Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,978,903 G→T 9.5% R72S (CGC→AGC)  PP_5241 ← LuxR family transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,978,9030GT 9.5% 128.5 / 3.5 42R72S (CGC→AGC) PP_5241LuxR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (19/19);  new base T (2/2);  total (21/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.69e-01

GCGGCTCGACAGTCTCGGCCAGGCTGCGCAGCAACGACCTGCCCAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGCCGGACCACACCTGGCTGAACAACTCGTCCTTGCCGACCACGCG‑GCCCTTGGCCCTGATCAGCGTGGCCAGCACGTCGAAAGCACGCCCACCCAACAG  >  NC_002947/5978762‑5979047
                                                                                                                                             |                                                                                                                                                 
gCGGCTCGACAGTCTCGGCCAGGCTGCGCAGCAACGACCTGCCCAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAg                                                                                                                                            <  8:189920/149‑1 (MQ=255)
gCGGCTCGACAGTCTCGGCCAGGCTGCGCAGCAACGACCTGCCCAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAg                                                                                                                                            <  5:109481/149‑1 (MQ=255)
            tctcGGCCATGCTGCGCAGCAACGACCTGCCCAATGACTCACCAGGCTCCTCGAGGCTGATCTCCGCGGCCAGGCTATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGTCCTTGCGCAGCAAGGACACCTGAAcc                                                                                                                                >  5:327149/1‑149 (MQ=255)
              tcGGCCAGGCTGCGCAGCAACGACCTGCCCAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCTGCGCAAggcctttg                                                                                                                                     <  8:39792/142‑7 (MQ=255)
              tcGGCCAGGCTGCGCAGCAACGACCTGCCCAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCTGCGCAAggcctttg                                                                                                                                     >  7:39792/1‑136 (MQ=255)
                   cAGGCTGCGCAGCAACGACCTGCCCAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGt                                                                                                                         <  4:328526/149‑1 (MQ=255)
                      gCTGCGCAGCAACGACCTGCCCAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCTGCGCAAggcctt                                                                                                                                       >  8:3454/1‑128 (MQ=255)
                      gCTGCGCAGCAACGACCTGCCCAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCTGCGCAAggcctt                                                                                                                                       <  7:3454/132‑5 (MQ=255)
                      gCTGCGCAGCAACGACCTGCCCAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTAt                                                                                                                      >  6:149768/1‑149 (MQ=255)
                         gcgcAGCAACGACCTGCCCAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGt                                                                                                                   >  6:282692/1‑149 (MQ=255)
                          cgcAGCAACGACCTGCCCAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTc                                                                                                                  <  4:77922/149‑1 (MQ=255)
                               caACGACCTGCCCAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGTATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGa                                                                                                             <  7:117699/149‑1 (MQ=255)
                               caACGACCTGCCCAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGa                                                                                                             <  5:282692/149‑1 (MQ=255)
                                aaCGACCTGCCCAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGac                                                                                                            >  3:71966/1‑149 (MQ=255)
                                 aCGACCTGCCCAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTc                                                                                                               >  6:23347/1‑145 (MQ=255)
                                 aCGACCTGCCCAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTc                                                                                                               <  5:23347/145‑1 (MQ=255)
                                      cTGCCCAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGt                                                                                                      >  8:152996/1‑149 (MQ=255)
                                        gCCCAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGc                                                                                                    >  6:22148/1‑149 (MQ=255)
                                         cccAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGcc                                                                                                   >  6:173392/1‑149 (MQ=255)
                                         cccAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGc                                                                                                    <  1:218222/148‑1 (MQ=255)
                                         cccAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGc                                                                                                    <  5:149768/148‑1 (MQ=255)
                                          ccAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGCCg                                                                                                  <  5:173392/149‑1 (MQ=255)
                                           cAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCACGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGCCgg                                                                                                 <  6:145884/149‑1 (MQ=255)
                                            aaTGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGCCGGa                                                                                                >  3:336105/1‑149 (MQ=255)
                                            aaTGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGCCGGa                                                                                                <  4:71966/149‑1 (MQ=255)
                                                             ctcGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGCCGGACCACACCTGGCTGaac                                                                                >  7:219998/1‑148 (MQ=255)
                                                                gAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGCCGGACCACACCTGGCTGaacaac                                                                             <  7:152996/148‑1 (MQ=255)
                                                                        tCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGCCGGACCACACCTGGCTGAACAACTCGTCCTTg                                                                    >  7:276876/1‑149 (MQ=255)
                                                                                     gCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGCCGGACCACACCTGGCTGAACAACTCGTCCTTGCCGACCACGCG‑Gc                                                      <  4:336105/149‑1 (MQ=255)
                                                                                           gCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGCCGGACCACACCTGGCTGAACGACTCGTCCTTGCCGACCACGCG‑GCCCTTgg                                                <  5:22148/149‑1 (MQ=255)
                                                                                            ccccGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGCCGGACCACACCTGGCTGAACAACTCGTCCTTGCCGACCACGCG‑GCCCTTGGc                                               <  8:219998/149‑1 (MQ=255)
                                                                                            ccccGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCAACCACCGTGCCGGACCACACCTGGCTGAACAACTCGTCCTTGCCGACCACGCG‑GCCCTTGGc                                               >  2:157788/1‑149 (MQ=255)
                                                                                                      gAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGCCGGACCACACCTGGCTGAACAACTCGTCCTTGcc                                                                  >  8:127075/1‑121 (MQ=255)
                                                                                                               ggATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGCCGGACCACACCTGGCTGAACAACTCGTCCTTGCCGACCACGCG‑GCCCTTGGCCCTGATCAGCGTGGCCAg                             >  2:243195/1‑148 (MQ=255)
                                                                                                                gATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCAACCACCGTGCCGGACCACACCTGGCTGAACAACTCGTCCTTGCCGACCACGCG‑GCCCTTGGCCCTGATCAGCGTGGCCa                              <  1:157788/146‑1 (MQ=255)
                                                                                                                           ggTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGaccac                                                                                                         >  4:141266/1‑61 (MQ=255)
                                                                                                                           ggTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGCCGGACCACACCTGGCTGAACAACTCGTCCTTGCCGACCACGCg‑g                                                       >  4:339074/1‑110 (MQ=255)
                                                                                                                           ggTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGCCGGACCACACCTGGCTGAACAACTCGTCCTTGCCGACCACGCg‑g                                                       <  3:339074/110‑1 (MQ=255)
                                                                                                                               gCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGCCGGACCACACCTGGCTGAACAACTCGTCCTTGCCGACCACGCGCGCCCTTGGCCCTGATCAGCGTGGCCAGCACGTCGAAAGCACg              <  1:243195/148‑1 (MQ=255)
                                                                                                                                ccAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGCCGGACCACACCTGGCTGAACAACTCGTCCTTGCCGACCACGCG‑GCCCTTGGCCCTGATCAGCGTGGCCAGCACGTCGAAAGCACGcc            >  8:333752/1‑148 (MQ=255)
                                                                                                                                      gCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGCCGGACCACACCTGGCTGAACAACTCGTCCTTGCCGACCACGCG‑GCCCTTGGCCCTGATCAGCGTGGCCAGCACGTCGAAAGCACGCCCACCCaa     >  8:224311/1‑149 (MQ=255)
                                                                                                                                          tGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGCCGGACCACACCTGGCTGAACAACTCGTCCTTGCCGACCACGCG‑GCCCTTGGCCCTGATCAGCGTGGCCAGCACGTCGAAAGCACGCCCACCCAACAg  >  5:166381/1‑148 (MQ=255)
                                                                                                                                             |                                                                                                                                                 
GCGGCTCGACAGTCTCGGCCAGGCTGCGCAGCAACGACCTGCCCAATGCCTCACCAGGCTCCTCGAGGCTGATCTGCGCGGCCAGGCGATAGCCCCGGCGCGGAACGGTCTGGATCAGGCCACGGTCGCCAAAGGCCTTGCGCAGCAAGGACACCTGAACCTGCAAGTTATTGTCCTCGACCACCGTGCCGGACCACACCTGGCTGAACAACTCGTCCTTGCCGACCACGCG‑GCCCTTGGCCCTGATCAGCGTGGCCAGCACGTCGAAAGCACGCCCACCCAACAG  >  NC_002947/5978762‑5979047

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑