Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 4,531,694 G→T 7.4% A171S (GCC→TCC)  PP_4015 → HflD‑like high frequency lysogenization protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029474,531,6940GT 7.4% 188.3 / 2.2 54A171S (GCC→TCC) PP_4015HflD‑like high frequency lysogenization protein
Reads supporting (aligned to +/- strand):  ref base G (25/25);  new base T (2/2);  total (27/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.59e-01

CTTCCAGTGGAGCCTTGTATCAGGACACCCTGAGCACCTTGCGCCAGCGCATCCAGGTGCATGGCGACATGCGCTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACATGATGCGCAGCCCCAACTGACGGGCTGGGCAGCCCGCTT  >  NC_002947/4531572‑4531829
                                                                                                                          |                                                                                                                                       
cTTCCAGTGGAGCCTTGTATCAGGACACCCTGAGCACCTTGCGCCAGCGCATCCAGGTGCATGGCGACATGCGCTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATccgcgc                                                                                                                            >  1:336136/1‑136 (MQ=255)
  tCCAGTGGAGCCTTGTATCAGGACACCCTGAGCACCTTGCGCCAGCGCATCCAGGTGCATGGCGACATGCGCTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATccgcgccg                                                                                                                          <  1:283786/136‑1 (MQ=255)
             cTTGTATCAGGACCCCCTGAGCACCTTGCGCCAGCGCATCCAGGTGCATGGCGACATGCGCTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTgg                                                                                                               <  2:322495/136‑1 (MQ=255)
                  aTCAGGACACCCTGAGCACCTTGCGCCAGCGCATCCAGGTGCATGGCGACATGCGCTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCa                                                                                                          >  1:333313/1‑136 (MQ=255)
                          acCCTGAGCACCTTGCGCCAGCGCATCCAGGTGCATGGCGACATGCGCTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTgggcg                                                                                                  <  2:403132/136‑1 (MQ=255)
                          acCCTGAGCACCTTGCGCCAGCGCATCCAGGTGCATGGCGACATGCGCTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTgggcg                                                                                                  <  2:23158/136‑1 (MQ=255)
                           cccTGAACACCTTGCGCCAGCGCATCCAGGTGCATGGCGACATGCGCTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTgggcgg                                                                                                 >  2:356239/1‑136 (MQ=255)
                            ccTGAGCACCTTGCGCCAGCGCATCCAGGTGCATGGCGACATGCGCTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTgggcggg                                                                                                >  1:113621/1‑136 (MQ=255)
                              tGAGCACCTTGCGCCAGCGCATCCAGGTGCATGGCGACATGCGCTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTgggcctgtc                                                                                              >  1:89045/1‑131 (MQ=255)
                              tGAGCACCTTGCGCCAGCGCATCCAGGTGCATGGCGACATGCGCTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCa                                                                                              >  1:204421/1‑136 (MQ=255)
                              tGAGCACCTTGCGCCAGCGCATCCAGGTGCATGGCGACATGCGCTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCa                                                                                              >  1:147633/1‑136 (MQ=255)
                              tGAGCACCTTGCGCCAGCGCATCCAGGTGCATGGCGACATGCGCTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCa                                                                                              >  1:521573/1‑136 (MQ=255)
                              tGAGCACCTTGCGCCAGCGCATCCAGGTGCATGGCGACATGAGCTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCa                                                                                              >  2:322996/1‑136 (MQ=255)
                                  cACCTTGCGCCAGCGCATCCAGGTGCATGGCGACATGCGCTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGt                                                                                          >  1:314503/1‑136 (MQ=255)
                                   aCCTTGCGCCAGCGCATCCAGGTGCATGGCGACATGCGCTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGtt                                                                                         >  2:3243/1‑136 (MQ=255)
                                      ttGCGCCAGCGCATCCAGGTGCATGGCGACATGCGCTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGc                                                                                      <  1:356239/136‑1 (MQ=255)
                                          gcCAGCGCATCCAGGTGCATGGCGACATGCGCTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCt                                                                                  >  2:416671/1‑136 (MQ=255)
                                          gcCAGCGCATCCAGGTGCATGGCGACATGCGCTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCt                                                                                  >  1:57927/1‑136 (MQ=255)
                                                  aTCCAGGTGCATGGCGACATGCGCTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCa                                                                          >  1:42198/1‑136 (MQ=255)
                                                              ggCGACATGCGCTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGt                                                              >  1:134251/1‑136 (MQ=255)
                                                                 gACATGCGCTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGc                                                           <  1:342545/136‑1 (MQ=255)
                                                                      gcgcTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTgaac                                                      <  2:57786/136‑1 (MQ=255)
                                                                      gcgcTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCAGCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTgaac                                                      <  2:54461/136‑1 (MQ=255)
                                                                      gcgcTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCGGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTgaac                                                      <  2:146577/136‑1 (MQ=255)
                                                                           tCCTGCAGCAGCCAAACATTGACTCTTAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCTCCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACt                                                 <  2:147633/136‑1 (MQ=255)
                                                                                  gcagcCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGAc                                          <  1:425816/136‑1 (MQ=255)
                                                                                  gcagcCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGAc                                          <  1:3243/136‑1 (MQ=255)
                                                                                        caacacTGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACatgatg                                    <  2:632448/136‑1 (MQ=255)
                                                                                         aacaaTGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTgaac                                                      <  2:151141/117‑1 (MQ=255)
                                                                                         aacaaTGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTgaac                                                      >  1:151141/1‑117 (MQ=255)
                                                                                         aacaaTGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACATGATgc                                   >  1:467082/1‑136 (MQ=255)
                                                                                         aacaaTGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACATGATgc                                   >  1:359240/1‑136 (MQ=255)
                                                                                           caaTGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACATGATgcgc                                 >  2:598162/1‑136 (MQ=255)
                                                                                              tGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGGATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACATGATGCGCAGc                              <  2:348319/136‑1 (MQ=255)
                                                                                                  tCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACATGATGCGCAGCCCCa                          >  1:167528/1‑136 (MQ=255)
                                                                                                   cGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTc                                                                           >  2:308248/1‑86 (MQ=255)
                                                                                                   cGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTc                                                                           <  1:308248/86‑1 (MQ=255)
                                                                                                   cGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACATGATGCGCAGCCCCaa                         >  2:414987/1‑136 (MQ=255)
                                                                                                   cGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACATGATGCGCAGCCCCaa                         <  2:113621/136‑1 (MQ=255)
                                                                                                   cGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACATGATGCGCAGCCCCaa                         <  2:314503/136‑1 (MQ=255)
                                                                                                   cGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTCGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACATGATGCGCAGCCCCaa                         >  2:665459/1‑136 (MQ=255)
                                                                                                     aaGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCTGCCGGCGCAAGTTGCTGAACGAACTGTACGACATGATGCGCAGCCCCAACt                       <  2:224466/136‑1 (MQ=255)
                                                                                                      aGATCCGCGCCCTGCTGCTGTCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACATGATGCGCAGCCCCAACTg                      >  1:569054/1‑136 (MQ=255)
                                                                                                        aTCCGCGCCCTGCTGCTGTCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACATGATGCGCAGCCCCAACTGAc                    <  2:569054/136‑1 (MQ=255)
                                                                                                                ccTGCTGCTGGCCGGCAGCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACATGATGCGCAGCCCCAACTGACGGGCTggg            <  1:646910/136‑1 (MQ=255)
                                                                                                                  tgctgctgTCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACATGATGCGCAGc                              <  2:484380/116‑1 (MQ=255)
                                                                                                                  tgctgctgTCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACATGATGCGCAGc                              >  1:484380/1‑116 (MQ=255)
                                                                                                                  tgctgctgGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACATGATGCGCAGCCCCAACTGACGGGCTGGGCa          >  2:129644/1‑136 (MQ=255)
                                                                                                                    ctgctgGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACATGATGCGCAGCCCCAACTGACGGGCTGGGCAGc        <  2:368557/136‑1 (MQ=255)
                                                                                                                    ctgctgGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACATGATGCGCAGCCCCAACTGACGGGCTGGGCAGc        <  2:167528/136‑1 (MQ=255)
                                                                                                                     tgctgGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACatgat                                     <  2:260090/106‑1 (MQ=255)
                                                                                                                     tgctgGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACATGATGCGCAGCCCCAACTGACGGGCTGGGCAGcc       <  2:55932/136‑1 (MQ=255)
                                                                                                                     tgctgGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACAGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACatgat                                     >  1:260090/1‑106 (MQ=255)
                                                                                                                     ggctgGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACATGATGCGCAGCCCCAACTGACGGGCTGGGCAGcc       <  1:392166/135‑1 (MQ=255)
                                                                                                                          gCCGGAATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGGACGACATGATGCGCAGCCCCAACTGACGGGCTGGGCAGCCCGCtt  <  2:336136/136‑1 (MQ=255)
                                                                                                                          |                                                                                                                                       
CTTCCAGTGGAGCCTTGTATCAGGACACCCTGAGCACCTTGCGCCAGCGCATCCAGGTGCATGGCGACATGCGCTTCCTGCAGCAGCCCAACAATGCCTCGAAGATCCGCGCCCTGCTGCTGGCCGGCATCCGCGCCGCGCGACTGTGGCGGCAGCTGGGCGGGCACCGTTGGCAGCTGGTGTTCAGCCGGCGCAAGTTGCTGAACGAACTGTACGACATGATGCGCAGCCCCAACTGACGGGCTGGGCAGCCCGCTT  >  NC_002947/4531572‑4531829

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: ‑