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.97.0% 143.0 / ‑0.6 33coding (928/1017 nt)waaJUDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base . (15/17);  total (15/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

AATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGA  >  NC_000913/3801028‑3801109
                                            |                                     
aaTTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttt                                   >  1:2560732/1‑49 (MQ=255)
 aTTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttttt                                  <  1:942438/49‑1 (MQ=255)
  ttCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttttta                                 >  1:1207516/1‑48 (MQ=255)
     cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaat                              <  1:3579290/49‑2 (MQ=255)
     cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt                            <  1:1109812/50‑1 (MQ=255)
     cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt                            >  1:345103/1‑50 (MQ=255)
          atatAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaata                       <  1:2704807/50‑1 (MQ=255)
           tataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataa                      >  1:290675/1‑50 (MQ=255)
             taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataat                     <  1:1356177/49‑1 (MQ=39)
             taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataat                     <  1:3148331/49‑1 (MQ=39)
             taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAAtt                    <  1:2002918/50‑1 (MQ=255)
                  atgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAttt               <  1:539743/50‑1 (MQ=255)
                  atgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAttt               <  1:3588601/50‑1 (MQ=255)
                  atgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAtt                <  1:309533/49‑1 (MQ=39)
                   tgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTc              <  1:1134934/50‑1 (MQ=255)
                    gTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCg             >  1:732256/1‑50 (MQ=255)
                     ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCg             >  1:2703740/1‑49 (MQ=39)
                     ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCg             <  1:2838094/49‑1 (MQ=39)
                      tGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCa           >  1:1076348/1‑50 (MQ=255)
                      tGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCa           >  1:2756287/1‑50 (MQ=255)
                       gCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAt          >  1:2648756/1‑50 (MQ=255)
                       gCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAt          >  1:3902208/1‑50 (MQ=255)
                         aCTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtct        <  1:3165196/50‑1 (MQ=255)
                         aCTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtct        >  1:825064/1‑50 (MQ=255)
                         aCTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtct        <  1:234405/50‑1 (MQ=255)
                            aaaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGt     >  1:2433769/1‑50 (MQ=255)
                             aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCg      <  1:3569056/48‑1 (MQ=39)
                             aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg    <  1:1656571/50‑1 (MQ=255)
                             aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg    <  1:658019/50‑1 (MQ=255)
                             aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg    <  1:3746718/50‑1 (MQ=255)
                              aaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTgg   <  1:888242/50‑1 (MQ=255)
                              aaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg    >  1:1650912/1‑49 (MQ=39)
                               aGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg    >  1:3249036/1‑48 (MQ=39)
                               aGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg    >  1:827194/1‑48 (MQ=39)
                                 aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGga  >  1:2115344/1‑48 (MQ=39)
                                 aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGga  >  1:3036934/1‑48 (MQ=39)
                                            |                                     
AATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGA  >  NC_000913/3801028‑3801109

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: ‑