Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913_3_pae_tpiA 1,188,870 C→T 35.5% 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_tpiA1,188,8700CT35.5% 22.7 / 24.4 33A303T (GCT→ACT) phoQsensory histidine kinase in two‑component regulatory system with PhoP
Reads supporting (aligned to +/- strand):  ref base C (6/14);  new base T (5/6);  total (12/21)
Fisher's exact test for biased strand distribution p-value = 4.52e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.69e-01

GCTGAGGTGAGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTT  >  NC_000913_3_pae_tpiA/1188728‑1189014
                                                                                                                                              |                                                                                                                                                
ccTGAGGTGAGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACt                                                                                                                                            <  1:243378/148‑1 (MQ=255)
    aGGTGAGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATACCTGagg                                                                                                                                        >  2:690642/1‑147 (MQ=255)
           aTTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGCATCACTGACGCTCATCt                                                                                                                                 >  1:632582/1‑149 (MQ=255)
            ttGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTCTGAAATGCGCCTAATCTCCGCCAGCATTACCGGCTCAGAATCACTGACGCACATCtt                                                                                                                                >  2:116519/1‑149 (MQ=255)
              gTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTATCGGCTCAGCAGCACTGACGCTCATCtttt                                                                                                                              <  2:84749/149‑1 (MQ=255)
                ccAGCAGTGTGGCGGCCTGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGCATCACTGACGCTCATCTTTTCa                                                                                                                            <  1:316240/149‑1 (MQ=255)
                          ggCGACCGGATGCAGCTCGCGGCTGAGCAATCTCCCGCCCCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCagag                                                                                                                  <  1:4211/149‑1 (MQ=255)
                             ggccGGAGGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAAc                                                                                                               <  1:715016/147‑1 (MQ=255)
                                         cTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACttt                                                                                                   >  1:736446/1‑149 (MQ=255)
                                          tCGCGGCTGAGTAATGTGCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTg                                                                                                  <  2:569379/149‑1 (MQ=255)
                                             cgGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCACCCTACTTTgcag                                                                                               >  2:42821/1‑149 (MQ=255)
                                                   aggagtGTCCCGCCGGGCATACTGGCACTATGCAGGTAGTAGCCAATTTGCTGTGAAATGCTGCTGATTTGCACCAGCATTACCGGCTCAGCATCACTGACGCTCACCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGc                                                                                         <  2:126666/144‑1 (MQ=255)
                                                   aGCGATGTTCCGCCGCGCAGCCTGGAACGAGGCCGGCACGAGCCAGTACGCTGTTAAACTCGGCGGAGTTGCTCCGATATGACCGGCTCATGAACTCTGACGCTCCTCTTTTCACTACGGAGGGCTCGCAGCGTACTTTGCAGCACCGc                                                                                         <  2:501004/149‑1 (MQ=255)
                                                        tGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTg                                                                                    <  1:378783/149‑1 (MQ=255)
                                                               ccgcGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGtttt                                                                             <  1:81347/149‑1 (MQ=255)
                                                               ccgcGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGtttt                                                                             >  1:34475/1‑149 (MQ=255)
                                                                  cgcATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGCATCACTGACGCTCAACTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAg                                                                          >  1:653397/1‑149 (MQ=255)
                                                                   gcATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGCATCACTGACGCTCATCTTTGCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGa                                                                         <  1:477780/149‑1 (MQ=255)
                                                                    cATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGAc                                                                        >  1:709559/1‑149 (MQ=255)
                                                                     aTACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAACATCACTGACGCTCATCTTTTCACTACCCAGAGAACGCAACGTCCTTTGCAGCACCACCAGTGGCGTTATCacgcg                                                                       >  2:148753/1‑145 (MQ=255)
                                                                       aCTGGCACGAGGCAGGTAGTAGCCAACTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTAt                                                                     <  2:659043/149‑1 (MQ=255)
                                                                           gCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGt                                                                 <  1:627014/149‑1 (MQ=255)
                                                                                    aGGTAGGACCCAATTTGCTGTGACATGCGGCTGATTTGCTCCAGCATTACCGGCGCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGt                                                        <  2:274590/149‑1 (MQ=255)
                                                                                      gtagtaGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCTAGCATTGCCGGCTCAGCATCACTGACGCTGATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGa                                                      <  2:475525/149‑1 (MQ=255)
                                                                                        agtagCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGc                                                    <  2:309608/149‑1 (MQ=255)
                                                                                              cAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTa                                              <  2:589185/149‑1 (MQ=255)
                                                                                                         gAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTc                                   <  1:180763/149‑1 (MQ=255)
                                                                                                                             cAGCATTACCGGCTCAGTATCACTGACGCTCATATTTTCACTACGCAGAGAACGCAGCGTGCTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTCACGTTCGCGTTCACttt               >  1:25836/1‑149 (MQ=255)
                                                                                                                             cAGCATTACCGGCTCAGTATCACTGACGCCCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCTTCGTATGGCGTTTGTCGTAACCTTCCCGTTCACttt               >  2:157632/1‑149 (MQ=255)
                                                                                                                                    cccGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACaa        <  1:504326/148‑1 (MQ=255)
                                                                                                                                    aCCGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACaa        <  1:504320/149‑1 (MQ=255)
                                                                                                                                     ccGGCGCAGCATCCATGACTCTCGTCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCATACTATGGGTCAGGTCGGTGAGCGTCGCACGGTATTTGTCGTAACGTTCGCGTTCACTTTTGAACAAt       <  2:36959/149‑1 (MQ=255)
                                                                                                                                      cGGCTCAGTATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCTGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATc      >  1:336743/1‑149 (MQ=255)
                                                                                                                                          ccagcagCCCTAACGTTCAGCTTTTCATTACGCAGAGAACGCAGCGTACTTTGCAGTACCGCCAGCGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTGCGCGTTCACTTTTTAACAATCGGtt  <  2:29843/148‑1 (MQ=255)
                                                                                                                                              |                                                                                                                                                
GCTGAGGTGAGATTGTCCAGCAGTGGGGCGACCGGATGCAGCTCGCGGCTGAGCAATGTCCCGCCGCGCATACTGGCACGATGCAGGTAGTAGCCAATTTGCTGTGAAATGCGGCTGATTTGCTCCAGCATTACCGGCTCAGCATCACTGACGCTCATCTTTTCACTACGCAGAGAACGCAGCGTACTTTGCAGCACCGCCAGTGGCGTTTTCAGACTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTT  >  NC_000913_3_pae_tpiA/1188728‑1189014

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑