Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,173,363	Δ2 bp	intergenic (‑1/+1)	gatC ← / ← gatC	pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,173,361	0	C	.	100.0%	35.4 / NA	9	pseudogene (2/442 nt)	gatC	pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (7/2);  total (7/2)
*	NC_000913	2,173,362	0	C	.	100.0%	35.4 / NA	9	pseudogene (1/442 nt)	gatC	pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (7/2);  total (7/2)

GATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTC  >  NC_000913/2173295‑2173411                                                                   ||                                                  gATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATaccacc                                                   <  1:1300/68‑1 (MQ=255) gATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATaccacc                                                   <  1:399869/68‑1 (MQ=255)     aCCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATaccaccgc                                                 <  1:36116/66‑3 (MQ=255)     aCCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATaccaccgc                                                 >  2:36116/1‑64 (MQ=255)            acacaAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTcc                                      >  2:341351/1‑68 (MQ=255)                       aaTTAATATGGTGAGTGGGATAAAAATCAGGCTTTCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACg                           <  1:553618/68‑1 (MQ=255)                            aaaTGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACg                           >  1:71021/1‑63 (MQ=255)                            aaaTGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACg                           <  2:71021/63‑1 (MQ=255)                            aaaTGGTGAGTGGGATAAAAATCAGGCATGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGAACCGCCGGa                      >  1:73596/1‑68 (MQ=255)                             aaTGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGAt                     >  2:397182/1‑68 (MQ=255)                                ggTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCaa                  >  1:540063/1‑68 (MQ=255)                                                aTCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTc  >  1:344132/1‑68 (MQ=255)                                                aTCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTc  >  1:666448/1‑68 (MQ=255)                                                                   ||                                                  GATTACCCGGCACACAAACAGCAATTAAAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACTC  >  NC_000913/2173295‑2173411

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑