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%	68.9 / NA	16	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 . (9/7);  total (9/7)
*	NC_000913	2,173,362	0	C	.	93.8%	60.1 / ‑1.7	16	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 (1/0);  new base . (8/7);  total (9/7)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACT  >  NC_000913/2173322‑2173410                                        ||                                                 aactGGCGAGCGGCAGAAAAATCAGGCCCGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGa                     <  1:683427/65‑1 (MQ=255) aaaTGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGa                     <  1:349580/68‑1 (MQ=255)    tGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCcagca                                <  1:827446/54‑1 (MQ=255)    tGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCcagca                                >  2:827446/1‑54 (MQ=255)    tGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCCACGCCGGATCa                  >  2:998138/1‑68 (MQ=255)     ggTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCaa                 >  1:290885/1‑68 (MQ=255)     ggTGAGTGGGATAAAAATCAGGCTTGCCGATA‑CA‑CCCGCCGTATGTCACAGCAGCAACGCCGGATCac                 >  2:821095/1‑67 (MQ=255)      gTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAg                <  2:685410/68‑1 (MQ=255)      gTGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAg                <  2:993250/68‑1 (MQ=255)       tGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAgg               >  2:985169/1‑68 (MQ=255)       tGAGTGGGATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGACGGATCAAgg               >  2:848794/1‑68 (MQ=255)              gATAAAAATCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCa        <  2:290885/68‑1 (MQ=255)                    aaTCAGGCTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACt  >  1:325599/1‑68 (MQ=255)                    aaTCAGGCTTGACGATACAA‑‑CCGCCGTATGTCACAGCAGCACCGCCGGATCACGGCCAATCAGGCACt  >  1:935833/1‑68 (MQ=255)                           cTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAAc   <  1:482163/60‑1 (MQ=255)                           cTTGCCGATACCA‑‑CCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAAc   >  2:482163/1‑60 (MQ=255)                                        ||                                                 AAATGGTGAGTGGGATAAAAATCAGGCTTGCCGATACCACCCCGCCGTATGTCCCAGCAGCAACGCCGGATCAAGGCCAATCAGGAACT  >  NC_000913/2173322‑2173410

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑