Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913_3_pae_tpiA 1,188,870 C→T A303T (GCT→ACT)  phoQ ← sensory histidine kinase in two‑component regulatory system with PhoP

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_tpiA1,188,8700CT97.9% 157.8 / NA 48A303T (GCT→ACT) phoQsensory histidine kinase in two‑component regulatory system with PhoP
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (22/25);  minor base G (0/1);  total (22/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGAGGTGAGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTT  >  NC_000913_3_pae_tpiA/1188730‑1189014
                                                                                                                                            |                                                                                                                                                
tGAGGTGAGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTAGCGGCTCAGTATCACTGa                                                                                                                                          >  1:208105/1‑149 (MQ=255)
tGAGGTGAGAGTGTCCAGCAGTGGGGCGACCGGATGCAGCCCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGa                                                                                                                                          <  2:592304/149‑1 (MQ=255)
 gAGGTGAGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAACTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGAc                                                                                                                                         <  1:568574/149‑1 (MQ=255)
              ccAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCa                                                                                                                            <  1:661697/149‑1 (MQ=255)
               cagcagTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCCCTGCCGCTCATCTTTTctc                                                                                                                           >  2:69112/1‑147 (MQ=255)
               cagcagTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCAc                                                                                                                           >  1:433575/1‑149 (MQ=255)
                 gcagTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGTTCATCTTTTCACTa                                                                                                                         <  2:518428/149‑1 (MQ=255)
                            aCCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACg                                                                                                              <  2:102571/149‑1 (MQ=255)
                            aCCGCATGCAGCTCGCGGCTGAGGAATGTCCCGCCGCGAATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACg                                                                                                              <  2:514732/149‑1 (MQ=255)
                              cGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCa                                                                                                            <  2:471892/149‑1 (MQ=255)
                                        tCGCGGCGGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGTCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTg                                                                                                  <  2:378328/149‑1 (MQ=255)
                                                 aGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGc                                                                                         <  1:229288/149‑1 (MQ=255)
                                                   cAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCa                                                                                       <  2:208105/149‑1 (MQ=255)
                                                     aTGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGt                                                                                     <  2:19022/149‑1 (MQ=255)
                                                      tGTCCCGCCGCGCATACTGGCACGATGCAGGGAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTg                                                                                    <  2:452316/149‑1 (MQ=255)
                                                        tCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGc                                                                                  <  1:795100/149‑1 (MQ=255)
                                                             ccgcGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGtttt                                                                             >  1:770446/1‑149 (MQ=255)
                                                               gcgcATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCa                                                                           <  1:130998/149‑1 (MQ=255)
                                                                     aCTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTAt                                                                     <  1:619315/149‑1 (MQ=255)
                                                                     aCTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTAt                                                                     <  1:617569/149‑1 (MQ=255)
                                                                                  aGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCTTTTTCAGACTATGGTTCATGTCGGt                                                        >  2:142103/1‑149 (MQ=255)
                                                                                    gtagtaGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTgc                                                                                                 >  1:220170/1‑106 (MQ=255)
                                                                                    gtagtaGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTgc                                                                                                 <  2:220170/106‑1 (MQ=255)
                                                                                          gCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTAAGGTCGGTGAGcgtcg                                                >  2:563690/1‑149 (MQ=255)
                                                                                             aaTTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGt                                                                 >  2:17638/1‑129 (MQ=255)
                                                                                             aaTTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGt                                                                 <  1:17638/129‑1 (MQ=255)
                                                                                                    tgtgAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTAttt                                      >  1:765634/1‑149 (MQ=255)
                                                                                                    tgtgAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTAttt                                      >  1:765873/1‑149 (MQ=255)
                                                                                                      tgAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCGGAGAACGCAGCGGACTTTGCAGCACCGCCAGTGGCGGTTTCAGACTTTGGGTCAGGTCGGTGAGGGTCGTACGGGCTTTGt                                    >  2:456353/1‑149 (MQ=255)
                                                                                                      tgAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGt                                    <  1:489075/149‑1 (MQ=255)
                                                                                                                 tGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTcg                         >  2:546716/1‑149 (MQ=255)
                                                                                                                    tttGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGa                                                                         >  1:684104/1‑98 (MQ=255)
                                                                                                                    tttGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGa                                                                         <  2:684104/98‑1 (MQ=255)
                                                                                                                       gCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTc                                   >  2:69846/1‑133 (MQ=255)
                                                                                                                       gCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTc                                   <  1:69846/133‑1 (MQ=255)
                                                                                                                        cTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCAc                  >  2:479493/1‑149 (MQ=255)
                                                                                                                         tCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACt                 >  2:43923/1‑149 (MQ=255)
                                                                                                                         tCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACt                 >  1:710877/1‑149 (MQ=255)
                                                                                                                         tCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATCGGTCAGGTCGGTGAGCGTCGTACGGTGTTTGTCGTAACGTTCGCGttacct                 >  1:338363/1‑145 (MQ=255)
                                                                                                                               aTTGCCGGCTCAGGAGCACGGGCGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCTCGTTCACTTTTTaa           <  2:303847/149‑1 (MQ=255)
                                                                                                                                ttACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTc                                   >  2:439098/1‑124 (MQ=255)
                                                                                                                                ttACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTc                                   <  1:439098/124‑1 (MQ=255)
                                                                                                                                    cGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATc      >  2:403877/1‑149 (MQ=255)
                                                                                                                                     ggCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCg     <  1:77011/149‑1 (MQ=255)
                                                                                                                                      gCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTGCTTTGCAGCACCGCCAGTGGCGTTTTCAGACTAt                                                                     <  2:209387/84‑1 (MQ=255)
                                                                                                                                      gCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTAt                                                                     >  1:209387/1‑84 (MQ=255)
                                                                                                                                      gCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAACGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCgg    <  1:142103/149‑1 (MQ=255)
                                                                                                                                        tCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGGCGTAACGTTCGCGTTCACTTTTTAACAATCGGtt  >  1:383289/1‑149 (MQ=255)
                                                                                                                                            |                                                                                                                                                
TGAGGTGAGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTT  >  NC_000913_3_pae_tpiA/1188730‑1189014

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑