Table 1. Comparison of 5′ RACE/primer extension 5′ end determination and 5′RNA-seq identified TSSs in B. burgdorferi B31.

Gene	ORF annotationa	5′ RACE/primer extension 5′ end position	Reference	5′ RNA-seq TSS position	Avg. TAP+ read countb	Avg. TAP- read countc	TAP+:TAP- Ratio	Nucleotide position difference (nts)d
ospAe	BB_A15	9421	(94)	9421	19 421	1407	13.8	0
chbC	BB_B04	3849	(95)	3849	1693	28.5	59.4	0
bb0360 operon	BB_0360-0364	368 456	(71)	368 456	3941.5	123.5	31.9	0
antigen IpLA7	BB_0365	374 265	(96)	374 190	1097.5	172.5	6.4	75
cheYI operon	BB_0551	561 955	(97)	561 958	1433	55.5	25.8	3
bbb22	BB_B22	19 338	(78)	19 336	3020.5	160.5	18.8	2
bbb23	BB_B23	21 082	(78)	21 080	1609	59.5	27.0	2
bpur	BB_0047	46 423	(98)	46 423	191	60	3.2	0
bdrF2operon	BB_G29	24 469	(99)	24 347	222	11	20.2	122
	BB_G31	26 453		Nonef	N/Ag	N/A	N/A	N/A
	BB_G33	28 014		28 017	293.5	25.5	11.5	3

^aB. burgdorferi gene annotations with one letter code signifying plasmid amplicon (50,90).

^bAverage normalized read counts from two biological replicated 5′RNA-seq TAP+ libraries, for a given TSS.

^cAverage normalized read counts from two biological replicated 5′RNA-seq TAP- libraries, for a given TSS.

^dDifferences in TSS positions from 5′ RACE/primer extension compared to 5′RNA-seq.

^eThe two previously published TSSs for the ospC gene were not included, as these data were acquired using a B. burgdorferi strain other than B31 (100–102). Nonetheless, the 5′RNA-seq defined TSS for ospC was found to be located one and four nucleotides away from the two previously defined sites of transcription initiation.

^fNo TSS was identified within 300 nucleotides of BB_G31 ORF.

^gNot applicable.