Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,986,861	C→T	100%	intergenic (+141/‑58)	PP_5245 → / → kefB‑III	AraC family transcriptional regulator/glutathione‑regulated potassium/H+ antiporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,986,861	0	C	T	94.3%	153.8 / ‑0.2	54	intergenic (+141/‑58)	PP_5245/kefB‑III	AraC family transcriptional regulator/glutathione‑regulated potassium/H+ antiporter
Reads supporting (aligned to +/- strand):  ref base C (2/1);  new base T (23/27);  total (26/28)
Fisher's exact test for biased strand distribution p-value = 5.97e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.64e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTAGCGCTGCCTTCTTCGCGGGCGCGCCCGCTCCCACAGAGATAGCACAGGCCTTGAGCCCAGGTAAGCGCCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTCAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTCTGCAAACCGCGGTGATCTTCCTGCTTGCCGCCGTCCTCGCCGTCCCCCTGGCCAAGCGCCTGCAAC  >  NC_002947/5986717‑5987006                                                                                                                                                 |                                                                                                                                                   ttAGCGCTGCCTTCTTCGCGGGCGCGCCCGCTCCCACAGAGATAGCACAGGCCTTGAGCCCAGGTAAGCGCCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGaa                                                                                                                                                <  4:288724/149‑1 (MQ=255)      gcTGCCTTCTTCGCGGGCGCGCCCGCTCCCACAGAGATAGCACAGGCCTTGAGCCCAGGTAAGCGCCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTc                                                                                                                                           <  2:102098/149‑1 (MQ=255)       cTGCCTTCTTCGCGGGCGCGCCCGCTCCCACAGAGATAGCACAGGCCTTGAGCCCAGGTAAGCGCCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTcc                                                                                                                                          <  6:159783/149‑1 (MQ=255)          ccTTCTTCGCGGGCGCGCCCGCTCCCACAGAGATAGCACAGGCCTTGAGCCCAGGTAAGCGCCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGt                                                                                                                                        >  3:218414/1‑148 (MQ=255)          ccTTCTTCGCGGGCGCGCCCGCTCCCACAGAGATAGCACAGGCCTTGAGCCCAGGTAAGCGCCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTCAGAATTGTCCGt                                                                                                                                        >  4:122941/1‑148 (MQ=255)                gagcgGGCGCGCCCGCTCCCACAGAGATAGCACAGGCCTTGAGCCCAGGTAAGCGCCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTg                                                                                                                                 >  1:221965/3‑149 (MQ=255)                          gcCCGCTCCCACAGAGATAGCACAGGCCTTGAGCCCAGGTAAGCGCCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCt                                                                                                                       >  1:241906/1‑149 (MQ=255)                            ccGCTCCCACAGAGATAGCACAGGCCTTGAGCCCAGGTAAGCGCCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCt                                                                                                                       >  8:123858/1‑147 (MQ=255)                            ccGCTCCCACAGAGATAGCACAGGCCTTGAGCCCAGGTAAGCGCCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCt                                                                                                                       <  7:123858/147‑1 (MQ=255)                             cGCTCCAACATATATAGCAAAGGCCTTTCGCCCAGGTATGGGCCGGAACGGATTGTCACTCTGTAAAGTACAATTTTTCTTCCCGTAATATTATTGTCTTACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGcc                                                                                                                    <  2:241906/149‑1 (MQ=255)                                tCCCACAGAGATAGCACTGGCCTTGAGCCCAGGTAAGCGCCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTAAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCg                                                                                                                 >  3:30891/1‑149 (MQ=255)                                      agagATAGCACAGGCCTTGAGCCCAGGTAAGCGCCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCt                                                                                                           >  6:22156/1‑149 (MQ=255)                                          aTAGCACAGGCCTTGAGCCCAGGTAAGCGCCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATg                                                                                                       <  2:221965/149‑1 (MQ=255)                                           tAGCACAGGCCTTGAGCCCAGGTAAGCGCCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATgg                                                                                                      <  3:156382/149‑1 (MQ=255)                                             gCACTGGCCTTGAGCCCAGGTAAGCGCCGGCACCGATTGTCACTGTTGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGa                                                                                                     <  6:14934/148‑1 (MQ=255)                                              cacaGGCCTTGAGCCCAGGTAAGCGCCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGaa                                                                                                                                                >  7:85373/1‑104 (MQ=255)                                              cacaGGCCTTGAGCCCAGGTAAGCGCCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGaa                                                                                                                                                <  8:85373/104‑1 (MQ=255)                                                 aGGCCTTGAGCCCAGGTAAGCGCCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTAc                                                                                                 >  6:156991/1‑148 (MQ=255)                                                        gAGCCCAGGTAAGCGCCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCaa                                                                                          <  3:318351/148‑1 (MQ=255)                                                             cAGGTAAGCGCCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCcac                                                                                    <  7:259570/149‑1 (MQ=255)                                                               ggTAAGCGCCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCGCATGGAGTACGAGCCAATGCCacac                                                                                  <  4:218414/149‑1 (MQ=255)                                                                   aGCGCCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAg                                                                             >  7:31587/1‑149 (MQ=255)                                                                    gcgcCGGCACCGATTGTAACTCTGTACAGGACAATTTTTCTTCCCTTGAGATGATTGTCTGACGCCACACTACACCTTAGAATTGTCCGTCATACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCTATGCCACACG‑TAg                                                                             <  2:297820/148‑1 (MQ=255)                                                                     cgcCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACg                                                                                                                         >  7:56832/1‑104 (MQ=255)                                                                     cgcCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACg                                                                                                                         <  8:56832/104‑1 (MQ=255)                                                                     cgcCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGc                                                                           <  8:31587/149‑1 (MQ=255)                                                                        cGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGc                                                                        <  5:22156/149‑1 (MQ=255)                                                                            aCCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTc                                                                    >  7:191556/1‑149 (MQ=255)                                                                                    tCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTCTg                                                                  <  1:94444/143‑1 (MQ=255)                                                                                    tCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTCTg                                                                  >  1:320877/1‑143 (MQ=255)                                                                                    tCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTCTg                                                                  <  2:320877/143‑1 (MQ=255)                                                                                    tCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTCTg                                                                  >  2:94444/1‑143 (MQ=255)                                                                                    tCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTCTGCAAAcc                                                            >  1:117015/1‑149 (MQ=255)                                                                                    tCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCAACACG‑AAGGCAGCCTTCTGCAAAcc                                                            >  2:64789/1‑149 (MQ=255)                                                                                                  acaATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTCTGCAAACCGCGGTGATCTTCCt                                              <  8:13928/149‑1 (MQ=255)                                                                                                      tttttCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTCTGCAAACCGCGGTGATCTTCCTGCtt                                          >  3:152820/1‑149 (MQ=255)                                                                                                          tcttcCCGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTCTGCAAACCGCGGTGATCTTCCTGCTTgcc                                       <  5:156991/148‑1 (MQ=255)                                                                                                              cccGTCAGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACGAAAGGCAGCCTTCTGCAAACCGCGGTGATCTTCCTGCTTgccgcc                                    <  1:64789/148‑1 (MQ=255)                                                                                                                    aGATGATTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTCTGCAAACCGCGGTGATCTTCCTGCTTGCCGCCGTCCTCGc                            >  2:265188/1‑149 (MQ=255)                                                                                                                         atTGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTCTGCAAACCGCGGTGATCTTCCTGCTTGCCGCCGTCCTCGCCGTcc                       >  5:131243/1‑149 (MQ=255)                                                                                                                          ttGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGcc                                                                       >  6:122527/1‑100 (MQ=255)                                                                                                                          ttGTCTGACGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGcc                                                                       <  5:122527/100‑1 (MQ=255)                                                                                                                               tGACGCCACACTACCCCTTTGAATTGTCGTGCAAACTGTTCGAACGCTGCCCCGTCAGCTCATGGAGTACGAGCCAATGCGACACG‑AAGGGAGCCTTCTGCAAACCGCGGTGATCTTCCTGCTTGCCGCCGTCCTCGCCGTCCCCGTgg                 <  4:30891/149‑1 (MQ=255)                                                                                                                                  cGCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTCTGCAAACCGCGGTGATCTTCCTGCTTGCCGCCGTCCTCGCCGTCCCCCTGGCCa              <  1:265188/149‑1 (MQ=255)                                                                                                                                   gCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTCTGCAAACCGCGGTGATCTTCCTGCTTgcc                                       <  4:251361/123‑1 (MQ=255)                                                                                                                                   gCCACACTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTCTGCAAACCGCGGTGATCTTCCTGCTTgcc                                       >  3:251361/1‑123 (MQ=255)                                                                                                                                     cacaCTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTTCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTCTGCAAACCGCGGTGATCTTCCTGCTTGCCGCCGTCCTCGCCGTCCCCCTGGCCAAgc           <  7:127664/149‑1 (MQ=255)                                                                                                                                     cacaCTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTCTGCAAACCGCGGTGATCTTCCTGCTTGCCGCCGTCCTCGCCGTCCCCCTGGCCAAgc           >  5:211665/1‑149 (MQ=255)                                                                                                                                        acTACCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTCTGCAAACCGCGGTGATCTTCCTGCTTGCCGCCGTCCTCGCCGTCCCCCTGGCCAAGCGcc        <  6:131243/149‑1 (MQ=255)                                                                                                                                          tACCCCTCAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTCTGCAAACCGCGGTGATCTTCCTGCTTGCCGCCGTCCTCGCCGTCCCCCTGGCCAAGCGCCt       >  7:243159/1‑148 (MQ=255)                                                                                                                                           aCCCCTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTCTGCAAACCGCGGTGATCTTCCTGCTTGCCGCCGTCCTCGCCGTCCCCCTGGCCAAGCGCCTg      >  1:181818/1‑148 (MQ=255)                                                                                                                                            ccccTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTCTGCAAACCGCGGTGATCTTCCTGCTTGCCGACGTCCTCGCCGTCCCCCTGGCCAAGCGCCTGc     >  5:30708/1‑148 (MQ=255)                                                                                                                                            ccccTCAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTCTGCAAACCGCGGTGATCTTCCTGCTTGCCGCCGTCCTCGCCGTCCCCCTGGCCAAGCGCCt       <  8:243159/146‑1 (MQ=255)                                                                                                                                              ccTTAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTCTGCAAACCGCGGTGATCTTCCTGCTTGCCGCCGTCCTCGCCGTCCCCCTGGCCAAGCGCCTGCAAc  >  4:44519/1‑149 (MQ=255)                                                                                                                                                 |                                                                                                                                                   TTAGCGCTGCCTTCTTCGCGGGCGCGCCCGCTCCCACAGAGATAGCACAGGCCTTGAGCCCAGGTAAGCGCCGGCACCGATTGTCACTCTGGACAGGACAATTTTTCTTCCCGTCAGATGATTGTCTGACGCCACACTACCCCTCAGAATTGTCCGTCAAACTGTTCGAACGCTGCCCCGGCAGCTCATGGAGTACGAGCCAATGCCACACG‑AAGGCAGCCTTCTGCAAACCGCGGTGATCTTCCTGCTTGCCGCCGTCCTCGCCGTCCCCCTGGCCAAGCGCCTGCAAC  >  NC_002947/5986717‑5987006

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑