Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,636,925	G→C	R77P (CGC→CCC)	creC →	sensory histidine kinase CreC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,636,925	0	G	C	96.9%	103.3 / ‑2.8	32	R77P (CGC→CCC)	creC	sensory histidine kinase CreC
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base C (13/18);  total (13/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.97e-01

AGCCTGAGGGGCCTGTAATGCGTATCGGCATGCGGTTGTTGCTGGGCTATTTTTTACTGGTGGCGGTGGCAGCCTGGTTCGTACTGGCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCGCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAGGGCAAAGTATTGTTCGATTCGGCAAATAAAGCCGTTGGACAGGATTATTCGCGCTGGAATGACGTCTGGCTAACGTTGCGTGGTCAGTATGGTGCGCGCAGCACGTTGCAAAATCCTGCCGATCCCGAAAGTTCTGTGATGTATGTTGCCGCACCGATT  >  NC_000913/4636679‑4637157                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                         aGCCTGAGGGGCCTGTAATGCGTATCGGCATGCGGTTGTTGCTGGGCTATTTTTTACTGGGGGCGGGGGCAGCCTGGTTCGTACTGGCCATTTTTGTCAAAGCAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGGTGATCGACACCGCAACGTTGATGGCGGAGCTGGCGCGGACCGATTTGCTCTCTGGGGACCCAACGCCTGGGCAACTGGCGCAGGCGGTTAATCAGCTACAACATCccccc                                                                                                                                                                                                                                      >  2:191296/1‑250 (MQ=255)      gAGGGGCCTGTAATGCGTATCGGCATGCGGTTGTTGCTGGGCTATTTTTTACTGGTGGCGGTGGCAGCCTGGTTCGTACTGGCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTcg                                                                                                                                                                                                                                 <  2:57561/251‑1 (MQ=255)           cccTGTAATGCGTATCGGCATGCGGTTGTTGCTGGGCTATTTTTTACTGGTGGCGGTGGCAGCCTGGTTCGTACTGGCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTGATCCACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGCTTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCCGGCGTTTAATCAGCTACAACATCCCCCGttttccgccc                                                                                                                                                                                                                            >  2:136233/2‑244 (MQ=255)             cTGTAATGCGTATCGGCATGCGGTTGTTGCTGGGCTATTTTTTACTGGTGGCGGTGGCAGCCTGGTTCGTACTGGCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGAAGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCCCGTCCCGGTTTGCTCTCCGGGGACCCCACGCCTGGGCCACTTGCGCAAGGGTTTAATCAGCTACCACCTCCCCCGGTTcgccccca                                                                                                                                                                                                                           >  2:93470/1‑245 (MQ=255)                     cGTATCGGCATGCGGTTGTTGCTGGGCTATTTTTTACTGGTGGCGGTGGCAGCCTGGTTCGTACTGGCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTgg                                                                                                                                                                                                                  >  1:226998/1‑251 (MQ=255)                      gTATCGGCATGCGGTTGTTGCTGGGCTATTTTTTACTGGTGGCGGTGGCAGCCTGGTTCGTACTGGCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGc                                                                                                                                                                                                                 <  1:38141/251‑1 (MQ=255)                        aTCGGCATGCGGTTGTTGCTGGGCTATTTTTTACTGGTGGCGGTGGCAGCCTGGTTCGTACTGGCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGCAt                                                                                                                                                                                                               <  1:139725/251‑1 (MQ=255)                                gCGGTTGTTGCTGGGCTATTTTTTACTGGTGGCGGTGGCAGCCTGGTTCGTACTGGCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAg                                                                                                                                                                                                       <  1:197177/251‑1 (MQ=255)                                                                cggtggcAGCCTGGTTCGTACTGGCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGAt                                                                                                                                                                       <  2:198829/251‑1 (MQ=255)                                                                      cAGCCTGGTTCGTAATGGCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCCACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGCCTATATGACCGATgcgc                                                                                                                                                                   >  2:115812/1‑249 (MQ=255)                                                                       aGCCTGGTTCGTACTGGCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATAGCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAgg                                                                                                                                                                <  2:210990/251‑1 (MQ=255)                                                                        gCCTGGTTCGTACTGGCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAggg                                                                                                                                                               <  1:131971/251‑1 (MQ=255)                                                                                      ggCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAGGGCAAAGTATTGtt                                                                                                                                                   <  1:198635/249‑1 (MQ=255)                                                                                           tttttGTCAAAGAAGTTCAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGCATTCACAAAGTGCGCAATGAATATCATGTCTATCTGACCGATGCGCAGGGCAAAGTATTGTTCGATTCg                                                                                                                                            >  2:178382/1‑251 (MQ=255)                                                                                                           tAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAGGGCAAAGTATTGTTCGATTCGGCAAATAAAGCCGtt                                                                                                                             <  1:127761/250‑1 (MQ=255)                                                                                                             aaCCGGGCGTGCGAAGAGCAACGGAGGGGCCGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAGGGCAAAGTATTGTTCGATTCGGCAAATAAAGCCGTTggc                                                                                                                          >  2:214278/1‑250 (MQ=255)                                                                                                                                     aGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAGGGCAAAGTATTGTTCGATTCGGCAAATAAAGCCGTTGGACAGGATTATTCGCGCTGGAATGAc                                                                                                  <  1:43161/251‑1 (MQ=255)                                                                                                                                      ggggACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAGGGCAAAGTATTGTTCGATTCGGCAAATAAAGCCGTTGGACAGGATTATTCGCGCTGGAATGACg                                                                                                 >  1:132645/1‑251 (MQ=255)                                                                                                                                            gTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACAT‑GCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAGGGCAAAGTATTGTTCGATTCGGCAAATAAAGCCGTTGGACAGGATTATTCGCGCTGGAATGACGTCTGGCt                                                                                          <  1:14689/251‑1 (MQ=255)                                                                                                                                             ttGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAAATGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAGGGCAAAGTATTGTTCGATTCGGCAAATAAAGCCGTTGGACAGGATTATTAGCGCTGGAATGACGTCTGGCt                                                                                          >  2:139881/1‑251 (MQ=255)                                                                                                                                                           aaCGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAGGGCAAAGTATTGTTCGATTCGGCAAATAAAGCCGTTGGACAGGATTATTCGCGCTGGAATGACGTCTGGCTAACGTTGCGTGGTc                                                                            <  1:7561/251‑1 (MQ=255)                                                                                                                                                                                            gCTCTCTGGGGACCCAACGCATGTGCAACTGGCGCAGGCGGTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAGGGCAAAGTATTGTTCGATTCGGCAAATAAAGCCGTTGGACAGGATTATTCGCGCTGGAATGACGTCTGGCTAACGTTGCGTGGTCAGTATGGTGCGCGCAGCACGTTGCAAAATCCt                                            <  2:83188/250‑1 (MQ=255)                                                                                                                                                                                            gCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCTGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAGGGCAAAGGATTATTCGATTCGGCAAATAAAGCCGTTGGACAGGATTATTCGCGCTGGAATGACGTCTGGCTAACGTTGCGTGGTCAGTATGGTTCCCGCAGCACGTTGCAAAATCCTg                                           <  1:204679/251‑1 (MQ=255)                                                                                                                                                                                            gCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAGGGCAAAGTATTGTTCGATTCGGCAAATAAAGCCGTTGGACAGGATTATTCGCGCTGGAATGACGTCTGGCTAACGTTGCGTGGTCAGTATGGTGCGCGCAGCACGTTGCAAAATCCTg                                           <  2:54456/251‑1 (MQ=255)                                                                                                                                                                                                 ctGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAGGGCAAAGTATTGTTCGATTCGGCAAATAAAGCCGTTGGACAGGATTATTCGCGCTGGAATGACGTCTGGCTAACGTTGCGTGGTCAGTATGGTGCGCGCAGCACGTTGCAAAATCCTGCCGAt                                      >  2:179845/1‑251 (MQ=255)                                                                                                                                                                                                        cccAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAGGGCAAAGTATTGTTCGATTCGGCAAATAAAGCCGTTGGACAGGATTATTCGCGCTGGAATGACGTCTGGCTAACGTTGCGTGGTCAGTATGGTGCGCGCAGCACGTTGCAAAATCCTGCCGATCCCGaaa                               <  2:132645/251‑1 (MQ=255)                                                                                                                                                                                                        cccAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAGGGCAAAGTATTGTTCGATTCGGCAAATAAAGCCGTTGGACAGGATTATTCGCGCTGGAATGACGTCTGGCTAACGTTGCGTGGTCAGTATGGTGCGCGCAGCACGTTGCAAAATCCTGCCGATCCCGaaa                               <  1:210938/251‑1 (MQ=255)                                                                                                                                                                                                             cGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAGGGCAAAGTATTGTTCGATTCGGCAAATAAAGCCGTTGGACAGGATTATTCGCGCTGGAATGACGTCTGGCTAACGTTGCGTGGTCAGTATGGTGCGCGCAGCACGTTGCAAAATCCTGCCGATCCCGAAAGTTCt                          >  1:59302/1‑251 (MQ=255)                                                                                                                                                                                                                aTGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCACTATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAGGGCAAAGTATTGTTCGATTCGGCAAATAAAGCCGTTGGACAGGATTATTCGCGCTGGAATGACGTCTGGCTAACGTTGCGTGGTCAGTATGGTGCGCGCAGCACGTTGCAAAATCCTGCCGATCCCGACAGTTCtgtg                       >  1:229224/1‑251 (MQ=255)                                                                                                                                                                                                                 tGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAGGGCAAAGTATTGTTCGATTCGGCa                                                                                                                                         >  2:150629/1‑136 (MQ=255)                                                                                                                                                                                                                 tGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAGGGCAAAGTATTGTTCGATTCGGCa                                                                                                                                         <  1:150629/136‑1 (MQ=255)                                                                                                                                                                                                                                    tttAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGAGCAGGGCAAAGTATTGTTCGATTCGGCAAATAAAGCCGTTGGACAGGATTATTCGCGCTGGAATGACGTCTGGCTAACGTTGCGTGGTCAGTATGGTGCGCGCAGCACGTTGCAAAATCCTGCCGATCCCGAAAGTTCTGTGATGTATGTTGCCGCACCGAt   >  1:245565/1‑251 (MQ=255)                                                                                                                                                                                                                                      tAATCAGCTACAACATCCCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAGGGCAAAGTATTGTTCGATTCGGCAAGTAAAGCCGTTGGACAGGATTATTCGCGCTGGAATGACGTCTGGCTAACGTTGCGTGGTCAGTATGGTGCGCGCAGCACGTTGCAAAATCCTGCCGATCCCGAAAGTTCTGTGATGTATGTTGCCGCACCGAtt  <  1:194627/250‑1 (MQ=255)                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                         AGCCTGAGGGGCCTGTAATGCGTATCGGCATGCGGTTGTTGCTGGGCTATTTTTTACTGGTGGCGGTGGCAGCCTGGTTCGTACTGGCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAACGGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGGGACCCAACGCATGGGCAACTGGCGCAGGCGTTTAATCAGCTACAACATCGCCCGTTTCGCGCCAATATCGGTGGCATTAACAAAGTGCGCAATGAATATCATGTCTATATGACCGATGCGCAGGGCAAAGTATTGTTCGATTCGGCAAATAAAGCCGTTGGACAGGATTATTCGCGCTGGAATGACGTCTGGCTAACGTTGCGTGGTCAGTATGGTGCGCGCAGCACGTTGCAAAATCCTGCCGATCCCGAAAGTTCTGTGATGTATGTTGCCGCACCGATT  >  NC_000913/4636679‑4637157

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑