Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	246,301	C→G	100%	intergenic (+1/‑57)	phoB → / → phoR	DNA‑binding response regulator in two‑component regulatory system with PhoR (or CreC)/sensory histidine kinase in two‑component regulatory system with PhoB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	246,301	0	C	G	98.2%	183.7 / ‑3.6	54	intergenic (+1/‑57)	phoB/phoR	DNA‑binding response regulator in two‑component regulatory system with PhoR (or CreC)/sensory histidine kinase in two‑component regulatory system with PhoB
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base G (53/0);  total (54/0)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GTGCAGACCGTGCGCGGTACAGGATATCGTTTTTCAACCCGCTTTTAACGCCTTGCTCATCGGACGCAG  >  minE/246253‑246321                                                 |                     gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCgg        >  1:6295/1‑63 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCgg        >  1:1696913/1‑63 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:550898/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:218851/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:222151/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:2255212/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:264738/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:291756/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:336614/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:338717/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:341812/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:361571/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:423522/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:432001/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:491560/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:4973/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:2160717/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:640809/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:649673/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:666971/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:691051/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:700785/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:774959/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:776514/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:883828/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:925858/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:986962/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:1713949/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:1067626/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:109722/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:1099495/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:116127/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:1394792/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:1449328/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:1460712/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:1603672/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:1618575/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:1620174/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:1639385/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:1712941/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:1020779/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:1743322/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:1782938/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:1813698/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:1837883/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:1894804/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:1902224/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:1912864/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:1937090/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:2008194/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:2087417/1‑64 (MQ=255) gTGCAGACCGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:2139903/1‑64 (MQ=255) gTGCAGACAGTGCGCGGTACAGGGTATCGTTTTTCAACCCGCTTTTAAGGCCTTGCTCATCGGa       >  1:539335/1‑64 (MQ=255)   gCAGACCGTGCGCGGTACAGGATATCGTTTTTCAACCCGCTTTTAACGCCTTGCTCATCGGACGCag  >  1:1933191/1‑67 (MQ=255)                                                 |                     GTGCAGACCGTGCGCGGTACAGGATATCGTTTTTCAACCCGCTTTTAACGCCTTGCTCATCGGACGCAG  >  minE/246253‑246321

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑