Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,978,158 T→A 10.3% D9V (GAC→GTC)  PP_5240 ← two‑component system response regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,978,1580TA10.3% 106.9 / 5.5 39D9V (GAC→GTC) PP_5240two‑component system response regulator
Reads supporting (aligned to +/- strand):  ref base T (18/17);  new base A (2/2);  total (20/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.71e-01

CCCCGGCATTTTCAGGTCCAGCAACACACAGCCCGCCTCGCCCGCCAGTGGCGAAGCCAGGAATGCGTGCCCGGCGGAAAACGACAAGGTCTCGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCGAGGAGGTTGTGCATGGCCGCAAGCTCCAGCAGCGAGCGGGACTGCATCTTGTTCATGATGTTCTTCTTGTGCACCTTGGTCGTCACCTCGCTG  >  NC_002947/5978010‑5978306
                                                                                                                                                    |                                                                                                                                                    
ccccGGCATTTTCAGGTCCAGCAACACACAGCCCGCCTCGCCCGCCAGTCGCGCAGCCAGGACTGCGTGACCGCCGGAAAACGACAAGGTCTGGAACCCCGGCGAGCGCAGCAGGTTGGCCCGGCTTTTGCGCACCGACGCCtcgtcgtc                                                                                                                                                     >  2:6920/1‑150 (MQ=255)
           tCAGGTCCAGCAACACACAGCCCGCCTCGCCCGCCAGTGGCGAAGCCAGGAATGCGTGCCCGGCGGAAAACGACAAGGTCTCGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATg                                                                                                                                              >  2:272244/1‑146 (MQ=255)
           tCAGGTCCAGCAACACACAGCCCGCCTCGCCCGCCAGTGGCGAAGCCAGGAATGCGTGCCCGGCGGAAAACGACAAGGTCTCGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATg                                                                                                                                              <  1:272244/146‑1 (MQ=255)
               gTCCAGCAACACACAGCCCGCCTCGCCCGCCAGTGGCGAAGCCAGGAATGCGTGCCCGGCGGAAAACGACAAGGTCTCGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATg                                                                                                                                              >  2:181947/1‑142 (MQ=255)
               gTCCAGCAACACACAGCCCGCCTCGCCCGCCAGTGGCGAAGCCAGGAATGCGTGCCCGGCGGAAAACGACAAGGTCTCGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATg                                                                                                                                              <  1:181947/142‑1 (MQ=255)
               gTCCAGCAACACACAGCCCGCCTCGCCCGCCAGTGGCGAAGCCAGGAATGCGTGCCCGGCGGAAAACGACAAGGTCTCGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACAcccc                                                                                                                                      >  2:329370/1‑150 (MQ=255)
               gTCCAGCAACACACAGCCCGCCTCGCCCGCCAGTGGCGAAGCCAGGAATGCGTGCCCGGCGGAAAACGACAAGGTCTCGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACAcccc                                                                                                                                      >  1:45656/1‑150 (MQ=255)
                 ccAGCAACACACAGCCCGCCTCGCCCGCCAGTGGCGAAGCCAGGAATGCGTGCCCGGCGGAAAACGACAAGGTCTCGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACACCCctc                                                                                                                                    <  2:242242/150‑1 (MQ=255)
                           acaGCCCGCCTCGCCCGCCAGTGGCGAAGCCAGGAATGCGTGCCCGGCGGAAAACGACAAGGTCTCGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCAt                                                                                                                             <  1:132614/147‑1 (MQ=255)
                           acaGCCCGCCTCGCCCGCCAGTGGCGAAGCCAGGAATGCGTGCCCGGCGGAAAACGACAAGGTCTCGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCAt                                                                                                                             >  2:132614/1‑147 (MQ=255)
                           acaGCCCGCCTCGCCCGCCAGTGGCGAAGCCAGGAATGCGTGCCCGGCGGAAAACGACAAGGTCTCGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCATgcg                                                                                                                          >  2:298895/1‑150 (MQ=255)
                             aGCCCGCCTCGCCCGCCAGTGGCGAAGCCAGGAATGCGTGCCCGGCGGAAAACGACAAGGTCTCGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCATGcgcc                                                                                                                        >  2:292844/1‑150 (MQ=255)
                               cccGCCTCGCCCGCCAGTGGCGAAGCCAGGAATGCGTGCCCGGCGGAAAACGACAAGGTCTCGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCAt                                                                                                                             >  2:423787/1‑143 (MQ=255)
                               cccGCCTCGCCCGCCAGTGGCGAAGCCAGGAATGCGTGCCCGGCGGAAAACGACAAGGTCTCGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCAt                                                                                                                             <  1:423787/143‑1 (MQ=255)
                               cccGCCTCGCCCGCCAGTGGCGAAGCCAGGAATGCGTGCCCGGCGGAAAACGACAAGGTCTCGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCATGcgccgc                                                                                                                      <  1:329370/150‑1 (MQ=255)
                                     tCGCCCGCCAGTGGCGAAGCCAGGAATGCGTGCCCGGCGGAAAACGACAAGGTCTCGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGc                                                                                                                <  2:18918/150‑1 (MQ=255)
                                                        ccAGGAATGCGTGCCCGGCGGAAAACGACAAGGTCTCGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCgag                                                                                             >  2:371409/1‑150 (MQ=255)
                                                          aGGAATGCGTGCCCGGCGGAAAACGACAAGGTCTCGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCgagga                                                                                           <  1:298895/150‑1 (MQ=255)
                                                                      ccGGCGGAAAACGACAAGGTCTCGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCGAGGAGGTTGTGCATgg                                                                               >  2:279973/1‑150 (MQ=255)
                                                                             aaaaCGACAAGGTCTCGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTc                                                                                                              >  2:263811/1‑112 (MQ=255)
                                                                             aaaaCGACAAGGTCTCGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTc                                                                                                              <  1:263811/112‑1 (MQ=255)
                                                                              aaaCGACAAGGTCTCGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCGAGGAGGTTGTGCATGGCCGCAAGc                                                                       >  1:176814/1‑150 (MQ=255)
                                                                                           tcGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCGAGGAGGTTGTGCATGGCCGCAAGCTCCAGCagcgagc                                                          >  2:244072/1‑150 (MQ=255)
                                                                                              aaCCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCGAGGAGGTTGTGCATGGCCGCAAGCTCCAGCAGCGAGCggg                                                       >  1:320061/1‑150 (MQ=255)
                                                                                                     ccgAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCGAGGAGGTTGTGCATGGCCGCAAGCTCCAGCAGCGAGCGGGACTGCAt                                                <  1:174709/150‑1 (MQ=255)
                                                                                                            cagcagGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCTACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCGAGGAGGTTGTGCATGGCCGCAAGCTCCAGCAGCGAGCGGGACTGCATCTTGTTc                                         <  1:6920/150‑1 (MQ=255)
                                                                                                               cagGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCGAGGAGGTTGTGCATGGCCGCAAGCTCCAGCAGCGAGCGGGACTGCATCTTGTTCatg                                      <  2:45656/150‑1 (MQ=255)
                                                                                                               cagGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCGAGGAGGTTGTGCATGGCCGCAAGCTCCAGCAGCGAGCGGGACTGCATCTTGTTCatg                                      <  1:279973/150‑1 (MQ=255)
                                                                                                                  gtgggCCAGGTTTTTCCCCACCGAGGCATCGTCGTCGCCGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCGAGGAGGTTGTGCATGGCCGCAAGCTCCAGCAGCGAGCGGGACTGCATCTTGTTCatgatg                                   <  1:185879/147‑1 (MQ=255)
                                                                                                                    tGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCGAGGAGGTTGTGCATGGCCGCAAGCTCCAGCAGCGAGCGGGACTGCATCTTGTTCATGATGtt                                 <  1:239850/150‑1 (MQ=255)
                                                                                                                              tttGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCGAGGAGGTTGTGCATGGCCGCAAGCTCcagca                                                                <  2:247198/109‑1 (MQ=255)
                                                                                                                              tttGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCGAGGAGGTTGTGCATGGCCGCAAGCTCcagca                                                                >  1:247198/1‑109 (MQ=255)
                                                                                                                                     aCCGAGGCATCGTCGTCGACTATGCACACCGCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCGAGGAGGTTGTGCATGGCCGCAAGCTCCAGCAGCGAGCGGGACTGCATCTTGTTCATGATGTTCTTCTTGTGCACCTTgg                >  2:186997/1‑150 (MQ=255)
                                                                                                                                       gtgtgCATCGTCGACGACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCGAGGAGGTTGTGCATGGCCGCAAGCTCCAGCagcgagcg                                                         >  2:293482/5‑107 (MQ=255)
                                                                                                                                       gtgtgCATCGTCGACGACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCGAGGAGGTTGTGCATGGCCGCAAGCTCCAGCagcgagcg                                                         <  1:293482/103‑1 (MQ=255)
                                                                                                                                        tgtgCATCGTCGACGACGATGCCCACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCgagga                                                                                           <  2:338833/69‑1 (MQ=38)
                                                                                                                                        tgtgCATCGTCGACGACGATGCCCACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCgagga                                                                                           >  1:338833/4‑72 (MQ=38)
                                                                                                                                           gCATCGTCGTCGACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCGAGGAGGTTGTGCATGGCCGCAAGCTCCAGCAGCGAGCGGGACTGCATCTTGTTCa                                        <  1:289097/120‑1 (MQ=255)
                                                                                                                                           gCATCGTCGTCGACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCGAGGAGGTTGTGCATGGCCGCAAGCTCCAGCAGCGAGCGGGACTGCATCTTGTTCa                                        >  2:289097/1‑120 (MQ=255)
                                                                                                                                             aTCGTCGTCGACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCGAGGAGGTTGTGCATGGCCGCAAGCTCCAGCAGCGAGCGGGACTGCATCTTGTTCATGATGTTCTTCTTGTGCACCTTGGTCGTCAcc        >  2:214277/1‑150 (MQ=255)
                                                                                                                                                gtcgtcgACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCGAGGAGGTTGTGCATGGCCGCAAGCTCCAGCAGCGAGCGGGACTGCATCTTGTTCATGATGTTCTTCTTGTGCACCTTGGTCGTCACCTCg     <  2:320061/150‑1 (MQ=255)
                                                                                                                                                  cgtcgACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCGAGGAGGTTGTGCATGGCCGCAAGCTCCAGCAGCGAGCGGGACTGCATCTTGTTCATGATGTTCTTCTTGTGCACCTTGGTCGTCACCTCGCt   <  2:282355/150‑1 (MQ=255)
                                                                                                                                                   gtcgACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCGAGGAGGTTGTGCATGGCCGCAAGCTCCAGCAGCGAGCGGGACTGCATCTGGTTCATGATGTTCTTCTTGTGCACCTTGGTCGTCACCTCGccg  <  1:292844/150‑3 (MQ=255)
                                                                                                                                                    |                                                                                                                                                    
CCCCGGCATTTTCAGGTCCAGCAACACACAGCCCGCCTCGCCCGCCAGTGGCGAAGCCAGGAATGCGTGCCCGGCGGAAAACGACAAGGTCTCGAACCCCGCCGAGCGCAGCAGGTTGGCCAGGCTTTTGCGCACCGAGGCATCGTCGTCGACGATGCACACCCCTCTGCTCATGCGCCGCCCAGGCTCGCAGACCGCGCTCCGAGGAGGTTGTGCATGGCCGCAAGCTCCAGCAGCGAGCGGGACTGCATCTTGTTCATGATGTTCTTCTTGTGCACCTTGGTCGTCACCTCGCTG  >  NC_002947/5978010‑5978306

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: ‑