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.92.6% 101.1 / 5.1 27coding (928/1017 nt)waaJUDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase
Reads supporting (aligned to +/- strand):  ref base T (0/2);  new base . (10/15);  total (10/17)
Fisher's exact test for biased strand distribution p-value = 5.16e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

GCTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCATC  >  NC_000913/3801023‑3801117
                                                 |                                             
gCTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCt                                               >  1:1351248/1‑50 (MQ=255)
 cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtt                                              >  1:419995/1‑50 (MQ=255)
    taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttt                                           <  1:744639/50‑1 (MQ=255)
    taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttt                                           <  1:2235398/50‑1 (MQ=255)
    taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttt                                           >  1:1572652/1‑50 (MQ=255)
    taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttt                                            <  1:184554/49‑1 (MQ=255)
     aaTTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttt                                           >  1:1061980/1‑49 (MQ=255)
       ttCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttttaa                                        <  1:896583/50‑3 (MQ=255)
       ttCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttttaa                                        <  1:1018638/50‑3 (MQ=255)
       ttCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttttaa                                        <  1:1459703/50‑3 (MQ=255)
         ccTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaa                                       <  1:126485/49‑1 (MQ=255)
          cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaatc                                     <  1:854913/50‑3 (MQ=255)
          cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt                                    <  1:1440470/50‑1 (MQ=255)
             agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCa                                  <  1:267493/49‑1 (MQ=39)
             agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCa                                  <  1:1925903/49‑1 (MQ=39)
              gaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaat                                <  1:1607504/50‑1 (MQ=255)
               atatAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaat                                >  1:868488/1‑49 (MQ=39)
                tataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataa                              >  1:2191326/1‑50 (MQ=255)
                tataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataa                              >  1:1424153/1‑50 (MQ=255)
                tataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataa                              <  1:2194021/50‑1 (MQ=255)
                tataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataa                              <  1:1604995/50‑1 (MQ=255)
                 ataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataat                             >  1:672076/1‑50 (MQ=255)
                    atgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTg                           <  1:1567539/49‑1 (MQ=39)
                       atgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAtt                        <  1:1970210/49‑1 (MQ=39)
                        tgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTc                      <  1:1543052/50‑1 (MQ=255)
                          ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGc                    <  1:761471/50‑1 (MQ=255)
                            gCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAt                  >  1:1736796/1‑50 (MQ=255)
                               cTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtctc               <  1:76465/50‑1 (MQ=255)
                                 aaaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGt             >  1:1398768/1‑50 (MQ=255)
                                 aaaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGt             >  1:2099277/1‑50 (MQ=255)
                                  aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg            <  1:1610528/50‑1 (MQ=255)
                                   aaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTgg           <  1:668223/50‑1 (MQ=255)
                                      aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGgaga        <  1:2127225/50‑1 (MQ=255)
                                      aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGga          >  1:39009/1‑48 (MQ=39)
                                          ttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCa    >  1:1941392/1‑50 (MQ=255)
                                            atatC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCAt   <  1:1828491/49‑1 (MQ=39)
                                            atatC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCATc  >  1:1427247/1‑50 (MQ=255)
                                                 |                                             
GCTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCATC  >  NC_000913/3801023‑3801117

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑