Use of mRNA-seq to discriminate contributions to the transcriptome from the constituent genomes of the polyploid crop species Brassica napus

Higgins, Janet; Magusin, Andreas; Trick, Martin; Fraser, Fiona; Bancroft, Ian

doi:10.1186/1471-2164-13-247

Table 1 Summary of read alignments

From: Use of mRNA-seq to discriminate contributions to the transcriptome from the constituent genomes of the polyploid crop species Brassica napus

				Naive reference					Cured reference
Sample	Experiment	Type	No. sequence reads	No. sequence reads mapped to reference	Aligned reference sequence /bases	Average depth over aligned reference	No. unigenes with mapped sequence reads	Total sequence mapped to naive reference/Gb	No. sequence reads mapped to A genome	No. A genome unigenes with mapped sequence reads	No. sequence reads mapped to C genome	No. C genome unigenes with mapped sequence reads	Aligned reference sequence /bases	Average depth over aligned reference	Total sequence mapped to cured reference/ Gb	Increase sequence mapped to reference / %
B. napus 1 rep1	BCC_1_2*	Resynthesized (B. rapa cytoplasm)	30290727	11396746	27704492	32.9	60801	0.91	8136121	57101	7725545	57232	48716080	26.0	1.27	39.2
B. napus 1 rep2	BCC_2_2_rep*		32362747	12596459	27628537	36.4	60182	1.01	8974130	56758	8472600	56859	48927782	28.5	1.40	38.5
B. napus 1 rep3	BCC_3_2*		30212318	12688970	28367947	35.8	60953	1.02	8933134	57381	8523534	57505	50115239	27.9	1.40	37.6
B. napus 1 rep4	BCC_4_2*		29073842	12556527	27816387	36.1	60572	1.00	8886730	57072	8581997	57168	49020495	28.5	1.40	39.1
B. napus 2 rep1	BCC_1_4*	Resynthesized (B. oleracea cytoplasm)	28333122	11390102	28050282	32.5	61139	0.91	8138583	57406	7545728	57600	49388101	25.4	1.25	37.7
B. napus 2 rep2	BCC_2_4*		27156815	11209306	27415043	32.7	59994	0.90	7908682	56465	7619986	56551	48167524	25.8	1.24	38.5
B. napus 2 rep3	BCC_3_4*		29720775	12618159	28214425	35.8	61051	1.01	8828851	57410	8491265	57632	49691719	27.9	1.39	37.3
B. napus 2 rep4	BCC_4_4*		29830870	12580532	28294428	35.6	61303	1.01	8829979	57645	8473127	57779	49861276	27.8	1.38	37.5
Tapidor	TAP**	Winter	22841910	11026783	28473370	31.0	61776	0.88	6770387	57940	7281348	58231	48844912	23.0	1.12	27.4
Ningyou 7	NIN**	Chinese	23151184	10774087	28233727	30.5	61982	0.86	6640976	58055	6841509	58167	48266879	22.3	1.08	25.1
Altasweet	D3_ALT*	Swede	29080184	13239756	28730927	36.9	61251	1.06	8340513	58022	8806044	58177	49777567	27.6	1.37	29.5
Ceska	D31_CES*	Spring	28036702	13193597	29567877	35.7	61903	1.06	8050594	58512	8803320	58830	51209098	26.3	1.35	27.7
Aphid Resistant Rape	D8_AphRR*	Fodder	28334337	11879400	29161922	32.6	62434	0.95	7486610	58922	7881247	59083	50269176	24.5	1.23	29.4

* deposited under SRA accession ERA063602.
**deposited under SRA accession ERA036824.

Back to article page

ISSN: 1471-2164

Contact us

Submission enquiries: bmcgenomics@biomedcentral.com
General enquiries: ORSupport@springernature.com

BMC Genomics

Contact us