Predicted mutation
evidence seq id position mutation annotation gene description
RA CP000730 1,274,208 C→T S204L (TCA→TTA)  codY → CodY family transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,274,2080CT86.5% 87.4 / 5.2 37S204L (TCA→TTA) codYCodY family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (5/0);  new base T (14/18);  total (19/18)
Fisher's exact test for biased strand distribution p-value = 4.63e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGCATAGTGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAA  >  CP000730/1274070‑1274340
                                                                                                                                          |                                                                                                                                    
aGCATAGTGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTaa                                                                                                                                    >  2:162290/1‑141 (MQ=255)
   ctAGTGAAGCAGAAAAAGAAGCGCGCGATGAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGAGTGAACATATCTATGAAGAACTTGGCGGTGCGGAAGGCCGATTAGTCGCATTaaacg                                                                                                                                 >  2:406290/2‑139 (MQ=255)
   aTAGTGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAg                                                                                                                                 <  1:273758/141‑1 (MQ=255)
                    gaagCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGt                                                                                                                >  1:323894/1‑141 (MQ=255)
                    gaagCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTAGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGt                                                                                                                >  2:28380/1‑141 (MQ=255)
                    gaagCGCACGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGt                                                                                                                <  2:237877/141‑1 (MQ=255)
                       gcgcgcGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTAtt                                                                                                             <  2:45677/141‑1 (MQ=255)
                       gcgcgcGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTAtt                                                                                                             >  2:73059/1‑141 (MQ=255)
                             gATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGa                                                                                                       <  2:95573/141‑1 (MQ=255)
                             gATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGa                                                                                                       <  1:152218/141‑1 (MQ=255)
                                  aGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGACGGTACGGAAGGCCTCTTAATCGCATTCCAAGTCGCAGACAGAGTTGGTACTACTAGATgtgt                                                                                                  >  2:395618/1‑141 (MQ=255)
                                   gctgctATTACACTGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTAAGGAAGGCCTATTAATCGCATCAACAGTTGCAGATAGAGGTGGTATTACTAGATCTGTa                                                                                                 >  2:290132/1‑141 (MQ=255)
                                   gctgctATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGTCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGTTATTACTAGATCTGTa                                                                                                 >  2:342987/1‑141 (MQ=255)
                                    ctgctATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTaa                                                                                                >  1:97595/1‑141 (MQ=255)
                                                tGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCAc                                                                                    <  1:272623/141‑1 (MQ=255)
                                                   gaattaattCATTATCTTATTCTGAAAAAGAAGCGATTGTACATATCTTTGAAGAACTTGGCGGTACAGATGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGATATTACCAGATCTGTAATTGTAAATGCACGAc                                                                                 <  2:398917/140‑1 (MQ=255)
                                                   cAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTAc                                                                                 >  2:110191/1‑141 (MQ=255)
                                                      ttaattCATTATCTTATTCTGACAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTa                                                                              <  1:350313/141‑1 (MQ=255)
                                                           tCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTa                                                                         >  1:105639/1‑141 (MQ=255)
                                                             aTTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGa                                                                       >  1:115198/1‑141 (MQ=255)
                                                                            aaaaGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAAt                                                        <  1:162290/141‑1 (MQ=255)
                                                                                gaagCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAGATTAGAAAGTGCTGGTGTAATTGaa                                                    >  1:318178/1‑141 (MQ=255)
                                                                                  agCGATTGAACATGTCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTATTTGaagc                                                  >  1:191210/1‑139 (MQ=255)
                                                                                   gCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCa                                                 >  1:312409/1‑141 (MQ=255)
                                                                                   gCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCa                                                 >  2:385854/1‑141 (MQ=255)
                                                                                    cGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCAc                                                <  1:143896/141‑1 (MQ=255)
                                                                                    cGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCAc                                                <  1:150873/141‑1 (MQ=255)
                                                                                     gATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACg                                               <  1:403656/141‑1 (MQ=255)
                                                                                     gATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACg                                               <  1:283530/141‑1 (MQ=255)
                                                                                               atCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGa                                     >  1:32632/1‑141 (MQ=255)
                                                                                                          aCTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTAc                          <  1:8944/141‑1 (MQ=255)
                                                                                                           cTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACt                         >  1:7677/1‑141 (MQ=255)
                                                                                                                cGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCAt                    <  2:133507/141‑1 (MQ=255)
                                                                                                                  gTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTaa                                                                                                <  2:400349/63‑1 (MQ=255)
                                                                                                                  gTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTaa                                                                                                >  1:400349/1‑63 (MQ=255)
                                                                                                                               aTTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGa     <  1:28380/141‑1 (MQ=255)
                                                                                                                                  aaTCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGaaaa  <  1:267804/141‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                    
AGCATAGTGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAA  >  CP000730/1274070‑1274340

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: ‑