miRNA Polymorphism Validation

Type - 1 = "Variant exists in both RNAseq and trace data", 2 = "Variant only exists in RNAseq data", 3 = "Variant exists in only trace data".

I've scanned 27 of the 203 inferred variants. There are still 176 positions to scan.

miRNA Name

Variant Details

Image

dme-mir-13b-2

Species	Chrom	Pos	Ref base	Type	A	C	G	T	RNAseq Total	A	C	G	T	Trace Total	Decision	Partition
dp4	chrXL_group1e	7000802	A	2	0.1	0	0.025	0.875	40	1	0	0	0	7	Valid - polymorphic	3' MOR
droMoj3	scaffold_6473	13342566	A	2	0.145	0.012	0.024	0.819	83	1	0	0	0	8	Valid - polymorphic	5' MOR
droPer1	super_13	1553336	T	2	0.813	0	0	0.188	16	0	0	0	0	2	Valid - polymorphic	5' MOR
droPer1	super_13	1553337	G	2	0.875	0	0.063	0.063	16	0	0	0	0	2	Valid - polymorphic	5' MOR
droVir3	scaffold_12970	9304409	T	2	0.78	0.04	0	0.18	100	0	0	0	1	8	Valid - polymorphic	3' MOR
droVir3	scaffold_12970	9304410	G	2	0.91	0.03	0.02	0.04	100	0	0	1	0	8	Valid - polymorphic	3' MOR
droWil1	scaffold_180777	2053158	C	2	0.959	0.04	0.001	0	1362	0	1	0	0	10	Valid - polymorphic	3' MOR

[picture]

dme-mir-13b-2-as

Species	Chrom	Pos	Ref base	Type	A	C	G	T	RNAseq Total	A	C	G	T	Trace Total	Decision	Partition
dp4	chrXL_group1e	7000802	A	2	0.1	0	0.025	0.875	40	1	0	0	0	7	Invalid - antisense reads	NA
droMoj3	scaffold_6473	13342566	A	2	0.145	0.012	0.024	0.819	83	1	0	0	0	8	Invalid - antisense reads	NA
droPer1	super_13	1553336	T	2	0.813	0	0	0.188	16	0	0	0	0	2	Invalid - antisense reads	NA
droVir3	scaffold_12970	9304409	T	2	0.78	0.04	0	0.18	100	0	0	0	1	8	Invalid - antisense reads	NA
droWil1	scaffold_180777	2053158	C	2	0.959	0.04	0.001	0	1362	0	1	0	0	10	Invalid - antisense reads	NA

Valid - polymorphic

dme-mir-184

Species	Chrom	Pos	Ref base	Type	A	C	G	T	RNAseq Total	A	C	G	T	Trace Total	Decision	Partition
dp4	chr3	696774	A	2	0	0	0	1	21	1	0	0	0	27	Invalid- 3' RNA-editing	miR
droPer1	super_2	863216	A	2	0.222	0.056	0	0.722	18	1	0	0	0	10	Invalid- 3' RNA-editing	miR

[dp4 picture]

[droPer1 picture]

dme-mir-2a-1

Species

Chrom

Pos

Ref base

Type

RNAseq Total

Trace Total

Decision

Partition

droWil1

scaffold_180708

4284763

0.028

0.972

3446

Invalid - RNA- editing

3' MOR

[droWil1 picture]

dme-mir-2281

Species	Chrom	Pos	Ref base	Type	A	C	G	T	RNAseq Total	A	C	G	T	Trace Total	Decision	Partition
droSec1	super_0	11818543	T	2	0	1	0	0	91	0	0	0	1	4	Invalid- Antisense to the ortholog	miR*
droSim1	chr3R	11233927	C	3	0	0	0	0	0	0	0.4	0	0.6	15	Valid- Genomic Error	5' MOR

[droSec1 picture]

[droSim1 picture]

dme-mir-2495

Species

Chrom

Pos

Ref base

Type

RNAseq Total

Trace Total

Decision

Partition

droMoj3

scaffold_6500

1220508

0.8

0.2

Valid - Genomic Errror

miR*

[droMoj3 picture]

dme-mir-286

Species

Chrom

Pos

Ref base

Type

RNAseq Total

Trace Total

Decision

Partition

dp4

chr3

12677658

0.55

0.448

0.002

471

Valid - Polymorphic

miR*

[dp4 picture]

dme-mir-310

Species	Chrom	Pos	Ref base	Type	A	C	G	T	RNAseq Total	A	C	G	T	Trace Total	Decision	Partition
dp4	chr3	8680049	A	2	0.237	0	0	0.763	355	1	0	0	0	15	Valid - genomic error	miR
dp4	chr3	8680090	G	2	0	0.845	0.155	0	174	0	0	1	0	16	Valid - genomic error	miR*
droSim1	chr2R	15132610	T	3	0	0	0	0	9	0	0.625	0	0.375	8	Valid - genomic error	miR*

[dp4 picture]

[droSim1 picture]

dme-mir-4944

Species

Chrom

Pos

Ref base

Type

RNAseq Total

Trace Total

Decision

Partition

droEre2

scaffold_4770

15270508

0.55

0.45

Ambiguous- Polymorphic

miR*

[droEre1 picture]

dme-mir-4947

Species	Chrom	Pos	Ref base	Type	A	C	G	T	RNAseq Total	A	C	G	T	Trace Total	Decision	Partition
droEre2	scaffold_4820	3199338	T	2	0	0	1	0	38	0	0	0	1	10	Invalid - Antisense to the miRNA	--
droEre2	scaffold_4820	3199345	T	2	1	0	0	0	38	0	0	0	1	10	Invalid- Antisense to teh miRNA	--
droSec1	super_4	3696566	A	2	0	0	0	1	48	1	0	0	0	13	Invalid - Antisense to the miRNA	--
droSec1	super_4	3696573	A	2	0	1	0	0	48	1	0	0	0	13	Invalid - Antisense to the miRNA	--

[droSec1 picture]

[droEre2 picture]

dme-mir-6-1

Species	Chrom	Pos	Ref base	Type	A	C	G	T	RNAseq Total	A	C	G	T	Trace Total	Decision	Partition
droSim1	chr2R	14253986	A	3	0	0	0	0	0	0.471	0	0.529	0	17	Valid - polymorphic in different strains	loop
droSim1	chr2R	14253990	A	3	0	0	0	0	0	0.471	0	0	0.529	17	Valid - polymorphic in different strains	loop

[droSim1 picture]

dme-mir-6-3

Species	Chrom	Pos	Ref base	Type	A	C	G	T	RNAseq Total	A	C	G	T	Trace Total	Decision	Partition
droEre2	scaffold_4845	9748488	A	2	0.4	0.55	0	0.05	20	1	0	0	0	17	Invalid- genuine cross-mapped reads with 6-1, 6-2 ignored	miR*
droMoj3	scaffold_6496	20935971	A	2	0.417	0.556	0.028	0	36	1	0	0	0	11	Invalid- genuine cross-mapped reads with 6-1, 6-2 ignored	miR*
droSim1	chr2R	14253669	A	2	0.333	0.583	0.083	0	36	1	0	0	0	19	Invalid- genuine cross-mapped reads with 6-1, 6-2 ignored	miR*
droVir3	scaffold_12875	4113022	T	2	0	0.036	0.5	0.464	28	0	0	0	1	9	Invalid- genuine cross-mapped reads with 6-1, 6-2 ignored	miR*
droYak2	chr2R	13624555	T	2	0	0.125	0.625	0.25	16	0	0	0	1	13	Invalid- genuine cross-mapped reads with 6-1, 6-2 ignored	miR*

[droYak2 picture]

[droEre2 picture]

dme-mir-92a

Species

Chrom

Pos

Ref base

Type

RNAseq Total

Trace Total

Decision

Partition

droWil1

scaffold_181130

14578441

0.015

0.001

0.984

1504

Invalid - RNA-editing

5' MOR

[droWil1 image]

dme-mir-971

Species	Chrom	Pos	Ref base	Type	A	C	G	T	RNAseq Total	A	C	G	T	Trace Total	Decision	Partition
droAna3	scaffold_13117	3891875	A	2	0.359	0	0.641	0	485	0.875	0	0	0.125	8	Valid- RNA-editing	miR
droEre2	scaffold_4690	13914770	T	2	0.008	0.809	0	0.183	1061	0	0	0	1	8	Valid- RNA-editing	miR
droSec1	super_21	701307	A	2	0.38	0	0.62	0	526	1	0	0	0	7	Valid- RNA-editing	miR
droYak2	chrX	7229837	G	3	0	0	0	0	0	0.3	0	0.7	0	10	Valid- RNA-editing	miR
droYak2	chrX	7229859	A	2	0.579	0	0.413	0.008	126	1	0	0	0	10	Valid- RNA-editing	miR

[link]

dme-mir-977

Species

Chrom

Pos

Ref base

Type

RNAseq Total

Trace Total

Decision

Partition

droMoj3

scaffold_6328

2900876

0.001

0.656

0.343

1391

Valid - Polymorphic

miR

[droMoj3 picture]

dme-mir-978-as

Species	Chrom	Pos	Ref base	Type	A	C	G	T	RNAseq Total	A	C	G	T	Trace Total	Decision	Partition
droAna3	scaffold_13417	2460600	G	2	0.083	0.75	0.167	0	12	0	0	1	0	8	Ambiguous- unusual read pileup	miR*
droAna3	scaffold_13417	2460610	C	2	0.867	0.133	0	0	15	0	1	0	0	8	Ambiguous- unusual read pileup	3' MOR

[droAna3 picture]

dme-mir-985

Species

Chrom

Pos

Ref base

Type

RNAseq Total

Trace Total

Decision

Partition

droEre2

scaffold_4690

10993738

0.004

0.006

0.99

512

Valid- Genomic Error

miR

[droEre2 picture]

Updated: 8/26/2011