96
Chromosome 8
28434780
21599468
75.96
2421403
175648574
6.17
Chromosome 9
22696651
17062975
75.18
1948057
141312055
6.22
Chromosome 10
22685906
17010721
74.98
1920358
139302769
6.13
Chromosome 11
28386948
19744488
69.55
2119376
153739535
5.41
Chromosome 12
27566993
19042915
69.08
2230282
161784656
5.87
Total/ Averagec
370792118
284567882
76.30
32139778
2331419496
6.23
Nipponbare reference genome (Genbank accession - AACV000000000.1); bLength of the consensus sequence; cTotal number except for
the column of coverage ad sequencing depth, which are average values; dCoverage is calculated basedon consensus of 9002 A aligned
lengthto the Nipponbare reference. The value is slightly different from average coverage of respective chromosome.
Supporting Table S1c Coverage of the reads from resequencing of the elite inbred parent 9003 A with IlluminaGAIIx to the Nipponbare
genome.
Chromosome
a
Nipponbaregenome
(bp)a
Length of consensus
sequence aligned to
reference (bp)b
Coverage
(%)
Uniquely mapped reads
Total number
bp
Sequencing
depth (fold)
Chromosome 1
43261740
35961418
83.13
5422090
403023950
9.29
Chromosome 2
35954743
30192655
83.97
4736592
352070883
9.76
Chromosome 3
36192742
31578597
87.25
4815479
357934554
9.87
Chromosome 4
35498469
26700233
75.22
3872169
287818322
8.09
Chromosome 5
29737217
24529956
82.49
3756749
279239153
9.37
Chromosome 6
30731886
24461707
79.60
3722544
276696696
8.99
Chromosome 7
29644043
22904412
77.26
3390952
252049462
8.49
Chromosome 8
28434780
22494724
79.11
3351113
249088229
8.75
Chromosome 9
22696651
17814566
78.49
2662446
197899611
8.70
Chromosome 10
22685906
17739029
78.19
2697251
200486667
8.82
Chromosome 11
28386948
21285247
74.98
3044692
226311956
7.96
Chromosome 12
27566993
20595402
74.71
3026258
224941757
8.15
Total/ Averagec
370792118
296257946
79.53
44498335
3307561241
8.85
Nipponbare reference genome (Genbank accession - AACV000000000.1); bLength of the consensus sequence; cTotal number except for
the column of coverage ad sequencing depth, which are average values; dCoverage is calculated basedon consensus of 9003 A aligned
lengthto the Nipponbare reference. The value is slightly different from average coverage of respective chromosome.
Supporting Table S1d Coverage of the reads from resequencing of the elite inbred parent 9001 R with IlluminaGAIIxto the Nipponbare
genome.
Chromosome
a
Nipponbaregenome
(bp)a
Length of consensus
sequence aligned to
reference (bp)b
Coverage
(%)
Uniquely mapped reads
Total number
bp
Sequencing
depth (fold)
Chromosome 1
43261740
34558993
79.88
3635055
258743215
5.96
Chromosome 2
35954743
29184840
81.17
3204804
228117949
6.31
Chromosome 3
36192742
30806142
85.12
3264119
232339990
6.39
Chromosome 4
35498469
25090021
70.68
2689773
191458042
5.37
Chromosome 5
29737217
23684348
79.65
2537463
180616616
6.06
Chromosome 6
30731886
23810552
77.48
2552522
181688516
5.90
Chromosome 7
29644043
22037540
74.34
2302252
163874297
5.52
Chromosome 8
28434780
21147551
74.37
2240544
159481922
5.60
Chromosome 9
22696651
16786481
73.96
1786773
127182502
5.59
Chromosome 10
22685906
16896578
74.48
1826747
130027851
5.72
Chromosome 11
28386948
19565016
68.92
2041989
145348777
5.12
Chromosome 12
27566993
18499164
67.11
1961163
139595582
5.07
Total/ Averagec
370792118
282067226
75.60
30043204
2138475261
5.72
Nipponbare reference genome (Genbank accession - AACV000000000.1); bLength of the consensus sequence; cTotal number except for
the column of coverage ad sequencing depth, which are average values; dCoverage is calculated basedon consensus of 9001 R aligned
lengthto the Nipponbare reference. The value is slightly different from average coverage of respective chromosome.
Supporting Table S1e Coverage of the reads from resequencing of the elite inbred parent 9002 R with IlluminaGAIIx to the Nipponbare
genome.
Chromosome
a
Nipponbaregenome
(bp)a
Length of consensus
sequence aligned to
reference (bp)b
Coverage
(%)
Uniquely mapped reads
Total number
bp
Sequencing
depth (fold)
Chromosome 1
43261740
34495487
79.74
5031923
357316852
8.23
Chromosome 2
35954743
29299881
81.49
4528114
321541375
8.89
Chromosome 3
36192742
30782051
85.05
4553958
323376558
8.91
Chromosome 4
35498469
24956944
70.30
3675479
260995764
7.33
Chromosome 5
29737217
23650292
79.53
3536406
251120190
8.42
Chromosome 6
30731886
23474297
76.38
3495906
248244285
8.06
Chromosome 7
29644043
22151145
74.72
3206360
227683624
7.67
Chromosome 8
28434780
21315168
74.96
3137270
222777543
7.83
Chromosome 9
22696651
16918001
74.54
2484607
176431943
7.76
Chromosome 10
22685906
16964637
74.78
2532960
179865490
7.92
Chromosome 11
28386948
19764664
69.63
2855748
202786665
7.14
Chromosome 12
27566993
18580320
67.40
2731577
193969283
7.04
Total/ Averagec
370792118
282352887
75.71
41770308
2966109571
7.93
Nipponbare reference genome (Genbank accession - AACV000000000.1); bLength of the consensus sequence; cTotal number except for
the column of coverage ad sequencing depth, which are average values; dCoverage is calculated basedon consensus of 9002 R aligned
lengthto the Nipponbare reference. The value is slightly different from average coverage of respective chromosome.
Supporting Table S1fCoverage of the reads from resequencing of the elite inbred parent 9003 R with IlluminaGAIIx to the Nipponbare
genome.
Chromosome
a
Nipponbaregenome
(bp)a
Length of consensus
sequence aligned to
reference (bp)b
Coverage
(%)
Uniquely mapped reads
Total number
bp
Sequencing
depth (fold)
Chromosome 1
43261740
35191528
81.35
5009052
372072383
8.57
Chromosome 2
35954743
29652431
82.47
4414448
327905197
9.09
Chromosome 3
36192742
31274967
86.41
4477239
332569313
9.16
Chromosome 4
35498469
25744124
72.52
3692726
274295687
7.70
Chromosome 5
29737217
24267501
81.61
3514401
261049706
8.76
Chromosome 6
30731886
23748118
77.28
3408261
253165627
8.22
Chromosome 7
29644043
22529380
76.00
3171872
235606652
7.93
Chromosome 8
28434780
21292920
74.88
3025887
224762886
7.89
Chromosome 9
22696651
17230536
75.92
2473529
183733734
8.08
Chromosome 10
22685906
17122571
75.48
2476333
183942015
8.09
Chromosome 11
28386948
20178490
71.08
2863227
212680502
7.48
Chromosome 12
27566993
19185839
69.60
2764216
205325964
7.44
Total/ Averagec
370792118
287418405
77.05
41291191
3067109667
8.20
Nipponbare reference genome (Genbank accession - AACV000000000.1); bLength of the consensus sequence; cTotal number except for
the column of coverage ad sequencing depth, which are average values; dCoverage is calculated basedon consensus of 9003 R aligned
lengthto the Nipponbare reference. The value is slightly different from average coverage of respective chromosome.
Supporting Table S2aPolymorphism in genomic DNA observed in the elite rice inbred 9001 A in comparision with Nipponbare.
Chromosome
No.
DNA
DNA Polymorphism/ No. of
Polymorphism
100kb
SNPs
SNP/
100 kb
No. of
Insertions
Insertions/ No. of
100 kb
Deletions
Deletions/
100kb
Chromosome 1
123372
284.9
103580
239.2
9890
22.8
9902
22.9
Chromosome 2
103338
287
86716
240.9
8147
22.6
8475
23.5
Chromosome 3
102371
282.7
85263
235.5
8515
23.5
8593
23.7
Chromosome 4
78230
220.4
65790
185.3
6018
17.0
6422
18.1
Chromosome 5
73374
247
61284
206.3
6002
20.2
6088
20.5
Chromosome 6
85465
277.5
72595
235.7
6277
20.4
6593
21.4
Chromosome 7
79534
267.8
68012
229.0
5585
18.8
5937
20.0
Chromosome 8
75010
264.1
63341
223.0
5774
20.3
5895
20.8
Chromosome 9
59757
263.3
50483
222.4
4586
20.2
4688
20.7
Chromosome 10
66854
294.5
57327
252.5
4691
20.7
4836
21.3
Chromosome 11
84081
296.1
72020
253.6
6026
21.2
6035
21.3
Chromosome 12
57600
208.8
48785
176.8
4384
15.9
4431
16.1
Totala/ Averageb
988986a
266.2 b
835196a
225.0 b
75895a
20.3 b
77895a
20.9b
Supporting Table S2b Polymorphism in genomic DNA observed in the elite rice inbred 9002 A in comparision with Nipponbare.
Chromosome
No.
DNA
Polymorphism
DNA Polymorphism/ No. of
100kb
SNPs
SNP/ No. of
Insertions/ No. of
100 kb Insertions
100 kb
Deletions
Deletions/
100kb
Chromosome 1
110969
256.3
96655
223.2
7145
16.5
7169
16.6
Chromosome 2
96823
269.1
84842
235.8
5950
16.5
6031
16.8
Chromosome 3
91782
253.5
79857
220.6
5953
16.4
5972
16.5
Chromosome 4
71245
200.7
62340
175.6
4315
12.2
4590
12.9
Chromosome 5
67364
226.8
58327
196.4
4490
15.1
4547
15.3
Chromosome 6
78553
255
68945
223.8
4685
15.2
4923
16.0
Chromosome 7
74815
251.8
66067
222.4
4285
14.4
4463
15.0
Chromosome 8
65995
232.3
57718
203.2
4068
14.3
4209
14.8
Chromosome 9
54620
240.6
47831
210.7
3331
14.7
3458
15.2
Chromosome 10
60938
268.5
53708
236.6
3577
15.8
3653
16.1
Chromosome 11
78564
276.6
69245
243.8
4610
16.2
4709
16.6
Chromosome 12
61027
221.1
53240
192.9
3858
14.0
3929
14.2
912695a
246.0b
798775a
215.4b
56267a
15.1b
57653a
15.5b
Totala/ Averageb
Supporting Table S2c Polymorphism in genomic DNA observed in the elite rice inbred 9003 A in comparision with Nipponbare.
Chromosome
No.
DNA
DNA Polymorphism/ No. of
Polymorphism
100kb
SNPs
SNP/
100 kb
No. of
Insertions/ No. of
Insertions
100 kb
Deletions
Deletions/
100kb
Chromosome 1
133281
307.8
103260
238.5
15025
34.7
14996
34.6
Chromosome 2
111021
308.4
86230
239.5
12404
34.5
12387
34.4
Chromosome 3
108684
300.3
84950
234.7
12127
33.5
11607
32.1
Chromosome 4
82387
232.1
63940
180.1
9084
25.6
9363
26.4
Chromosome 5
74565
251.1
57462
193.5
8588
28.9
8515
28.7
Chromosome 6
91771
298
72691
236.0
9596
31.2
9484
30.8
Chromosome 7
90614
305.1
72789
245.1
8848
29.8
8977
30.2
Chromosome 8
74011
260.6
55913
196.9
9099
32.0
8999
31.7
Chromosome 9
65789
289.9
51927
228.8
6972
30.7
6890
30.4
Chromosome 10
76543
337.1
61754
272.0
7273
32.0
7516
33.1
Chromosome 11
88948
313.2
70076
246.7
9557
33.7
9315
32.8
Chromosome 12
63495
230.1
47112
170.7
8162
29.6
8221
29.8
1061109a
286.1b
828104 a
223.5b
116735 a
31.4b
116270 a
31.3b
Totala/ Averageb
Supporting Table S2d Polymorphism in genomic DNA observed in the elite riceinbred 9001 R in comparision with Nipponbare.
Chromosome
No.
DNA
DNA Polymorphism/ No. of
Polymorphism
100kb
SNPs
SNP/
100 kb
No. of
Insertions/ No. of
Deletions/
Insertions
100 kb
Deletions
100kb
Chromosome 1
111847
258.3
101265
233.9
5173
11.9
5409
12.5
Chromosome 2
88709
246.4
79923
222.0
4298
11.9
4488
12.5
Chromosome 3
86590
239.2
77943
215.3
4297
11.9
4350
12.0
Chromosome 4
69601
196.1
63326
178.4
2979
8.4
3296
9.3
Chromosome 5
62752
211.3
56513
190.3
3099
10.4
3140
10.6
Chromosome 6
67493
219.2
61105
198.4
3036
9.9
3352
10.9
Chromosome 7
69805
235.1
63486
213.8
3050
10.3
3269
11.0
Chromosome 8
63322
223
57200
201.4
2954
10.4
3168
11.2
Chromosome 9
54426
239.7
49360
217.4
2456
10.8
2610
11.5
Chromosome 10
61320
270.1
56079
247.0
2536
11.2
2705
11.9
Chromosome 11
76877
270.7
70146
247.0
3308
11.6
3423
12.1
Chromosome 12
67174
243.3
61471
222.7
2799
10.1
2904
10.5
879916a
237.7b
797817 a
215.6b
39985 a
10.7b
42114 a
11.3b
Totala/ Averageb
Supporting Table S2e Polymorphism in genomic DNA observed in the elite rice inbred 9002 R in comparision with Nipponbare.
Chromosome
No.
DNA
DNA Polymorphism/ No. of
Polymorphism 100kb
SNPs
SNP/
100 kb
No. of
Insertions/ No. of
Insertions
100 kb
Deletions
Deletions/
100kb
Chromosome 1
132176
305.3
116683
269.5
7676
17.7
7817
18.1
Chromosome 2
108609
301.7
95612
265.6
6403
17.8
6594
18.3
Chromosome 3
105830
292.3
92677
256.0
6619
18.3
6534
18.0
Chromosome 4
93437
263.2
83177
234.3
5002
14.1
5258
14.8
Chromosome 5
77728
261.7
68163
229.5
4705
15.8
4860
16.4
Chromosome 6
88584
287.6
78637
255.3
4765
15.5
5182
16.8
Chromosome 7
84683
285.1
75260
253.4
4495
15.1
4928
16.6
Chromosome 8
82798
291.5
72957
256.9
4859
17.1
4982
17.5
Chromosome 9
67956
286.1
57440
253.0
3755
16.5
3761
16.6
Chromosome 10
76651
337.6
68350
301.1
4120
18.1
4181
18.4
Chromosome 11
91878
323.4
81717
287.7
5097
17.9
5064
17.8
Chromosome 12
82713
299.7
73885
267.7
4366
15.8
4462
16.2
1093043a
294.6b
964558a
260.8b
61862a
16.6b
63623a
17.1b
Totala/ Averageb
Supporting Table S2f Polymorphism in genomic DNA observed in the elite rice inbred 9003 R in comparision with Nipponbare.
Chromosome
No.
DNA
DNA Polymorphism/
Polymorphism 100kb
No. of
SNPs
SNP/
100 kb
No. of Insertions/
Insertions
100 kb
No. of Deletions/
Deletions
100kb
Chromosome 1
156426
361.3
131214
303.0
12632
29.2
12580
29.1
Chromosome 2
131801
366.2
110574
307.2
10757
29.9
10470
29.1
Chromosome 3
125774
347.5
104710
289.3
10692
29.5
10372
28.7
Chromosome 4
103684
292.1
87683
247.0
7828
22.1
8173
23.0
Chromosome 5
84467
284.4
70163
236.2
7094
23.9
7210
24.3
Chromosome 6
109707
356.2
93107
302.3
8224
26.7
8376
27.2
Chromosome 7
103142
347.6
87747
295.4
7600
25.6
7795
26.6
Chromosome 8
93206
328.6
78967
278.1
7088
25.0
7151
25.5
Chromosome 9
74456
328.1
62847
276.9
5800
25.6
5809
25.6
Chromosome 10
86271
380.1
73773
325.0
6217
27.4
6281
27.7
Chromosome 11
104763
368.9
89563
315.4
7650
26.9
7550
26.6
Chromosome 12
91297
330.8
78468
284.3
6417
23.3
6412
23.2
2445994a
341.0b
2249816a
288.3b
97999a
26.3b
98179a
26.4b
Totala/ Averageb
Table S3. Cross validation of SNPs detected by combined assembly
Chromosome
Total
SNPs
SNPs
validated by
cross
checking
with
individual
assembly
(A)
SNPs with
only one
variant
(B)
SNPs with
more than
one variant
and freq
more than
50% (C)
Total
SNPs
validated
by cross
checking
(A+B+C)
SNPs
validated by
cross
checking
(%)
Chromosome 1
284078
108933
42498
132422
283853
99.92
Chromosome 2
243923
91950
34890
116873
243713
99.91
Chromosome 3
211527
82043
39183
90182
211408
99.94
Chromosome 4
236006
74917
28312
132514
235743
99.89
Chromosome 5
162723
59877
25931
76803
162611
99.93
Chromosome 6
201956
73530
33331
94923
201784
99.91
Chromosome 7
188046
69030
32301
86565
187896
99.92
Chromosome 8
197285
66199
27245
103654
197098
99.91
Chromosome 9
151888
52563
21808
77406
151777
99.93
Chromosome 10
176433
61011
29707
85535
176253
99.90
Chromosome 11
224589
76665
34200
113499
224364
99.90
Chromosome 12
216598
66907
20665
128763
216335
99.88
Total
2495052
2492835
99.91
883625
370071
1239139
A - SNPs validated by cross checking with individual assembly.
B - SNPs with only one variant. (For individual assembly, SNPs identification was very stringent with
additional filtering settings: more than 90% frequency and minimum coverage of 4X. This was done to
avoid calling spurious SNPs even though it resulted in the loss of some true SNPs. Since, the number of
SNPs is huge we decided to go with such stringent parameters for individual assembly. But in the
combined assembly, we had more coverage depth as reads from all six genotypes were mapped to the
reference genome which has resulted in identifying SNPs with only single variant across the individuals
but with a minimum coverage of 10X in this case.)
C - SNPs with more than one variant and minimum frequency of major allele more than 50%. (In the
combined assembly, the depth of coverage was more than for the individual assembly, as reads from all
six genotypes were mapped to the reference genome, which has resulted in identifying SNPs with more
than one variant across the individuals but with a minimum coverage of 10X in this case. The filtering
with minimum frequency of more than 50% gives a robust estimate of true SNPs. Additional analysis
revealed that out of the total SNPs in combined assembly, only 214 SNPs were found to be with a
coverage of less than 20X and less than 50% frequency).
Unmapped
3.17 X 106
Unmapped
3.61 X 106
Organelle
2.74 X 106
Organelle
4.77 X 106
Total reads
51.86 X 106
Multi
10.74 X 106
Multi
8.62 X 106
Total reads
44.58 X 106
Nuclear
43.47 X 106
Nuclear
38.66 X 106
Unique
32.72 X 106
Unique
30.04 X 106
(a)
(b)
Unmapped
4.28 X 106
Unmapped
4.21 X 106
Organelle
3.30 X 106
Organelle
4.74 X 106
Multi
11.77 X 106
Multi
9.62 X 106
Total reads
50.71 X 106
Total reads
61.12 X 106
Nuclear
41.76 X 106
Nuclear
53.54 X 106
Unique
32.14 X 106
Unique
41.77 X 106
(d)
(c)
Unmapped
4.96 X 106
Unmapped
5.28 X 106
Organelle
4.06 X 106
Organelle
5.36 X 106
Multi
12.65 X 106
Total reads
67.78 X 106
Multi
11.64 X 106
Total reads
61.95 X 106
Nuclear
57.15 X 106
Nuclear
52.93 X 106
Unique
44.50 X 106
Unique
41.29 X 106
(e)
(f)
Supporting FigureS1 Classificationof the reads from sequence of each of the six elite
indica rice inbreds mapped onto the Nipponbare genome genotypes (a) 9001 A
vsNipponbare; (b) 9001 R vsNipponbare; (c) 9002 A vsNipponbare; (d) 9002 R
vsNipponbare; (e) 9003 A vsNipponbare; (f) 9003 R vsNipponbare.. The total number
of reads generated through resequencing is in the centre circle. The number of reads
mapped onto nuclear genome, organelle genome and unmapped reads are shown in the
middle circle. The outer circle represents reads with unique mapping, multiple mapping
on the chromosomes as well as the reads mapped to organelle and unmapped reads.
20
Chr. 10
(53708)
0
20
0
0
0
[28.4 Mb]
0
Chr. 11
(70076)
10
10
20
30
20
SNPs (No.)
SNPs (No.)
SNPs (No.)
SNPs (No.)
SNPs (No.)
SNPs (No.)
[22.7 Mb]
10
20
[22.7 Mb]
10
20
10
20
500
0
500
0
Chr. 7
(87747)
0
0
Chr. 8
(78967)
0
SNPs (No.)
0
Chr. 9
(62487)
0
0
Chr. 10
(73773)
0
1000
1000
0
[27.6 Mb]
20
10
20
30
10
20
30
[36.0 Mb]
10
20
30
[36.2 Mb]
10
20
30
10
20
10
20
10
20
10
20
10
20
[22.7 Mb]
10
20
[22.7 Mb]
10
20
10
20
40
[43.2 Mb]
0
Chr. 11
(89563)
0
20
Chr. 12
(78468)
0
20
(d)
SNPs (No.)
0
SNPs (No.)
1000
500
0
[27.6 Mb]
SNPs (No.)
[35.5 Mb]
1000
500
0
[29.7 Mb]
1000
500
0
30 [30.7 Mb]
1000
500
0
[29.6 Mb]
1000
500
0
[28.4 Mb]
1000
500
0
1000
500
0
1000
1000
500
0
[28.4 Mb]
500
10
500
[22.7 Mb]
500
10
Chr. 12
(73885)
0
500
[22.7 Mb]
500
[28.4 Mb]
500
20
1000
10
Chr. 11
(81717)
500
[28.4 Mb]
500
[22.7 Mb]
500
20
1000
10
Chr. 10
(68350)
500
[27.6 Mb]
1000
[29.6 Mb]
500
[22.7 Mb]
1000
20
1000
10
SNPs (No.)
0
[28.4 Mb]
500
30 [30.7 Mb]
500
[28.4 Mb]
Chr. 9
(57440)
20
SNPs (No.)
0
1000
SNPs (No.)
SNPs (No.)
SNPs (No.)
SNPs (No.)
SNPs (No.)
0
500
Chr. 6
(93107)
10
Chr. 8
(72957)
1000
SNPs (No.)
20
0
1000
[29.7 Mb]
500
[29.6 Mb]
500
20
1000
SNPs (No.)
20
1000
(b)
10
[28.4 Mb]
500
[35.5 Mb]
Chr. 5
(70163)
0
SNPs (No.)
0
30
20
500
10
Chr. 7
(75260)
20
20
1000
[36.2 Mb]
1000
30 [30.7 Mb]
SNPs (No.)
20
SNPs (No.)
0
500
30
Chr. 4
(87683)
10
1000
20
0
[29.7 Mb]
Chr. 6
(78637)
10
0
SNPs (No.)
20
500
20
10
[29.6 Mb]
0
1000
10
1000
20
20
500
[36.0 Mb]
500
[35.5 Mb]
Chr. 5
(68163)
0
SNPs (No.)
30
1000
SNPs (No.)
SNPs (No.)
SNPs (No.)
SNPs (No.)
SNPs (No.)
SNPs (No.)
SNPs (No.)
SNPs (No.)
30
20
500
1000
20
Chr. 3
(104710)
10
1000
1000
Chr. 2
(110574)
500
[36.2 Mb]
0
10
Chr. 12
(61471)
30
Chr. 4
(83177)
10
Chr. 11
(70416)
20
20
10
30 [30.7 Mb]
1000
[43.2 Mb]
0
SNPs (No.)
SNPs (No.)
0
500
10
Chr. 10
(56079)
40
30
500
10
1000
10
Chr. 9
(49360)
20
0
1000
Chr. 1
(1312214)
20
1000
Chr. 3
(92677)
10
Chr. 8
(57200)
10
[29.7 Mb]
(e)
1000
[36.0 Mb]
500
10
Chr. 7
(63486)
20
0
[27.6 Mb]
0
10
0
10
Chr. 6
(61105)
20
500
[43.2 Mb]
Chr. 2
(95612)
500
10
Chr. 5
(56513)
10
[35.5 Mb]
500
1000
SNPs (No.)
40
30
1000
10
Chr. 4
(63326)
30
1000
SNPs (No.)
SNPs (No.)
20
SNPs (No.)
SNPs (No.)
0
10
20
500
1000
1000
Chr. 1
(116683)
500
1000
Chr. 3
(77943)
10
(c)
1000
10
[36.2 Mb]
1000
[28.4 Mb]
Chr. 12
(47112)
(a)
Chr. 2
(79923)
20
500
[27.6 Mb]
30
0
[22.7 Mb]
1000
0
20
20
500
0
20
20
500
[22.7 Mb]
Chr. 10
(61754)
10
500
20
500
[22.7 Mb]
10
1000
SNPs (No.)
SNPs (No.)
SNPs (No.)
20
500
[36.0 Mb]
0
[28.4 Mb]
Chr. 9
(51927)
10
0
20
500
[22.7 Mb]
500
30
0
[29.6 Mb]
Chr. 8
(55913)
10
Chr. 9
(47831)
1000
10
Chr. 1
(101265)
20
500
[28.4 Mb]
500
SNPs (No.)
Chr. 12
(53240)
0
0
20
1000
1000
Chr. 7
(72789)
10
Chr. 8
(57718)
0
20
[43.2 Mb]
500
30 [30.7 Mb]
20
500
[29.6 Mb]
500
SNPs (No.)
1000
Chr. 6
(72691)
10
0
10
40
1000
[29.7 Mb]
SNPs (No.)
Chr. 11
(69245)
20
SNPs (No.)
1000
Chr. 5
(57462)
500
30 [30.7 Mb]
30
500
[35.5 Mb]
SNPs (No.)
SNPs (No.)
1000
30
SNPs (No.)
SNPs (No.)
SNPs (No.)
SNPs (No.)
SNPs (No.)
1000
SNPs (No.)
SNPs (No.)
SNPs (No.)
1000
20
0
20
20
0
[36.2 Mb]
0
10
Chr. 7
(66067)
10
Chr. 12
(48785)
1000
0
1000
30
500
[29.7 Mb]
500
10
Chr. 11
(72020)
20
Chr. 6
(68945)
10
Chr. 10
(57327)
20
Chr. 4
(63940)
10
SNPs (No.)
SNPs (No.)
SNPs (No.)
SNPs (No.)
SNPs (No.)
1000
0
1000
10
500
1000
500
[35.5 Mb]
500
10
Chr. 9
(50483)
30
Chr. 5
(58327)
10
Chr. 8
(63341)
20
0
0
1000
[36.0 Mb]
Chr. 3
(84950)
10
500
1000
30
500
[36.2 Mb]
1000
1000
0
20
500
[43.2 Mb]
0
10
Chr. 7
(68012)
30
20
0
10
Chr. 6
(72595)
1000
Chr. 4
(62340)
0
40
30
Chr. 2
(86230)
10
500
10
Chr. 5
(61284)
SNPs (No.)
1000
1000
Chr. 3
(79857)
20
500
[36.0 Mb]
500
10
Chr. 4
(65790)
0
1000
0
30
Chr. 1
(103260)
500
10
Chr. 2
(84842)
20
1000
1000
[43.2 Mb]
SNPs (No.)
1000
40
30
500
10
Chr. 3
(85263)
20
SNPs (No.)
SNPs (No.)
1000
SNPs (No.)
Chr. 2
(86716)
SNPs (No.)
10
SNPs (No.)
0
SNPs (No.)
Chr. 1
(96655)
500
SNPs (No.)
1000
SNPs (No.)
SNPs (No.)
Chr. 1
(103580)
[28.4 Mb]
500
0
[27.6 Mb]
(f)
Supporting Figure S2 Distribution of SNPs identified between each of the six elite
indica rice inbreds and Nipponbare in the 12 rice chromosomes (a) 9001 A; (b) 9001 R;
(c) 9002; (d) 9002 R; (e) 9003 A; (f) 9003 R. The x-axis represents the physical distance
along each chromosome, split into 100kb windows. The total size of each chromosome
is shown in brackets. The y-axis indicates the number of SNPs. The total number of
SNPs in each chromosome is shown in the parenthesis.
20
0
0
Chr. 11
(4610)
50
0
20
[28.4 Mb]
Chr. 12
(3858)
50
0
20
0
0
0
10
0
10
0
Insertions (No.)
Insertions (No.)
Chr. 12
(2799)
20
0
50
Chr. 7
(4495)
0
20
0
20
50
Chr. 9
(6755)
0
Chr. 10
(4120)
50
Chr. 11
(5097)
0
[22.7 Mb]
100
50
0
[28.4 Mb]
100
Chr. 12
(4366)
50
0
[27.6 Mb]
Insertions (No.)
Insertions (No.)
Insertions (No.)
Insertions (No.)
Insertions (No.)
Insertions (No.)
Insertions (No.)
Chr. 2
(10757)
Insertions (No.)
Chr. 3
(10692)
[36.2 Mb]
10
20
30
10
20
[29.7 Mb]
10
20
30 [30.7 Mb]
10
20
[29.6 Mb]
10
20
10
20
[22.7 Mb]
10
20
[22.7 Mb]
10
20
10
20
0
20
30
50
Insertions (No.)
Chr. 4
(7828)
Insertions (No.)
[35.5 Mb]
Chr. 5
(7094)
0
20
100
50
0
100
50
0
100
50
0
50
Chr. 6
(8224)
0
20
50
0
100
50
0
100
50
0
50
Chr. 7
(7600)
0
20
50
0
Chr. 8
(7088)
50
0
20
50
Chr. 9
(5800)
0
50
Chr. 10
(6217)
0
Chr. 11
(7650)
[22.7 Mb]
100
50
0
[28.4 Mb]
100
Chr. 12
(6417)
50
0
10
20
(d)
0
[27.6 Mb]
10
20
30
10
20
30
[36.0 Mb]
10
20
30
[36.2 Mb]
10
20
30
10
20
[29.7 Mb]
10
20
30 [30.7 Mb]
10
20
[29.6 Mb]
10
20
10
20
[22.7 Mb]
10
20
[22.7 Mb]
10
20
10
20
40
[43.2 Mb]
50
0
100
50
0
100
50
0
[35.5 Mb]
100
50
0
100
50
0
100
50
0
100
50
0
[28.4 Mb]
100
50
0
[22.7 Mb]
100
20
50
100
[28.4 Mb]
100
10
[27.6 Mb]
100
[29.6 Mb]
100
20
[28.4 Mb]
100
30 [30.7 Mb]
100
10
[28.4 Mb]
100
[29.7 Mb]
100
20
[35.5 Mb]
0
[36.2 Mb]
Insertions (No.)
30
100
10
[22.7 Mb]
100
20
0
10
[28.4 Mb]
100
(b)
30
50
[36.0 Mb]
0
10
Chr. 8
(4859)
30
50
[29.6 Mb]
50
Chr. 1
(12632)
100
10
100
20
50
30 [30.7 Mb]
20
100
20
20
100
[43.2 Mb]
100
10
Chr. 6
(4765)
Insertions (No.)
50
10
0
[29.7 Mb]
100
20
50
10
Chr. 5
(4705)
40
30
100
10
[35.5 Mb]
20
Insertions (No.)
30
0
0
Insertions (No.)
20
50
10
10
(e)
Insertions (No.)
Chr. 4
(5002)
100
20
[36.0 Mb]
50
[27.6 Mb]
50
[36.2 Mb]
0
10
Insertions (No.)
Insertions (No.)
Insertions (No.)
Insertions (No.)
Insertions (No.)
30
Insertions (No.)
20
20
20
100
10
Insertions (No.)
Insertions (No.)
Insertions (No.)
Insertions (No.)
Insertions (No.)
Chr. 11
(3308)
Chr. 3
(6619)
Insertions (No.)
0
50
10
Chr. 12
(8162)
[28.4 Mb]
50
[36.0 Mb]
100
10
Chr. 10
(2536)
30
50
10
Chr. 9
(2456)
20
100
10
Chr. 8
(2954)
Chr. 2
(6403)
Insertions (No.)
Insertions (No.)
Insertions (No.)
Chr. 7
(3050)
20
100
10
Insertions (No.)
0
10
Chr. 11
(9557)
[22.7 Mb]
50
[43.2 Mb]
Insertions (No.)
Insertions (No.)
50
10
Chr. 6
(3036)
40
30
100
10
Chr. 5
(3099)
20
Insertions (No.)
Insertions (No.)
Chr. 4
(2979)
20
100
Insertions (No.)
0
Insertions (No.)
Chr. 1
(7676)
50
10
Chr. 10
(7273)
30
[43.2 Mb]
100
[22.7 Mb]
50
20
(c)
Insertions (No.)
Insertions (No.)
Chr. 3
(4297)
20
100
10
Insertions (No.)
Insertions (No.)
Chr. 2
(4298)
Chr. 9
(6972)
10
40
0
[28.4 Mb]
50
[27.6 Mb]
100
10
20
100
30
50
[29.6 Mb]
Chr. 8
(9099)
(a)
Chr. 1
(5173)
20
50
Insertions (No.)
10
0
100
Insertions (No.)
10
100
Chr. 7
(8848)
20
100
30 [30.7 Mb]
Insertions (No.)
Insertions (No.)
[22.7 Mb]
100
20
50
10
Chr. 10
(3577)
50
Chr. 6
(9596)
100
[22.7 Mb]
100
20
0
10
Chr. 9
(3331)
50
10
50
10
0
[29.7 Mb]
100
[28.4 Mb]
100
20
0
50
[35.5 Mb]
Chr. 5
(8588)
10
0
30
0
[29.6 Mb]
Chr. 8
(4068)
20
Insertions (No.)
20
50
20
0
Insertions (No.)
0
100
Chr. 4
(9084)
50
100
[36.2 Mb]
50
10
Chr. 7
(4285)
30
100
30 [30.7 Mb]
50
Insertions (No.)
20
100
20
50
10
Chr. 6
(4685)
0
Chr. 3
(12127)
100
[36.0 Mb]
100
[29.7 Mb]
50
Insertions (No.)
Insertions (No.)
Insertions (No.)
Insertions (No.)
Insertions (No.)
Insertions (No.)
Insertions (No.)
20
100
Insertions (No.)
Insertions (No.)
0
30
0
10
[35.5 Mb]
20
50
Insertions (No.)
Chr. 12
(4384)
Insertions (No.)
Chr. 11
(6026)
30
Chr. 5
(4490)
10
Chr. 10
(4691)
20
Insertions (No.)
Insertions (No.)
Insertions (No.)
0
50
Chr. 2
(12404)
100
10
100
Chr. 1
(15025)
[43.2 Mb]
0
[36.2 Mb]
Chr. 4
(4315)
10
Chr. 9
(4586)
30
50
10
Chr. 8
(5774)
20
100
10
Chr. 7
(5585)
Chr. 3
(5953)
40
30
50
10
0
20
100
[36.0 Mb]
50
10
Chr. 6
(6277)
Chr. 2
(5950)
100
10
Chr. 5
(6002)
30
0
10
Insertions (No.)
0
20
50
[43.2 Mb]
50
10
Chr. 4
(6018)
40
30
100
10
Chr. 3
(8515)
20
Insertions (No.)
Chr. 2
(8147)
Insertions (No.)
10
100
Insertions (No.)
0
Insertions (No.)
Chr. 1
(7145)
50
Insertions (No.)
100
Insertions (No.)
Insertions (No.)
Chr. 1
(9890)
100
50
0
100
50
0
[28.4 Mb]
100
50
0
[27.6 Mb]
(f)
Supporting FigureS3 Distribution of insertions identified between each of the six elite
indica rice inbreds and Nipponbare in the 12 rice chromosomes (a) 9001 A; (b) 9001 R;
(c) 9002; (d) 9002 R; (e) 9003 A; (f) 9003 R. The x-axis represents the physical distance
along each chromosome, split into 100kb windows. The total size of each chromosome
is shown in brackets. The y-axis indicates the number of SNPs. The total number of
SNPs in each chromosome is shown in the parenthesis.
20
Deletions (No.)
Deletions (No.)
Deletions (No.)
Deletions (No.)
Deletions (No.)
Deletions (No.)
Deletions (No.)
Deletions (No.)
Deletions (No.)
Deletions (No.)
20
30 [30.7 Mb]
10
20
[29.6 Mb]
10
20
10
20
[22.7 Mb]
10
20
[22.7 Mb]
10
20
10
20
0
50
0
50
0
100
50
0
100
50
0
Deletions (No.)
Deletions (No.)
100
100
Chr. 10
(4181)
50
0
100
Chr. 11
(5064)
100
0
0
0
0
[27.6 Mb]
20
20
(d)
[27.6 Mb]
Deletions (No.)
Deletions (No.)
Deletions (No.)
Deletions (No.)
Deletions (No.)
20
30
[36.0 Mb]
10
20
30
[36.2 Mb]
10
20
30
10
20
[29.7 Mb]
10
20
30 [30.7 Mb]
10
20
[29.6 Mb]
10
20
10
20
[22.7 Mb]
10
20
[22.7 Mb]
10
20
10
20
[43.2 Mb]
50
0
[35.5 Mb]
100
50
0
100
Chr. 8
(7151)
Chr. 12
(6412)
0
10
40
0
50
0
50
0
100
50
0
[28.4 Mb]
100
50
0
100
50
0
100
50
0
[28.4 Mb]
50
10
100
Chr. 11
(7550)
30
50
[22.7 Mb]
50
10
Chr. 12
(4462)
50
100
Chr. 10
(6281)
20
0
[22.7 Mb]
0
10
50
Chr. 7
(7795)
Chr. 9
(5809)
20
0
100
[28.4 Mb]
50
[28.4 Mb]
100
20
0
10
50
[29.6 Mb]
50
[22.7 Mb]
50
20
20
[27.6 Mb]
100
30 [30.7 Mb]
0
10
100
20
50
10
[28.4 Mb]
100
100
Chr. 6
(8376)
10
[28.4 Mb]
100
[29.7 Mb]
0
[22.7 Mb]
50
20
50
100
Chr. 9
(3761)
(b)
10
100
[35.5 Mb]
100
[28.4 Mb]
0
20
[29.7 Mb]
50
[36.2 Mb]
Chr. 5
(7210)
0
Deletions (No.)
20
50
10
Deletions (No.)
Chr. 8
(4982)
30
50
[29.6 Mb]
0
20
20
100
Deletions (No.)
20
20
0
10
Deletions (No.)
0
30
Chr. 4
(8173)
10
Chr. 7
(4928)
20
50
30 [30.7 Mb]
50
10
10
[35.5 Mb]
0
Deletions (No.)
Deletions (No.)
20
50
20
100
Chr. 3
(10372)
10
Chr. 6
(5182)
10
Deletions (No.)
Chr. 11
(3423)
30
50
[36.0 Mb]
0
[35.5 Mb]
0
20
100
30
50
[29.7 Mb]
50
10
Deletions (No.)
Deletions (No.)
Deletions (No.)
Deletions (No.)
Deletions (No.)
Deletions (No.)
100
Chr. 10
(2705)
20
Deletions (No.)
30
20
0
10
Chr. 5
(4860)
10
20
100
[43.2 Mb]
Chr. 2
(10470)
50
Deletions (No.)
Deletions (No.)
20
0
100
40
30
0
[36.2 Mb]
Chr. 4
(5258)
50
100
20
50
10
100
100
Deletions (No.)
30
0
10
Chr. 12
(2904)
20
100
[36.0 Mb]
50
100
10
(e)
Chr. 1
(12580)
10
Chr. 3
(6534)
10
Chr. 9
(2610)
30
0
100
Chr. 8
(3168)
20
50
10
Chr. 7
(3269)
[43.2 Mb]
0
100
Chr. 6
(3352)
40
30
Chr. 2
(6594)
10
Chr. 5
(3140)
[36.2 Mb]
0
[27.6 Mb]
0
Deletions (No.)
100
20
50
10
Chr. 4
(3296)
20
50
Deletions (No.)
Deletions (No.)
Deletions (No.)
100
Chr. 12
(8221)
100
Deletions (No.)
Deletions (No.)
Chr. 1
(7817)
10
Chr. 3
(4350)
Deletions (No.)
0
30
0
[28.4 Mb]
50
20
(c)
0
100
20
100
10
50
[22.7 Mb]
0
10
50
Deletions (No.)
Chr. 2
(4488)
20
50
[27.6 Mb]
100
10
Chr. 11
(9315)
Deletions (No.)
Deletions (No.)
Deletions (No.)
Deletions (No.)
Deletions (No.)
0
100
(a)
Chr. 1
(5409)
Chr. 10
(7516)
[36.0 Mb]
100
[22.7 Mb]
50
10
Chr. 12
(3929)
20
100
[28.4 Mb]
0
Chr. 9
(6890)
Deletions (No.)
20
50
10
0
30
50
[28.4 Mb]
50
10
0
20
100
[22.7 Mb]
Chr. 11
(4709)
10
0
20
[43.2 Mb]
100
[29.6 Mb]
Chr. 8
(8999)
10
50
20
50
10
40
0
Deletions (No.)
100
20
0
100
[22.7 Mb]
Chr. 10
(3653)
10
Chr. 12
(4431)
20
0
Chr. 7
(8977)
30
50
30 [30.7 Mb]
50
Deletions (No.)
Deletions (No.)
100
Chr. 11
(6035)
10
50
20
100
10
Chr. 9
(3458)
0
Chr. 6
(9484)
Deletions (No.)
Deletions (No.)
100
Chr. 10
(4836)
0
20
100
[29.7 Mb]
50
[28.4 Mb]
50
20
100
10
0
20
Chr. 5
(8515)
10
0
[35.5 Mb]
0
[29.6 Mb]
Chr. 8
(4209)
10
Chr. 9
(4688)
20
50
30
Deletions (No.)
Deletions (No.)
Deletions (No.)
100
Deletions (No.)
10
100
20
50
10
Chr. 7
(4463)
0
Chr. 4
(9363)
0
50
[36.2 Mb]
100
30 [30.7 Mb]
50
30
Deletions (No.)
Deletions (No.)
Chr. 8
(5895)
20
100
20
0
10
Chr. 6
(4923)
0
Chr. 3
(11607)
50
100
[36.0 Mb]
50
[29.7 Mb]
50
30
0
10
0
20
100
20
50
[35.5 Mb]
Chr. 5
(4547)
10
Chr. 7
(5937)
30
100
Deletions (No.)
100
20
50
Chr. 2
(12387)
100
[43.2 Mb]
0
10
Chr. 4
(4590)
40
30
50
[36.2 Mb]
0
10
Chr. 6
(6593)
30
50
20
100
10
Chr. 3
(5972)
20
0
[36.0 Mb]
0
10
Chr. 5
(6088)
30
50
10
Chr. 4
(6422)
20
50
10
Deletions (No.)
100
0
Chr. 1
(14996)
100
[43.2 Mb]
Chr. 2
(6031)
10
Chr. 3
(8593)
40
30
Deletions (No.)
Deletions (No.)
Chr. 2
(8475)
20
Deletions (No.)
Deletions (No.)
100
10
50
Deletions (No.)
Deletions (No.)
100
Chr. 1
(7169)
0
Deletions (No.)
Deletions (No.)
100
50
Deletions (No.)
Deletions (No.)
100
Deletions (No.)
Chr. 1
(9902)
[28.4 Mb]
100
50
0
[27.6 Mb]
(f)
Supporting FigureS4 Distribution of deletions identified between each of the six elite
indica rice inbreds and Nipponbare in the 12 rice chromosomes (a) 9001 A; (b) 9001 R;
(c) 9002; (d) 9002 R; (e) 9003 A; (f) 9003 R. The x-axis represents the physical distance
along each chromosome, split into 100kb windows. The total size of each chromosome
is shown in brackets. The y-axis indicates the number of SNPs. The total number of
SNPs in each chromosome is shown in the parenthesis.
100000
100000
75000
75000
50000
50000
25000
25000
0
0
-8
-7
-6
-5 -4
-3
-2
-1 +1 +2 +3 +4 +5 +6 +7
-8
-7
-6
-5 -4
-3
-2
(a)
-1 +1 +2 +3 +4 +5 +6 +7
(b)
100000
100000
75000
75000
50000
50000
25000
25000
0
0
-8
-7
-6
-5 -4
-3
-2
-8
-1 +1 +2 +3 +4 +5 +6 +7
-7
-6
-5 -4
-3
-2
(c)
(d)
100000
100000
75000
75000
50000
50000
25000
25000
0
-1 +1 +2 +3 +4 +5 +6 +7
0
-8
-7
-6
-5 -4
-3
-2
-1 +1 +2 +3 +4 +5 +6 +7
(e)
-8
-7
-6
-5 -4
-3
-2
-1 +1 +2 +3 +4 +5 +6 +7
(f)
Supplementary Figure S5 Distribution of InDel polymorphisms in each of the elite
indica rice inbreds compared to Nipponbare genome based on their length (a) 9001 A;
(b) 9001 R; (c) 9002; (d) 9002 R; (e) 9003 A; (f) 9003 R. The x-axis shows the number
of nucleotides of deletions (yellowish orange) and insertions (olive green). The y-axis
shows the number of InDels at each length.
CDS
744
Synonymous 21265
UTRs
26737
Synonymous 20100
UTRs
3266
UTRs
3211
Introns & Reg.
Sequences
15497
CDS
44609
Introns & Reg.
Sequences
127693
UTRs
25542
Genic
199039
Genic
11074
Genic
10394
Intergenic
31041
Intergenic
29591
Intergenic
608996
Non repeat
regions
75896
Non repeat
regions
77896
Non repeat
regions
39985
Non repeat
regions
835254
Non repeat
regions
42115
Non repeat
regions
797840
Repeat
regions
17979
Repeat
regions
15659
Repeat
regions
240891
SNP
Insertion
SNP
Deletion
Insertion
Non-synonymous
Introns & Reg.
Sequences
122347
Synonymous 23429
UTRs
2113
Introns & Reg.
Sequences
12139
CDS
40983
CDS
486
CDS
528
UTRs
2181
21501
UTRs
25605
Deletion
(b)
CDS
447
Synonymous 19482
Repeat
regions
10213
Repeat
regions
8840
Repeat
regions
228037
(a)
UTRs
30315
CDS
49270
Introns & Reg.
Sequences
142642
Genic
14637
Genic
14767
Non-synonymous
25841
Introns & Reg.
Sequences
11996
Intergenic
41500
CDS
698
UTRs
2306
UTRs
2354
Introns & Reg.
Sequences
12998
Introns & Reg.
Sequences
12941
Genic
15790
Genic
222227
Genic
188935
Genic
15993
Intergenic
46073
Intergenic
43016
Intergenic
47633
Intergenic
742370
Intergenic
609926
Non repeat
regions
56267
Non repeat
regions
61863
Non repeat
regions
57653
Repeat
regions
13447
Repeat
regions
11973
Repeat
regions
231916
SNP
Insertion
SNP
Deletion
Insertion
CDS
1729
CDS
1417
UTRs
4978
Intergenic
88312
UTRs
34185
UTRs
4299
UTRs
4196
Introns & Reg.
Sequences
18162
Introns & Reg.
Sequences
19041
CDS
57935
Introns & Reg.
Sequences
152550
Genic
27429
Genic
23984
Genic
24688
Genic
244670
Intergenic
88844
Intergenic
641625
Non-synonymous
30569
Introns & Reg.
Sequences
20946
Genic
28424
Genic
186515
Synonymous 27366
UTRs
4753
Introns & Reg.
Sequences
22029
CDS
42577
CDS
1626
CDS
1348
Non-synonymous
Introns & Reg.
Sequences
117879
Deletion
(d)
22354
UTRs
26059
Repeat
regions
16717
Repeat
regions
14511
Repeat
regions
290394
(c)
Synonymous 20223
Non repeat
regions
63626
Non repeat
regions
964597
Non repeat
regions
798861
Intergenic
73311
Intergenic
74197
Intergenic
824179
Non repeat
regions
116736
Non repeat
regions
97999
Non repeat
regions
116273
Non repeat
regions
8284140
SNP
Introns & Reg.
Sequences
8949
Introns & Reg.
Sequences
8584
CDS
42103
Genic
188844
Intergenic
58208
Intergenic
636215
Repeat
regions
250114
UTRs
1547
UTRs
1473
Introns & Reg.
Sequences
121199
Genic
19688
Intergenic
56389
Non-synonymous
22003
Introns & Reg.
Sequences
15323
Genic
19507
CDS
578
CDS
337
CDS
1154
Non-synonymous
23344
Non repeat
regions
1068849
Repeat
regions
24478
Insertion
(e)
Repeat
regions
27347
Deletion
Repeat
regions
317171
SNP
Repeat
regions
19510
Insertion
Non repeat
regions
98181
Repeat
regions
22174
Deletion
(f)
Supporting FigureS6 Annotation of SNPs, Insertions and Deletions identified between
each of the six elite rice genotypes and Nipponbare (a) 9001 A vsNipponbare; (b) 9001
R vsNipponbare; (c) 9002 A vsNipponbare; (d) 9002 R vsNipponbare; (e) 9003 A
vsNipponbare; (f) 9003 R vsNipponbare. SNPs, Insertions and Deletions between each
of the inbreds and Nipponbare were classified based on the annotations of the
Nipponbare reference genome.
8000
7271
8000
6000
6000
4000
4000
2000
2000
700
1184
621
600
Number of genes
700
960
Number of genes
Number of genes
1131
700
7404
7107
700
700
623
600
600
700
700
605
600
600
500
500
500
500
500
400
400
400
400
400
300
300
300
300
300
200
200
200
200
200
107
82
100
100
100
36
14
3
2
4
2
2
1.76
1.0
6.0
4.0
8.0
12.0
10.0
41
7
2
00
0
89
100
100
25
1.68
1.0
14.0
8.0
6.0
4.0
12.0
10.0
14.0
16.2
1.77
1.0
(a)
2
1
12.0
10.0
14.0
15.8
Number of non-synonymous SNPs/ kb
(c)
8000
8.0
6.0
4.0
Number of non-synonymous SNPs/ kb
Number of non-synonymous SNPs/ kb
8000
4
00
(e)
8000
7473
8385
7078
6000
4000
2000
6000
6000
4000
4000
2000
2000
1860
1285
670
600
600
Number of genes
700
700
Number of genes
Number of genes
973
700
700
625
600
600
700
700
500
500
500
500
500
500
400
400
400
400
400
400
300
300
300
300
200
200
200
200
80
100
100
300
300
34
10
3
100
100
43
11
2
1
6
3
1.69
4.0
6.0
8.0
10.0
Number of non-synonymous SNPs/ kb
(b)
12.0
14.0
15.0
65
17
3
9
6
1
0
1
00
00
1.0
186
200
200
142
100
100
00
649
600
600
1.0
1.86
4.0
6.0
8.0
10.0
Number of non-synonymous SNPs/ kb
(d)
12.0
14.0
16.2
1.0
2.06
4.0
6.0
8.0
10.0
12.0
14.0
16.0
18.0
20.0
Number of non-synonymous SNPs/ kb
(f)
Supporting FigureS7Degree of distribution and skewness of non-synonymous SNPs
per kb in genes among each of the six elite inbred lines and Nipponbare. (a) 9001 A
vsNipponbare – 9,185 genes were annotated by 23,344 non-synonymous SNPs; (b)
9001 R vsNipponbare – 8,851 genes were annotated by 22,003 non-synonymous SNPs ;
(c) 9002 A vsNipponbare– 8,807 genes were annotated by 21,501 non-synonymous
SNPs; (d) 9002 R vsNipponbare – 9,591 genes were annotated by 25,841 nonsynonymous SNPs; (e) 9003 A vsNipponbare – 9,337 genes were annotated by 22,354
non-synonymous SNPs; (f) 9003 R vsNipponbare – 11,179 genes were annotated by
30,569 non-synonymous SNPs. The outlier value calculation indicated that the
genotypes had 783, 800, 740, 833, 800 and 934 genes (light green bars) which had
higher non-synonymous SNPs per kb in a gene (as indicated by the respective outlier
values – with a perpendicular dotted line in the x-axis) respectively.