Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,354,452 C→A 8.5% Y218* (TAC→TAA)  PP_2949 → permease

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,354,4520CA 8.5% 145.4 / 3.4 48Y218* (TAC→TAA) PP_2949permease
Reads supporting (aligned to +/- strand):  ref base C (21/22);  new base A (2/2);  total (24/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.73e-01

TCGCGGACATTGGGTGGTTGGCAGGTGATCAGCTGGGCGTTGCTGGTAGCGTTGCCGTTCATGCTGCTGCTGACGGTGGTCAATCTTCCAGCCCCTGATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTGCGGCAGTGGGCCAATTGCAACTCTTTCAGCCGTTCATGGGGCTTGGGCTGGCAGCGTTGCTTCTGCACGAGCATGTCAGC  >  NC_002947/3354309‑3354599
                                                                                                                                               |                                                                                                                                                   
tcGCGGACATTGGGTGGTTGGCAGGTGATCAGCTGGGCGTTGCTGGTAGCGTTGCCGTTCATGCTGCTGCTGACGGTGGTCAATCTTCCAGCCCCTGATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCa                                                                                                                                               >  2:747929/1‑150 (MQ=255)
 cgcgGACATTGGGTGGTTGGCAGGTGATCAGCTGGGCGTTGCTGGTAGCGTTGCCGTTCATGCTGCTGCTGACGGTGGTCAATCTTCCAGCCCCTGATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCAc                                                                                                                                              <  2:529308/150‑1 (MQ=255)
      aCATTGGGTGGTTGGCAGGTGATCAGCTGGGCGTTGCTGGTAGCGTTGCCGTTCATGCTGCTGCTGACGGTGGTCAATCTTCCAGCCCCTGATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTc                                                                                                                                         >  1:232682/1‑150 (MQ=255)
                        gTGATCAGCTGGGCGTTGCTGGTAGCGTTGCCGTTCATGCTGCTGCTGACGGTGGTCAATCTTCCAGCCCCTGATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGttt                                                                                                                       <  2:283594/150‑1 (MQ=255)
                        gTGATCAGCTGGGCGTTGCTGGTAGCGTTGCCGTTCATGCTGCTGCTGACGGTGGTCAATCTTCCAGCCCCTGATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGttt                                                                                                                       >  1:523673/1‑150 (MQ=255)
                        gTGATCAGCTGGGCGTTGCTGGTAGCGTTGCCGTTCATGCCGCTAGTGAGGGGAGGCAATCTTCCAGCCCCTTATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCAGATCggaaga                                                                                                                       >  1:318129/1‑146 (MQ=255)
                                 tGGGCGTTGCTGGTAGCGTTGCCGTTCATGCTGCTGCTGACGGTGGTCAATCTTCCAGCCCCTGATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTgg                                                                                                              >  2:527642/1‑150 (MQ=255)
                                          cTGGTAGCGTTGCCGTTCATGCTGCTGCTGACGGTGGTCAATCTTCCAGCCCCTGATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAggg                                                                                                     >  2:648039/1‑150 (MQ=255)
                                          cTGGTAGCGTTGCCGTTCATGCTGCTGCTGACGGTGGTCAATCTTCCAGCCCCTGATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAggg                                                                                                     <  2:579540/150‑1 (MQ=255)
                                                gCGTTGCCGTTCATGCTGCTGCTGACGGTGGTCAATCTTCCAGCCCCTGATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTc                                                                                               >  2:751239/1‑150 (MQ=255)
                                                           cATGCTGCTGCTGACGGTGGTCAATCTTCCAGCCCCTGATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGAt                                                                                    >  1:671718/1‑150 (MQ=255)
                                                             ggctgctgatGAGGGTGGTCAATCTTCCAGCCCCTGATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTg                                                                                  <  2:216115/149‑1 (MQ=255)
                                                                   tgctgACGGTGGTCAATCTTCCAGCCCCTGATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCa                                                                                                                                        >  1:708475/1‑90 (MQ=255)
                                                                   tgctgACGGTGGTCAATCTTCCAGCCCCTGATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCa                                                                                                                                        <  2:708475/90‑1 (MQ=255)
                                                                      tgACGGTGGTCAATCTTCCAGCCCCTGATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTGCGGCAGTgg                                                                         <  2:523673/150‑1 (MQ=255)
                                                                      tgACGGTGGTCAATCTTCCAGCCCCTGATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTGCGGCAGCgg                                                                         <  1:751239/150‑1 (MQ=255)
                                                                      ggACGGTGGTCAAGTTTCCATCTCCTGATTACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTGCGGCAGTgg                                                                         <  2:232682/149‑1 (MQ=255)
                                                                         cGGTGGTCAATCTTCCAGCCCCTGATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTGCGGCAGTGGGcc                                                                      >  2:424505/1‑150 (MQ=255)
                                                                              gtCAATCTTCCAGCCCCTGATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATg                                                                                                                                   <  1:282042/84‑1 (MQ=255)
                                                                              gtCAATCTTCCAGCCCCTGATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATg                                                                                                                                   >  2:282042/1‑84 (MQ=255)
                                                                                cAATCTTCCAGCCCCTGATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTGCGGCAGTGGGCCAATTGCa                                                               >  1:498352/1‑150 (MQ=255)
                                                                                 aaTCTTCCAGCCCCTGATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTGCGGCAGTGGGCCAATTGCaa                                                              >  1:441798/1‑150 (MQ=255)
                                                                                 aaTCTTCCAGCCCCTGATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATACTGATCATGTTTTTGTTCTGTTACCGAGGGCTCGTCCAGGGGGGGGGTGCGGCAGTGGGCCAATTGCaa                                                              >  2:157663/1‑150 (MQ=255)
                                                                                                 atgaCTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTAAGTTTCACTGTTCAGCATGCTGATCGGGttt                                                                                                                       <  1:470215/77‑1 (MQ=255)
                                                                                                 atgaCTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTAAGTTTCACTGTTCAGCATGCTGATCGGGttt                                                                                                                       <  1:470191/77‑1 (MQ=255)
                                                                                                 atgaCTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTAAGTTTCACTGTTCAGCATGCTGATCGGGttt                                                                                                                       >  2:470215/1‑77 (MQ=255)
                                                                                                 atgaCTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTAAGTTTCACTGTTCAGCATGCTGATCGGGttt                                                                                                                       >  2:470191/1‑77 (MQ=255)
                                                                                                  tgaCTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTGCGGCAGTGGGCCAATTGCaa                                                              <  1:47595/133‑1 (MQ=255)
                                                                                                  tgaCTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTGCGGCAGTGGGCCAATTGCaa                                                              >  2:47595/1‑133 (MQ=255)
                                                                                                  tgaCCTTGCCAGGGTAAGTGCCCCTGCGTGGTTCCGCTTGCGCTACGTTTCCCTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCTAGGGCTCGTCCAGGCGGGGATTGCGGCAGTGGGCCAATTGCAACTCTTTCAGCCGTTCAt                                             <  1:157663/150‑1 (MQ=255)
                                                                                                    aCTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTGCGGCAGTGGGCCAATTGCAACTCTTTCAGCCGTTCATgg                                           <  1:648039/150‑1 (MQ=255)
                                                                                                      tttGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTGCGGCAGTg                                                                          <  1:12944/117‑1 (MQ=255)
                                                                                                      tttGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTGCGGCAGTg                                                                          >  2:12944/1‑117 (MQ=255)
                                                                                                         gCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTGCGGCAGTGGGCCAATTGCAACTCTTTCAGCCGTTCATGGGGCtt                                      <  2:498352/150‑1 (MQ=255)
                                                                                                         gCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTGCGGCAGTGGGCCAATTGCAACTCTTTCAGCCGTTCATGGGGCtt                                      <  1:527642/150‑1 (MQ=255)
                                                                                                           cAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTAGGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTTTGGTACGGAGGGCTCGTCCAGGGGGGGATTGCGGCAGTGGGCCAATTGCAACTCTTTCAGCCTTTCATGGTGCTTgg                                    >  1:35733/1‑150 (MQ=255)
                                                                                                                tAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTGCGGCAGTGGGCCAATTGCAACTCTTTCAGCCGTTCATGGGGCTTGGGCTgg                               <  2:63688/150‑1 (MQ=255)
                                                                                                                      ccccTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTGCGGCAGTGGGCCAATTGCAACTCTTTCAGCCGTTCATGGGGCTTGGGCTGGCAGCGt                         <  2:671718/150‑1 (MQ=255)
                                                                                                                         cTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTc                                                                                                                 <  1:733537/59‑1 (MQ=255)
                                                                                                                         cTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTc                                                                                                                 >  2:733537/1‑59 (MQ=255)
                                                                                                                                   cAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTtg                                                                                                                      <  1:668692/44‑1 (MQ=255)
                                                                                                                                   cAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTtg                                                                                                                      >  2:668692/1‑44 (MQ=255)
                                                                                                                                       tttGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTGCGGCAGTGGGCCAATTGCAACTCTTTCAGCCGTTCATGGGGCTTGGGCTGGCAGCGTTGCTTCTGCACGAGCAt        <  1:424505/150‑1 (MQ=255)
                                                                                                                                           gCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTGCGGCAGt                                                                           <  1:195939/79‑1 (MQ=255)
                                                                                                                                           gCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTGCGGCAGt                                                                           >  2:195939/1‑79 (MQ=255)
                                                                                                                                            cTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTGCGGCAGTGGGCCAATTGCAACTCTTTCAGCCGTTCATGGGGCtt                                      <  2:205116/115‑1 (MQ=255)
                                                                                                                                            cTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTGCGGCAGTGGGCCAATTGCAACTCTTTCAGCCGTTCATGGGGCtt                                      >  1:205116/1‑115 (MQ=255)
                                                                                                                                             tACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTGCGGCAGTGGGCCAATTGCAACTCTTTCAGCCGTTCATGGGGCTTGGGCTGGCAGCGTTGCTTCTGCACGAGCATGTCAGc  >  2:66873/1‑150 (MQ=255)
                                                                                                                                               |                                                                                                                                                   
TCGCGGACATTGGGTGGTTGGCAGGTGATCAGCTGGGCGTTGCTGGTAGCGTTGCCGTTCATGCTGCTGCTGACGGTGGTCAATCTTCCAGCCCCTGATGACTTTGCCAGGGTAAGTGCCCCTGCGTGGTTCAGCTTTGGCTACGTTTCACTGTTCAGCATGCTGATCGGGTTTGTGTTCTGGTACCGAGGGCTCGTCCAGGGGGGGATTGCGGCAGTGGGCCAATTGCAACTCTTTCAGCCGTTCATGGGGCTTGGGCTGGCAGCGTTGCTTCTGCACGAGCATGTCAGC  >  NC_002947/3354309‑3354599

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑