Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,636,767	C→T	A24A (GCC→GCT)	creC →	sensory histidine kinase CreC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,636,767	0	C	T	96.8%	82.2 / ‑5.8	31	A24A (GCC→GCT)	creC	sensory histidine kinase CreC
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (11/19);  total (11/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.66e-01

AGCAACTGATGGATAGCGTATGGGAAGATGCGCAGGACACCTACGATCGCACCGTCGATACCCACATTAAAACGCTGCGTGCCAAGCTGCGCGCCATCAACCCCGATCTTTCACCGATTAATACTCATCGCGGCATGGGATATAGCCTGAGGGGCCTGTAATGCGTATCGGCATGCGGTTGTTGCTGGGCTATTTTTTACTGGTGGCGGTGGCAGCCTGGTTCGTACTGGCCATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCGCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAGGGCAAAGTATTGT  >  NC_000913/4636536‑4637011                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                      aGCAACTAATGGATAGCGTGTGGGAAGATGCGCAGGACACCTACGATCGCACCGTTGATACCCACATTAAAACGTTGCGTGCCAAGCTGCGCGCCATCAACCCCGATCTTTCACCGATTAATACTCATCGCGGCATGGGATATAGCCTGAGGGGCCTGTAATGCGTATCGGCATGCGGTTGCTGCTGGGCTATTTTTTACTGGTGGCGGTGGCGGCCTGGTTCGTACTGGCTATTTTTGTCAAAG‑AAGTTa                                                                                                                                                                                                                                   <  1:80363/251‑1 (MQ=255)   cAACTGATGTATAGCATATGGGAAGACGCGCAGTACACCTACGATCGCACCGTCGATACCCACATTAAAACGCTGCGTGGCAAGCTGCGCGCCAGCAGCCCCGATCTTTCCCCGAATAATACTCAACGCTGCATGGGATATATTCTGAGGGGCCTGTAATGGTTATCCGCAGGCGGTTGTTGCTGGGCTAGTTGTTACTGGTGGCGGGGGCAGCCGGGTTCTTACTGGCCATTTTTGTCAAAG‑AAGTTaaa                                                                                                                                                                                                                                 <  1:15879/251‑1 (MQ=255)           ggATAGCGTGTGGGAAGATGCGCAGGACACCTACGATCGCACCGTTGATACCCACATTAAAACGTTGCGTGCCAAGCTGCGCGCCATCAACCCCGATCTTTCACCGATTAATACTCATCGCGGCATGGGATATAGCCTGAGGGGCCTGTAATGCGTATCGGCATGCGGTTGCTGCTGGGCTATTTTTTACTGGTGGCGGTGGCGGCCTGGTTCGTACTGGCTATTTTTGTCAAAG‑AAGTTAAACCGGGCgg                                                                                                                                                                                                                         >  1:137866/1‑250 (MQ=255)                     tGGGAAGATGCGCAGGACAACTACGATCGCACCGATGATACCCCCATTAAAACGTTGCGTGCCAAGCTGCGCGCCATCAACCCCGATCTTTCACCGATTAATACTCATCGCGGCATGGGATATAGCCTGAGGGGCCTGTAATGCGTATCGGAATGCGGTTGCTGCTGGGCTATTTTTTACTGGTGGCGGTGGCGGCCTGGTTCGTACTGGCTATTTTTGTTAAAGTAAGT‑AAACCGGGCGTGCGAGGAGc                                                                                                                                                                                                                >  2:253636/1‑250 (MQ=255)                               cgcAGGACACCTACGATCGCACCGTTGATACCCACATTAAAACGTTGCGTGCCAAGCTGCGCGCCATCAACCCCGATCTTTCACCGATTAATACTCATCGCGGCATGGGATATAGCCTGAGGGGCCTGTAATGCGTATCGGCATGCGGTTGCTGCTGGGCTATTTTTTACTGGTGGCGGTGGCGGCCTGGTTCGTACTGGCTATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGAGCAACGGAggggg                                                                                                                                                                                                     >  1:250591/1‑250 (MQ=255)                                       ccctccgaccgccccgtgtaTACCCACATTAAAACGTGGCGTGCCAAGTTGCGCGCCATCAACCCCGATCTGTCACCGATTAATACTCATCGCGGCATGGGATATAGCCTGAGTGGCCTGTAATGCGTATCGGCATGCGGTTGCTGCTGGGCTATTTTTTACTGGTGGCGGTGGCGGCCTGGTTCGTACTGGCTATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGAGCAACGGAGTGGACGTTAATc                                                                                                                                                                                             <  2:250591/232‑1 (MQ=255)                                                        tgATACCCACATTAAAACG‑TTCGTGCCAAGCTGCGCGCCATCAACCCCGATCTTTCACCGATTAATACTCATCGCGGCATGGGATATAGCCTGAGGGGCCTGTAATGCGTATCGGCATGCGGTTGCTGCTGGGCTATTTTTTACTGGTGGCGGTGGCGGCCTGGTTCGTACTGGCTATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTAATCGATACCGCAACGTTGCTg                                                                                                                                                                           >  1:74948/2‑251 (MQ=255)                                                                    tAAAACGTTGCGTGCCAAGCTGCGCGCCATCAACCCCGCTGTTTCACCGATTAATACTCATCGCGGCATGGGATATAGCCTGAGGGGCCTGTAATGCGTATCGGCATGCGGTTGCTGCTGGGCTATTTTTTACTGGTGGCGGTGGCGGCCTGGTTCGTACTGGCTATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTAATCGATACCGCAACGTTGCTGGCGGAGCTgg                                                                                                                                                                 <  2:67123/250‑1 (MQ=255)                                                                       aaCGTTGCGTGCCAAGCTGCGCGCCATCAACCCCGATCTTTCACCGATTAATACTCATCGCGGCATGGGATATAGCCTGAGGGGCCTGTAATGCGTATCGGCATGCGGTTGCTGCTGGGCTATTTTTTACTGGTGGCGGTGGCGGCCTGGTTCGTACTGGCTATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTAATCGATACCGCAACGTTGCTGGCGGAGCTGGcgcg                                                                                                                                                             >  1:245171/1‑251 (MQ=255)                                                                              cGTGCCAAGCTGCGCGCCATCAACCCCGATCTTTCACCGATTAATACTCATCGCGGCATGGGATATAGCCTGAGGGGCCTGTAATGCGTATCGGCATGCGGTTGCTGCTGGGCTATTTTTTACTGGTGGCGGTGGCGGCCTGGTTTGTACTGGCTATTTTTGTCAAAG‑AAGTTTAAACGGGCGTGCGAAGGGCAACGGAGGGGGCGGTAAATGATACCGCCACGTTGCTGGGGGGGCTGGggcgggccgct                                                                                                                                                      >  2:364210/1‑244 (MQ=255)                                                                                         ccgcgcCATCAACCCCGATCTTTCACCGTTTAATACTCATCGCGGCATGGGATACAGCCTGAGGGGCCTGTAATGCGTAGCGGCATGCGGTTGCTGCTGGGCTATTTTTTACTGGTGGCGGTGGCGGCCTGGTGCGTACTGGCTATTGTTGTCAAAG‑AAGTTAAACCGGTCATGCTAAGAGCAACGGATGGGACGTTAATCGATACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGctctct                                                                                                                                             <  1:216340/248‑1 (MQ=255)                                                                                                  aaaacccGATCTGTCACCTAGTAATTCTATTCGCGGCATGGGATATAGCCTGAGGGGCCTTGAATGCGTATCGGCATGCGGTTGCTGCTGGGCTATTTGTTACTGGTTGCGGTGGCGGCCTGGTTCGTACTGGCTATTTTTGGCAAAG‑AAGGTAAACCGGGCGGGCGAAGAGCAACGGAGGGGACGTTAATCGATACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAAc                                                                                                                                  <  2:302516/247‑1 (MQ=255)                                                                                                                cACCGATTAATACTCATCGCGGCATGGGATATAGCCTGAGGGGCTTGTAATGCGTATCGGCATGCGGTTGCTGCTTGGCTATTTTTTACTGGTGGCGGTGGCGGCCTGGTTCGTACTGGCTATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTAATCGATACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTg                                                                                                                     <  1:379396/250‑1 (MQ=255)                                                                                                                           gttgaTCGCGGTTTGGGATATAGTCTGGGGTGGCTGTAATGCGTATCGGCAGTCGGTTGCTGCCGGGATAGTTTTGACTGGTGGCGGTGGCGGCCTGGTTCGTACTGGCTATTTTTGGCCAAG‑AAGTTAAACCGGGCGGGCGAAGAGCAACTGAGGGGACGTTAATCGATACCGCAACGTTGCTGGCGGAGCGGGCGTGTCCCGAGTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGAGCTGGCGttt                                                                                                         <  2:207666/247‑1 (MQ=255)                                                                                                                                 cgcgGCATGGGATATAGCCTGAGGGGCCTGTAATGCGTATCGGCATGCGGTTGCTGCTGGGCTATTTTTTACTGGTGGCGGTGGCGGCCTGGTTCGTACTGGCTATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTAATCGATACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTTCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATc                                                                                                     >  1:373166/1‑249 (MQ=255)                                                                                                                                    ggCATGGGATATAGCCTGAGGGGCCTGTAATGCGTATCGGCATGCGGTTGCTGCTGGGCTATTTTTTACTGGTGGCGGTGGCGGCCTGGTTCGTACTGGCTATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTAATCGATACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTa                                                                                                <  1:364210/251‑1 (MQ=255)                                                                                                                                     gCATGGGATATATCCTGAGGGGCCTGTAATGCGTATCGGCATGCGGTTGCTGCTGGTCTATTTTTTACTGGTGGCGGTGGCGGCCTGGTTCGTACTGGCTATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTAATCGATACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTac                                                                                               <  1:194777/251‑1 (MQ=255)                                                                                                                                     gCATGGGATATAGCCTGAGGGGCCTGTAATGCGTATCGGCATGCGGTTGCTGCTGGGCTATTTTTTACTGGTGGCGGTGGCGGCCTGGTTCGTACTGGCTATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTAATCGATACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAAATGGCGCAGGCGTTTAATCAGcaac                                                                                               >  1:109948/1‑248 (MQ=255)                                                                                                                                                 gCCTTAGGTGCCTGTTATGCGTGTCGGCATGCGGTTGTTGCTGGGCTATTTTTGACTGGTGGCGGTGGCGGCCTGGGTTGTACTGGCTATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGATCAACGGAGGGGACGTTAATCGATACCGCAACGTTGCTGGCGGTGCTGGCGCGTCCCGATTTGCTCTCTGGGTACCCACCGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCGCCCGt                                                                                   <  2:9772/251‑1 (MQ=255)                                                                                                                                                       ggggCCTGTAATGCGTATCGGCATGCGGTTGCTGCTGGGCTATTTTTTACTGGTGGCTGTGGCGGCCTGGTTCGTACTGGCTATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTAATCGATACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCGCCCGTTTcgcg                                                                             <  1:209500/251‑1 (MQ=255)                                                                                                                                                       ggggCCTGTAATGCGTATCGGCATGCGGTTGCTGCTGGGCTATTTTTTACTGGTGGCGGTGGCGGCCTGGTTCGTACTGGCTATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTAATCGATACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCCACGCAAGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCGCCCGTTTcgcc                                                                             >  1:16459/1‑250 (MQ=255)                                                                                                                                                       ggggCCTGTAAGGCGTACCGGCATGCGGTTGCTGCTTGGCTATTTTTTACTGGTGGCGGTGGCGGCCTGGTTCGTACTGGCTATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTAATCGATACCGCAACGTTGCGGGCGGAGCTGGCGCGGCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCGCCCGTTTcgcg                                                                             <  1:52470/251‑1 (MQ=255)                                                                                                                                                             tGTAATGCGTATCGGCATGCGGTTGCTGCTGGGCTATTTTTTACTGGTGGCGGTGGCGGCCTGGTTCGTACTGGCTATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTAATCGATACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACt                                                                                                                      <  1:223895/204‑1 (MQ=255)                                                                                                                                                                aaTGCGTATCGGCATGCGGTTGCTGCTGGGCTAGTTTTTACTGGTGGCGGTGGCGGCCTGGTTCGTACTGGCTATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTAATCGATACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCGCCCGTTTCGCGCCAATATCg                                                                    <  1:323345/251‑1 (MQ=255)                                                                                                                                                                               catgttgctGCTTGGCTATTATTTACGGGAGGCGGTGGCGGCCTGGTTCGTACTGGCTATTGTTGTCAAAG‑AAGTTAAACCGGTCGTGCGAAGAGCAACGGAGGGGACGTTAAGCGATACCTCAACGTTGCTGGCGGAGCGGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCGCCCGTTGCGCGCCAATATCGGTGGCATTAACaaa                                                      <  2:282371/247‑1 (MQ=255)                                                                                                                                                                                 ggTTGCTGCTGGGCTCTTTTTTACTGGTGGCGGTGGCGGCCTGGTTCGGACTGGCTATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTAATCGATACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCGCCCGTTTCGCGCCAATATAGGTGGCATTAACaaa                                                      >  1:282371/1‑248 (MQ=255)                                                                                                                                                                                             gCTATTTTTTACTGGTGGCGGTGGCGGCCTGGTTCGTACTGGCTATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTAATCGATACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCGCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAatat                                       <  1:118215/251‑1 (MQ=255)                                                                                                                                                                                                aTTTTTTACTGGTGGCGGTGGCGGCCTGGTTCGTACTGGCTATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTAATCGATACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCGCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCAt                                    <  1:114126/251‑1 (MQ=255)                                                                                                                                                                                                                         cTGGTTCGTACTGGCTATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTAATCGATACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCGCCCATTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATTCGCAgggt            >  1:3618/1‑249 (MQ=255)                                                                                                                                                                                                                            gTTCGTACTGGCTATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTAATCGATACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTacaaca                                                                                           <  1:177844/168‑1 (MQ=255)                                                                                                                                                                                                                                  aCTGGCTATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTAATCGATACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCGCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATTCGCAGGGTAAAGTATTGt  <  1:253636/251‑1 (MQ=255)                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                      AGCAACTGATGGATAGCGTATGGGAAGATGCGCAGGACACCTACGATCGCACCGTCGATACCCACATTAAAACGCTGCGTGCCAAGCTGCGCGCCATCAACCCCGATCTTTCACCGATTAATACTCATCGCGGCATGGGATATAGCCTGAGGGGCCTGTAATGCGTATCGGCATGCGGTTGTTGCTGGGCTATTTTTTACTGGTGGCGGTGGCAGCCTGGTTCGTACTGGCCATTTTTGTCAAAG‑AAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCGCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAGGGCAAAGTATTGT  >  NC_000913/4636536‑4637011

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑