Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,801,078 (T)7→6 coding (922/1017 nt) waaJ ← UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,801,0720T.94.4% 143.2 / 4.9 36coding (928/1017 nt)waaJUDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase
Reads supporting (aligned to +/- strand):  ref base T (2/0);  new base . (17/17);  total (19/17)
Fisher's exact test for biased strand distribution p-value = 4.87e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.40e-02

TAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCAT  >  NC_000913/3801027‑3801116
                                             |                                            
taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttt                                          <  1:1779079/50‑1 (MQ=255)
    tCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaa                                      >  1:2116447/1‑50 (MQ=255)
     ccTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaat                                     >  1:575242/1‑49 (MQ=255)
      cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt                                   <  1:1821953/50‑1 (MQ=255)
        gagaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTc                                  >  1:1775177/1‑49 (MQ=39)
         agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTc                                  <  1:867824/48‑1 (MQ=39)
         agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTc                                  <  1:1731192/48‑1 (MQ=39)
         agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaa                                <  1:974593/50‑1 (MQ=255)
          gaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaat                               <  1:2052704/50‑1 (MQ=255)
            tataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataa                             >  1:1945079/1‑50 (MQ=255)
            tataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataa                             <  1:172585/50‑1 (MQ=255)
             ataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataat                            >  1:407763/1‑50 (MQ=255)
              taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAAtt                           <  1:89951/50‑1 (MQ=255)
              taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAAtt                           <  1:1168341/50‑1 (MQ=255)
              taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAAtt                           <  1:427752/50‑1 (MQ=255)
                 tgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAt                        >  1:1194111/1‑50 (MQ=255)
                   atgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAttt                      <  1:1603885/50‑1 (MQ=255)
                   atgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAtt                       <  1:2136112/49‑1 (MQ=39)
                    tgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTc                     <  1:1185613/50‑1 (MQ=255)
                      ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCg                    >  1:474001/1‑49 (MQ=39)
                        gCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCa                  <  1:1476023/49‑1 (MQ=39)
                           cTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtctc              <  1:1659835/50‑1 (MQ=255)
                           cTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtctc              <  1:1984065/50‑1 (MQ=255)
                              aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGt            <  1:2279848/49‑1 (MQ=39)
                               aaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg           >  1:256611/1‑49 (MQ=39)
                               aaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg           >  1:1566206/1‑49 (MQ=39)
                                  aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGgaga       <  1:2200784/50‑1 (MQ=255)
                                  aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGga         >  1:413035/1‑48 (MQ=39)
                                  aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGga         >  1:1589056/1‑48 (MQ=39)
                                   tGTTTATATC‑TTTTTTACATTCAATAATTGATTTCGCATCTCGTGGagag      >  1:1446372/1‑50 (MQ=255)
                                   tGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGagag      >  1:1449715/1‑50 (MQ=255)
                                   tGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGagag      >  1:1419526/1‑50 (MQ=255)
                                    gTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGt     >  1:118045/1‑50 (MQ=255)
                                      ttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCa   >  1:1615489/1‑50 (MQ=255)
                                      ttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCa   >  1:1058648/1‑50 (MQ=255)
                                       tataTC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCAt  >  1:1226585/1‑50 (MQ=255)
                                       tataTC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCAt  >  1:1313982/1‑50 (MQ=255)
                                             |                                            
TAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCAT  >  NC_000913/3801027‑3801116

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑