Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,979,975 T→A 10.9% L207* (TTA→TAA)  PP_5242 → GAF domain‑containing sensor histidine kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,979,9750TA10.9% 124.5 / 6.2 46L207* (TTA→TAA) PP_5242GAF domain‑containing sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base T (20/21);  new base A (3/2);  total (23/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.26e-01

GTGCCGACCCAGCAGAGCGGATCAGCGAACAGGGCACCCCGCTCGGCAACTGGGCCTACCTGGCGCCGGAGCAGGTTTGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAGCGAAGCGGACAGCAAGGTGCCGCACTCCCTCAGCCTGGTCCTGGCAAAGGCCTTGGCCAAA  >  NC_002947/5979831‑5980120
                                                                                                                                                |                                                                                                                                                 
gTGCCGACCCAGCAGAGCGGATCAGCGAACAGGGCACCCCGCTCGGCAACTGGGCCTACCTGGCGCCGGAGCAGGTTTGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTg                                                                                                                                               <  6:344741/149‑1 (MQ=255)
 tGCCGACCCAGCAGAGCGGATCAGCGAACAGGGCACCCCGCTCGGCAACTGGGCCTACCTGGCGCCGGAGCAGGTTTGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTgg                                                                                                                                              <  6:354585/149‑1 (MQ=255)
         cagcagAGCGGATCAGCGAACAGGGCACCCCGCTCGGCAACTGGGCCTACCTGGCGCCGGAGCAGGTTTGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAGGCGaa                                                                                                                                      <  6:271269/149‑1 (MQ=255)
         cagcagAGCGGATCAGCGAACAGGGCACCCCGCTCGGCAACTGGGCCTACCTGGCGCCGGAGCAGGTTTGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTAACTGGTAga                                                                                                                                          >  1:215028/1‑144 (MQ=255)
         cagcagAGCGGATCAGCGAACAGGGCACCCCGCTCGGCAACTGGGCCTACCTGGCGCCGGAGCAGGTTTGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTAACTGGTAga                                                                                                                                          <  2:215028/145‑2 (MQ=255)
                              aGGGCACCCCGCTCGGCAACTGGGCCTACCTGGCGCCGGAGCAGGTTTGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGac                                                                                                                 <  2:108755/149‑1 (MQ=255)
                                     cccGCTCGGCAACTGGGCCTACCTGGCGCCGGAGCAGGTTTGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGc                                                                                                          >  7:163403/1‑149 (MQ=255)
                                      ccGCTCGGCAACTGGGCCTACCTGGCGCCGGAGCAGGTTTGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCa                                                                                                         <  8:197607/149‑1 (MQ=255)
                                                      ccTACCTGGCGCCGGAGCAGGTTTGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGt                                                                                                                                             <  8:220937/97‑1 (MQ=255)
                                                      ccTACCTGGCGCCGGAGCAGGTTTGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGt                                                                                                                                             >  7:220937/1‑97 (MQ=255)
                                                       cTACCTGGCGCCGGAGCAGGTTTGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATg                                                                                        >  3:264363/1‑149 (MQ=255)
                                                           cTGGCGCCGGAGCAGGTTTGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTgg                                                                                    >  7:249264/1‑149 (MQ=255)
                                                             ggCGCCGGAGCAGGTTTGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGgtg                                                                                  >  3:177717/1‑149 (MQ=255)
                                                              gcgcCGGAGCAGGTTTGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGgtgt                                                                                 <  2:145826/149‑1 (MQ=255)
                                                                gcCGGAGCAGGTTTGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTAACTGGTAga                                                                                                                                          >  5:278256/1‑89 (MQ=255)
                                                                gcCGGAGCAGGTTTGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTAACTGGTAga                                                                                                                                          <  6:278256/90‑2 (MQ=255)
                                                                      gCAGGTTTGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGgt                                                                                   >  4:221001/1‑139 (MQ=255)
                                                                      gCAGGTTTGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGgt                                                                                   <  3:221001/139‑1 (MQ=255)
                                                                        aGGTTTGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCgcgg                                                                       <  8:163403/149‑1 (MQ=255)
                                                                          gTTTGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAg                                                                                                                                           <  5:294637/79‑1 (MQ=255)
                                                                          gTTTGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAg                                                                                                                                           >  6:294637/1‑79 (MQ=255)
                                                                           tttGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCgcgggcg                                                                    >  8:158247/1‑149 (MQ=255)
                                                                                              cagcGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAGCGAAGCGGACAGc                                                  >  8:227566/1‑148 (MQ=255)
                                                                                              cagcGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCAGCGGGCGGCCAGCGAAGCGGACAGc                                                  >  8:227570/1‑148 (MQ=255)
                                                                                                   accgacGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCTGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAGCGAAGCGGACAGCAAGGTg                                            <  7:227570/149‑1 (MQ=255)
                                                                                                   accgacGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAGCGAAGCGGACAGCAAGGTg                                            <  7:227566/149‑1 (MQ=255)
                                                                                                         gCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAGCGAAGCGGACAGCAAGGTGCCGCAc                                      >  1:159296/1‑149 (MQ=255)
                                                                                                             tGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAg                                                               <  6:67446/120‑1 (MQ=255)
                                                                                                             tGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAg                                                               >  5:67446/1‑120 (MQ=255)
                                                                                                                 aTCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAGCGAAGCGGACAGCAAGGTGCCGCACTCCCTCAg                              >  4:36499/1‑149 (MQ=255)
                                                                                                                 aTCTATGCCCTGGGGGCAATACACTACCAGTTACTGGTAGGCGAACAGCCCCAGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCAAGCTGGTGTGCAGCCGCGGGCGGCCAGCGAAGCGGACAGCAAGGTGCCGCACTCCCTCAg                              >  5:32386/1‑149 (MQ=255)
                                                                                                                    tATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAGCGAAGCGGACAGCAAGGTGCCGCACTCCCTCAGCCt                           >  7:240830/1‑149 (MQ=255)
                                                                                                                      tGCCCTGGGGGCAATCCTCTACCAGTTACTTGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAGCGAAGCGGACAGCAAGGTGCCGCACTCCCTCAGCCTg                          <  8:240830/148‑1 (MQ=255)
                                                                                                                           tGGGGGCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAGCGAAGCGGACAGCAAGGTGCCGCACTCCCTCAGCCTGGTCCTg                    >  3:24452/1‑149 (MQ=255)
                                                                                                                             ggggCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAGCGAAGCGGACAGCAAGGTGCCGCACTCCCTCAGCCTGGTCCTgg                   >  8:164812/1‑148 (MQ=255)
                                                                                                                                  aaTCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAGCGAAGCGGACAGCAAGGTGCCGCACTCCCTCAGCCTGGTCCTGGCAAAgg             >  5:29336/1‑149 (MQ=255)
                                                                                                                                    tCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCATGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAGCGAAGCGGACAGCAAGGTGCCGCACTCCCTCAGCCTGGTCCTGGCAAAGGcc           >  7:295671/1‑149 (MQ=255)
                                                                                                                                       cctACCAGTAACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAGCGAAGCGGACAGCAAGGTGCCGCACTCCCTCAGCCTGGTCCTGGCAAAGGCCTTg        >  6:46919/2‑149 (MQ=255)
                                                                                                                                         tACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAGCGAAGCGGACAGCAAGGTGCCGCACTCCCTCAGCCTGGTCCTGGCAAAGGCCTTg        <  8:249264/147‑1 (MQ=255)
                                                                                                                                         tACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAGCGAAGCGGACAGCAAGGTGCCGCACTCCCTCAGCCTGGTCCTGGCAAAGGCCTTg        <  7:164812/147‑1 (MQ=255)
                                                                                                                                         tACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAGCGAAGCGGACAGCAAGGTGCCGCACTCCCTCAGCCTGGTCCTGGCAAAGGCCTTg        <  4:264363/147‑1 (MQ=255)
                                                                                                                                         tACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAGCGAAGCGGACAGCAAGGTGCCGCACTCCCTCAGCCTGGTCCTGGCAAAGGCCTTGGc      >  5:90230/1‑149 (MQ=255)
                                                                                                                                          aCCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAGCGAAGCGGACAGCAAGGTGCCGCACTCCCTCAGCCTGGTCCTGGCAAAGGCCTTGGc      <  6:29336/148‑1 (MQ=255)
                                                                                                                                           ccAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAGCGAAGCGGACAGCAAGGTGCCGCACTCCCTCAGCCTGGTCCTGGCAAAGGCCTTGGc      <  4:24452/147‑1 (MQ=255)
                                                                                                                                             aGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAGCGAAGCGGACAGCAAGGTGCCGCACTCCCTCAGCCTGGTCCTGGCAAAGGCCTTGGCCaaa  <  3:36499/149‑1 (MQ=255)
                                                                                                                                             aGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAGCGAAGCGGACAGCAAGGTGCCGCACTCCCTCAGCCTGGTCCTGGCAAAGGCCTTGGCCaaa  <  2:159296/149‑1 (MQ=255)
                                                                                                                                                |                                                                                                                                                 
GTGCCGACCCAGCAGAGCGGATCAGCGAACAGGGCACCCCGCTCGGCAACTGGGCCTACCTGGCGCCGGAGCAGGTTTGCCCGCACGGTAGCAGCAGCGACCGACGCAGTGACATCTATGCCCTGGGGGCAATCCTCTACCAGTTACTGGTAGGCGAACTGCCGCTGGCCGGGCGCGACACCCTGCACTGGCGACAGCTGCATGCTGGTGTGCAGCCGCGGGCGGCCAGCGAAGCGGACAGCAAGGTGCCGCACTCCCTCAGCCTGGTCCTGGCAAAGGCCTTGGCCAAA  >  NC_002947/5979831‑5980120

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑