Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 790,778 G→A 100% intergenic (+277/‑197) kipA → / → ltaS possible allophanate hydrolase subunit 2/possible phosphatidylglycerol‑‑membrane‑oligosaccharide glycerophosphotransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730790,7780GA100.0% 202.6 / ‑7.8 64intergenic (+277/‑197)kipA/ltaSpossible allophanate hydrolase subunit 2/possible phosphatidylglycerol‑‑membrane‑oligosaccharide glycerophosphotransferase
Reads supporting (aligned to +/- strand):  ref base G (1/0);  major base A (36/25);  minor base T (2/0);  total (39/25)
Fisher's exact test for biased strand distribution p-value = 5.14e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AATTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTGTAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAATGTTA  >  CP000730/790648‑790913
                                                                                                                                  |                                                                                                                                       
aaTTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCaaa                                                                                                                                <  1:359608/140‑1 (MQ=255)
 aTTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCaaaa                                                                                                                               <  2:659986/140‑1 (MQ=255)
      gACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGCTAACAGTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACtt                                                                                                                          >  1:495145/1‑140 (MQ=255)
      gACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACtt                                                                                                                          <  1:382055/140‑1 (MQ=255)
      gACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACtt                                                                                                                          >  2:439817/1‑140 (MQ=255)
         tAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGtt                                                                                                                       <  2:328053/140‑1 (MQ=255)
           aaaTTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTaa                                                                                                                     <  2:555662/140‑1 (MQ=255)
           aaaTTACACTATCTTTATTAATTGAGCTATCCTTATTATTCCGATTTGATTACAAATTATAAATTTGTTATTTGATTTAGAATTGACAAGAGTGAAACTTAGCAAAGCAAATATGAGTATTAGCCCAAAATACTTGTTaa                                                                                                                     >  2:298166/1‑140 (MQ=255)
                 ctctATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCaaa                                                                                                               >  2:364327/1‑140 (MQ=255)
                           attaATTGAGCTATGCTTATTATTACATTTAGACGACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTCAAATCAAAGTTGAAAGCt                                                                                                     >  1:352233/1‑140 (MQ=255)
                           attaATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGAAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCt                                                                                                     >  1:27858/1‑140 (MQ=255)
                               aTTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGATACaa                                                                                                 >  1:288475/1‑140 (MQ=255)
                                   aGCTATGGTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATaa                                                                                             <  2:400532/140‑1 (MQ=255)
                                     cTATGCTTATTATTACGATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACg                                                                                           >  2:536958/1‑140 (MQ=255)
                                       aTGCTTATTATTACAATGTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGaa                                                                                         <  1:715448/140‑1 (MQ=255)
                                        tGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGaaa                                                                                        <  2:678578/140‑1 (MQ=255)
                                        tGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTGGAAAGCTACAAATAACGaaa                                                                                        <  1:439817/140‑1 (MQ=255)
                                          cTTATTATTACAATTTGGTTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAATCTACAAATAACGAAAAt                                                                                      <  2:516321/140‑1 (MQ=255)
                                          cTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGTATCATAGCCCAATATACAATGTAAATCAAAGTTGAAAGCTACAAATAACGAAAAt                                                                                      <  1:170432/140‑1 (MQ=255)
                                          cTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTTATTCAAACTGTAAAGCTACAAATAACGAAAAt                                                                                      <  1:172868/140‑1 (MQ=255)
                                          cTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAAt                                                                                      <  1:651326/140‑1 (MQ=255)
                                          cTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAAt                                                                                      <  1:628849/140‑1 (MQ=255)
                                           ttattattaCAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGTCCAAAATACTTTTTAAATCAAAGTTGAAAGCTACAAATAACCAGAAtt                                                                                     >  1:582741/1‑140 (MQ=255)
                                            tattattaCACTTTTATTAAAAATTTTAAATTTTTTAATTGAATGATAATATTAAATAAAGAAATTTACACAAGCAAATATGAGTTATAGCCCAAAGTATTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATta                                                                                    <  1:331742/140‑1 (MQ=255)
                                                   aCAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCTAAGTTTAAAGCTACAAATAACGAAAATTATAAACtt                                                                             >  1:376769/1‑140 (MQ=255)
                                                   aCAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATaaccca                                                                             <  2:703342/140‑5 (MQ=255)
                                                   aCAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACtt                                                                             >  1:703342/1‑140 (MQ=255)
                                                        ttGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATc                                                                        <  2:592037/140‑1 (MQ=255)
                                                           aTTACAACTTTTAAATTTTTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGa                                                                     <  2:495145/140‑1 (MQ=255)
                                                           aTTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTATTTCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGa                                                                     <  2:220345/140‑1 (MQ=255)
                                                            ttACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGaa                                                                    <  2:54162/140‑1 (MQ=255)
                                                            ttACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGaa                                                                    <  1:474216/140‑1 (MQ=255)
                                                              aCAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAg                                                                  >  2:134882/1‑140 (MQ=255)
                                                               cAAATTTTAAATTTGTCAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGt                                                                 >  1:431099/1‑140 (MQ=255)
                                                                     ttAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTaa                                                           >  1:230504/1‑139 (MQ=255)
                                                                         aTTTGTTAATTGAATGATATTTTTTTGTAAGGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAGGCTATAAATATTGAAAATTATAAATTTGAGTTTGAAAGTAAttattaaa                                                       >  1:353273/1‑138 (MQ=255)
                                                                         aTTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTGTAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAAATTGAATATGAAAGTAATTACtata                                                       >  2:16219/1‑140 (MQ=255)
                                                                          tttGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAACATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATaa                                                      >  1:703704/1‑140 (MQ=255)
                                                                           ttGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAAATATAAACTTGAATCTGAAAGTAATTACTATAAt                                                     >  1:272246/1‑140 (MQ=255)
                                                                             gTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAACGTTTGAAAGAACGAACATTATAAACTTGAATCTGAAAGTAATTACTATAATTa                                                   >  1:710285/1‑140 (MQ=255)
                                                                                 aTTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGAc                                               <  1:96660/140‑1 (MQ=255)
                                                                                      aTGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGt                                          >  1:398392/1‑140 (MQ=255)
                                                                                          taataTTAAATAAAGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAAATACTATAATTATGACAATGTTAAc                                      >  2:723997/1‑140 (MQ=255)
                                                                                                  aataaaGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAAc                              >  1:285285/1‑140 (MQ=255)
                                                                                                       aGAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGAAAATGTTAACTTTTAAACGCACt                         >  1:303644/1‑140 (MQ=255)
                                                                                                        gAAACTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACtt                        >  2:374951/1‑140 (MQ=255)
                                                                                                        gAAAATTACACAAGCAAATATGCGTTTTAGCCAAAAATACTTGTTAAATCAAAGTTGAATGCTACAAATAACGAAAATTATAACGTTGAATATGAAAGTAAATACATTATTTATGACAATTTTAACTTTTAAACGCAcgt                        >  2:554834/1‑138 (MQ=255)
                                                                                                          aaCTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTAAAATTATGACAATGTTAACTTTTAAACGCACttat                      >  2:689472/1‑140 (MQ=255)
                                                                                                           aCTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGCAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACttatt                     >  1:115419/1‑140 (MQ=255)
                                                                                                           aCTTACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAAATTTTAAACGCACttatt                     >  2:537353/1‑140 (MQ=255)
                                                                                                            cTTACATAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACttatta                    <  1:497788/140‑1 (MQ=255)
                                                                                                             ttACACAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTattaa                   >  2:310308/1‑140 (MQ=255)
                                                                                                               acacAAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACATGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTattaatt                 >  1:550507/1‑140 (MQ=255)
                                                                                                                cacaAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAGGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTattaatta                >  2:388069/1‑140 (MQ=255)
                                                                                                                cacaAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACATATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTGAACTTTTAAACGCACTTattaatta                >  1:446495/1‑140 (MQ=255)
                                                                                                                  caAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAAc              >  1:250894/1‑140 (MQ=255)
                                                                                                                  caAGCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCGACAAATAACGAAAATTATAAACTTGAATCTGACAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAAc              >  2:399828/1‑140 (MQ=255)
                                                                                                                     gCAAATATGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTAc           >  2:33723/1‑140 (MQ=255)
                                                                                                                         atatGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATaa       >  2:635761/1‑140 (MQ=255)
                                                                                                                         atatGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATCAACTCCATaa       >  2:161317/1‑140 (MQ=255)
                                                                                                                         agatGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCCCTTATTAATTAACTACATaa       >  2:7666/3‑140 (MQ=255)
                                                                                                                          tatGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAAt      >  2:485023/1‑140 (MQ=255)
                                                                                                                            tGAGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAATGt    <  1:77794/140‑1 (MQ=255)
                                                                                                                              aGTTATAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAATGTTa  <  1:364327/140‑1 (MQ=255)
                                                                                                                                  |                                                                                                                                       
AATTTTGACTAAAATTACTCTATATTTATTAATTGAGCTATGCTTATTATTACAATTTGATTACAAATTTTAAATTTGTTAATTGAATGATAATATTAAATAAAGAAACTTACACAAGCAAATATGAGTTGTAGCCCAAAATACTTGTTAAATCAAAGTTGAAAGCTACAAATAACGAAAATTATAAACTTGAATCTGAAAGTAATTACTATAATTATGACAATGTTAACTTTTAAACGCACTTATTAATTAACTACATAATGTTA  >  CP000730/790648‑790913

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: