A robust and cost-effective approach to sequence and analyze complete genomes of small RNA viruses

Dimitrov, Kiril M.; Sharma, Poonam; Volkening, Jeremy D.; Goraichuk, Iryna V.; Wajid, Abdul; Rehmani, Shafqat Fatima; Basharat, Asma; Shittu, Ismaila; Joannis, Tony M.; Miller, Patti J.; Afonso, Claudio L.

doi:10.1186/s12985-017-0741-5

Virology Journal

Table 2 Summary of sequencing and assembly data of 25 avian paramyxovirus isolates

From: A robust and cost-effective approach to sequence and analyze complete genomes of small RNA viruses

Isolate number	% PF reads^a	Number of raw read pairs	Number of filtered read pairs^b	Forward read quality^c	Reverse read quality^c	Identified virus	Final coverage depth^c	Number of reads used for consensus^d	Consensus nucleotide length	Missing positions at 5' end^e	Length of internal gaps	Missing positions at 3' end^e	Percent coverage^e
1002	2.49	409193	405137	2\|37\|38\|38\|38	2\|36\|37\|38\|38	NDV	0\|3680\|6088\|7868\|18004	390740	15124		68		99.55
1004	2.67	437755	432361	2\|37\|38\|38\|38	2\|34\|37\|38\|38	NDV	0\|4185\|6151\|7909\|14329	422150	15125		67		99.56
1007	4.20	688524	681691	2\|37\|38\|38\|38	2\|36\|37\|38\|38	NDV	0\|817\|3648\|7368\|19348	665220	15125		67		99.56
994	1.39	227500	226196	2\|37\|38\|38\|38	2\|36\|37\|38\|38	NDV	0\|1758\|2756\|4186\|14276	219609	15121		71		99.53
995	1.38	226050	224416	2\|36\|37\|38\|38	2\|34\|36\|37\|38	NDV	0\|2162\|2995\|4197\|9101	216240	15110		82		99.46
996	1.53	251238	250338	2\|37\|38\|38\|38	2\|34\|37\|37\|38	NDV	0\|2383\|3175\|4411\|9167	242158	15104	20	68		99.42
1001	3.79	621655	618002	2\|37\|38\|38\|38	2\|36\|37\|38\|38	NDV	0\|4653\|6784\|9510\|21623	594361	15122		70		99.54
997	1.72	281376	266251	2\|37\|38\|38\|38	2\|35\|37\|38\|38	NDV	0\|1937\|3026\|4030\|9645	233775	15104	22	66		99.42
999	1.70	279207	272105	2\|37\|38\|38\|38	2\|36\|37\|38\|38	NDV	0\|1728\|2583\|4496\|11915	241105	15108		84		99.45
1000	1.74	285079	280596	2\|37\|38\|38\|38	2\|35\|37\|38\|38	NDV	0\|2338\|3107\|4441\|8796	241724	15117		75		99.51
959	3.60	590494	588212	2\|37\|38\|38\|38	2\|37\|38\|38\|38	APMV-13	1\|2250\|3484\|5801\|23998	531520	16126	20			99.88
960	4.34	711909	709377	2\|37\|37\|38\|38	2\|37\|37\|38\|38	NDV	0\|3738\|5631\|7347\|19491	628837	15135	25	32		99.62
961	4.61	756197	753487	2\|36\|37\|38\|38	2\|35\|37\|38\|38	NDV	0\|4585\|6509\|8206\|14939	674667	15167	25			99.84
962	3.35	548833	547622	2\|37\|38\|38\|38	2\|35\|37\|38\|38	NDV	2\|4617\|6340\|8772\|14719	529553	15192				100.00
967	3.71	607876	597902	2\|37\|38\|38\|38	2\|36\|37\|38\|38	NDV	2\|2673\|3928\|6881\|26072	562657	15192				100.00
968	4.46	731692	727838	2\|37\|38\|38\|38	2\|35\|37\|38\|38	NDV	0\|2507\|4136\|7393\|22877	636218	15167	19			99.87
695	7.16	1156516	1129415	2\|36\|37\|38\|38	2\|35\|37\|38\|38	NDV	2\|1678\|3827\|6301\|32862	955829	15192				100.00
714	3.98	653603	643246	2\|37\|37\|38\|38	2\|36\|37\|38\|38	NDV	1\|2082\|3513\|6724\|35052	570825	15192				100.00
715	3.63	594802	580223	2\|37\|38\|38\|38	2\|36\|37\|38\|38	NDV	10\|2608\|5633\|8881\|28809	526885	15192				100.00
720	4.05	663757	657982	2\|37\|37\|38\|38	2\|35\|37\|38\|38	NDV	13\|3821\|6267\|9252\|27439	525313	15192				100.00
861	3.51	576077	574864	2\|37\|38\|38\|38	2\|35\|37\|38\|38	NDV	6\|3930\|6419\|8881\|27153	559394	15192				100.00
867	4.11	673510	668781	2\|37\|38\|38\|38	2\|36\|37\|38\|38	NDV	0\|4284\|6079\|9028\|23441	647586	15176	16			99.89
892	3.92	642753	642250	2\|37\|38\|38\|38	2\|35\|37\|38\|38	NDV	1\|5147\|7049\|9922\|18221	618591	15180	12			99.92
913	4.06	665640	661350	2\|36\|37\|38\|38	2\|35\|37\|38\|38	NDV	0\|2278\|3784\|7011\|31842	566280	15192				100.00
688	0.01	no data	NA	NA	NA	NA	NA		NA	NA	NA	NA	NA

NA not applicable
^a the fraction of reads assigned to each sample out of all number of reads that passed filter (i.e. pass-filter reads)
^b the number of paired reads remaining after host and internal control filtering
^c numbers represent distribution (minimum | lower quartile | median | upper quartile | maximum)
^d numbers of paired reads used to re-call the final consensus for each sequence
^e the missing nucleotides at the ends and the fraction of the expected full genome length covered by the consensus scaffold (i.e. not containing unknown nucleotides)

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ISSN: 1743-422X

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