Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 6,007,160 C→T 11.1% V152I (GTA→ATA)  PP_5261 ← LysR family transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029476,007,1600CT11.1% 92.0 / 3.4 36V152I (GTA→ATA) PP_5261LysR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (15/17);  new base T (2/2);  total (17/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

AGTCACGCTTGTCCACCGTGGGGTGCAGCAGTTCGACAGAGGCCAGCCTGCAAACATCCCAGGGCTCCTCGTCGAGCAGGTCCGGCGCGCCGACCGGGATCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTGGTCAG‑CTGCACTTCATTGCCCGGCTGCAGATGCCGAAAGCGGCTAAGGCACGCCAGCAACCAGCGCATGGTCA  >  NC_002947/6007013‑6007309
                                                                                                                                                   |                                                                                                                                                      
aggcACGCTTGTCCACCGTGGGGTGCAGCAGTTCGACAGAGGCCAGCCTGCAAACATCCCAGGGCTCCTCGTCGAGCAGGTCCGGCGCGCCGACCGGGATCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATAccc                                                                                                                                                      >  1:1205237/4‑150 (MQ=255)
 gTCACGCTTGTCCACCGTGGGGTGCAGCAGTTCGACAGAGGCCAGCCTGCAAACATCCCAGGGCTCCTCGTCGAGCAGGTCCGGCGCGCCGACCGGGATCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATAcccc                                                                                                                                                     <  2:576044/150‑1 (MQ=255)
 gTCACGCTTGTCCACCGTGGGGTGCAGCAGTTCGACAGAGGCCAGCCTGCAAACATCCCAGGGCTCCTCGTCGAGCAGGTCCGGCGCGCCGACCGGGATCAGTACCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATAcccc                                                                                                                                                     <  2:327674/150‑1 (MQ=255)
      gCTTGTCCACCGTGGGGTGCAGCAGTTCGACAGAGGCCAGCCTGCAAATTTCCCAGGGCTCCTCGTCGAGCAGGTCCGGCGCGCCGACCGGGATCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATACCCCGTCGc                                                                                                                                                <  1:734822/150‑1 (MQ=255)
                           gcagTTCGACAGAGGCCAGCCTGCAAACATCCCAGGGCTCCTCGTCGAGCAGGTCCGGCGCGCCGACCGGGATCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCaa                                                                                                                               >  1:1096403/1‑146 (MQ=255)
                           gcagTTCGACAGAGGCCAGCCTGCAAACATCCCAGGGCTCCTCGTCGAGCAGGTCCGGCGCGCCGACCGGGATCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCaa                                                                                                                               <  2:1096403/146‑1 (MQ=255)
                            cagTTCGACAGAGGCCAGCCTGCAAACATCCCAGGGCTCCTCGTCGAGCAGGTCCGGCGCGCCGACCGGGATCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGaa                                                                                                                          <  2:967940/150‑1 (MQ=255)
                                        ggCCAGCCTGCAAACATCCCAGGGCTCCTCGTCGAGCAGGTCCGGCGCGCCGACCGGGATCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCTCGCAATCGAATGGCTCCTGGtt                                                                                                              <  1:157620/150‑1 (MQ=255)
                                            aGCCTGCAAACATCCCAGGGCTCCTCGTCGAGCAGGTCCGGCGCGCCGACCGGGATCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGaaa                                                                                                          >  1:913327/1‑150 (MQ=255)
                                             gCCTGCAACCATCCCAGGGCTCCTCGTCGAGCAGGTCCGGCGCGCCGACCGGGATCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAAt                                                                                                         <  2:876521/150‑1 (MQ=255)
                                                            aGGGCTCCTCGTCGAGCAGGTCCGGCGCGCCGACCGGGATCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGAcat                                                                                          <  2:913327/150‑1 (MQ=255)
                                                               gCTCCTCGTCGAGCAGGTCCGGCGCGCCGACCGGGATCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTc                                                                                               >  2:347946/1‑142 (MQ=255)
                                                               gCTCCTCGTCGAGCAGGTCCGGCGCGCCGACCGGGATCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTc                                                                                               <  1:347946/142‑1 (MQ=255)
                                                                      gtcgAGCAGGTCCGGCGCGCCGACCGGGATCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGCATAcc                                                                                                                                                       <  2:301471/79‑1 (MQ=255)
                                                                      gtcgAGCAGGTCCGGCGCGCCGACCGGGATCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATAcc                                                                                                                                                       >  1:301471/1‑79 (MQ=255)
                                                                      gtcgAGCAGGTCCGGCGCGCCGACCGGGATCAGCGGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGgc                                                                                >  1:286187/1‑150 (MQ=255)
                                                                        cgAGCAGGTCCGGCGCGCCGACCGGGATCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGgcgc                                                                              <  2:218960/150‑1 (MQ=255)
                                                                          aGCAGGTCCGGCGCGCCGACCGGGATCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTg                                                                            >  2:1147308/1‑150 (MQ=255)
                                                                                       cgcCGACCGGGATCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTGGTCAG‑CTGCACtt                                                              <  2:9360/150‑1 (MQ=255)
                                                                                          cGACCGGGATCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTGGTCAG‑CTGCACTTCAt                                                           >  1:33327/1‑150 (MQ=255)
                                                                                            accgataTCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATATCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACatccatcc                                                                                    <  1:604536/118‑1 (MQ=255)
                                                                                            aCCGGGATCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATATCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACatccatcc                                                                                    >  2:604536/1‑124 (MQ=255)
                                                                                            aCCGGGATCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTGGTCAG‑CTGCACTTCATTg                                                         >  2:667163/1‑150 (MQ=255)
                                                                                             ccGGGATCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTGGTCAG‑CTGCACTTCATTGc                                                        <  2:789544/150‑1 (MQ=255)
                                                                                                                gAACAGCTTGCGCACCTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTGGTCAG‑CTGCACTTCATTGCCCGGCTGCAGATGCCGaaa                                     <  1:667163/150‑1 (MQ=255)
                                                                                                                  aCAGCTTGCGCACCTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTGGTCAG‑CTGCACTTCATTGCCCGGCTGCAGATGCCGAAAGc                                   >  1:692378/1‑150 (MQ=255)
                                                                                                                    aGCTTGCGCACCTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTGGCCAG‑CTGCACTTCATTGCCCGGCTGCAGATGCCGAAAGCgg                                 <  1:1147308/150‑1 (MQ=255)
                                                                                                                     gCTTGCGCACCTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTGGTCAG‑CTGCACTTCATTGCCCGGCTGCAGATGCCGAAAGCGGc                                >  1:268376/1‑150 (MQ=255)
                                                                                                                              ccTCCCACTCCGGCGGGAATATCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTGGTCAG‑CTGCACTTCATTGCCCGGCTGCAGATGCCGAAAGCGGCTAAGGCACg                       >  1:174314/1‑150 (MQ=255)
                                                                                                                              ccTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTGGTCAG‑CTGCGCTCCGTTGCCCGCCGCCAGATGCCTAAAGCGGCGAAGGCACg                       >  2:1036918/1‑150 (MQ=255)
                                                                                                                               cTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTGGTCAG‑CTGCACTTCATTGCCCGGCTGCAGATGCCGAAAGCGGCTAAGGCACGc                      >  2:983784/1‑150 (MQ=255)
                                                                                                                               cTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTGGTCAG‑CTGCACTTCATTGCCCGGCTGCAGATGCCGAAAGCGGCTAAGGCACGc                      <  1:214852/150‑1 (MQ=255)
                                                                                                                                tCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTGGTCAG‑CTGCACTTCATTGCCCGGCTGCAGATGCCGAAAGCGGCTAAGGCACGcc                     >  2:1140726/1‑150 (MQ=255)
                                                                                                                                 cccACTCCGGCGGGAATATCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTGGTCAG‑CTGCACTTCATTGCCCGGCTGCAGATGCCGAAAGCGGCTAAGGCACGCCa                    <  2:174314/150‑1 (MQ=255)
                                                                                                                                 cccACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGCTCAACATACGTTTGCTGCCTTCACCGACAGC‑CAACATTACCCGGCTGCAGATGCCGAAAGCGGCTACGTCACGCCa                    >  1:444589/1‑150 (MQ=255)
                                                                                                                                    aCTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTGGTCAG‑CTGCACTTCATTGCCCGGCTGCAGATGCCGAAAGCGGCTAAGGCACGCCAGCa                 <  1:1198917/150‑1 (MQ=255)
                                                                                                                                      tCCGGCGGTGATACCCCGTCTCTGAGCAACACGGCGCAATCGAATGGCTCCTGGTGGGATTCCGCATGGTCGACAGCCATCCAGGCGCTGTTCAG‑CTGCACTTCAGTGCCCGGCTGCAGATGCCGAAAGCGGGTAAGGCAGGCGAGCAAc               <  2:33327/150‑1 (MQ=255)
                                                                                                                                               aaTACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTGGTCAG‑CTGCACTTCATTGCCCGGCTGCAGATGCCGAAAGCGGCTAAg                            >  1:879310/1‑128 (MQ=255)
                                                                                                                                               aaTACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTGGTCAG‑CTGCACTTCATTGCCCGGCTGCAGATGCCGAAAGCGGCTAAg                            <  2:879310/128‑1 (MQ=255)
                                                                                                                                                  aCCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTGGTCAG‑CTGCACTTCATTGCCCGGCTGCAGa                                             <  2:759052/108‑1 (MQ=255)
                                                                                                                                                  aCCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTGGTCAG‑CTGCACTTCATTGCCCGGCTGCAGa                                             >  1:759052/1‑108 (MQ=255)
                                                                                                                                                   ccccGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTGGTCAG‑CTGCACTTCATTGCCCGGCTGCAGATGCCGAAAGCGGCTAAGGCACGCCAGCAACCAGCGCATGGTCa  >  1:78258/1‑150 (MQ=255)
                                                                                                                                                   ccccGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTGGTCAG‑CTGCACTTCATTGCCCGGCTGCAGATGCCGAAAGCGGCTAAGGCACGCCAGCAACCAGCGCATGGTCa  <  1:1140726/150‑1 (MQ=255)
                                                                                                                                                   |                                                                                                                                                      
AGTCACGCTTGTCCACCGTGGGGTGCAGCAGTTCGACAGAGGCCAGCCTGCAAACATCCCAGGGCTCCTCGTCGAGCAGGTCCGGCGCGCCGACCGGGATCAGTAGCTCAGGGAACAGCTTGCGCACCTCCCACTCCGGCGGGAATACCCCGTCGCTGAGCAACACCGCGCAATCGAATGGCTCCTGGTTGAAATCCACATGGTCGACATCCATCCAGGCGCTGGTCAG‑CTGCACTTCATTGCCCGGCTGCAGATGCCGAAAGCGGCTAAGGCACGCCAGCAACCAGCGCATGGTCA  >  NC_002947/6007013‑6007309

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑