Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,832,784 T→C 7.3% C156R (TGC→CGC)  rfaQ → lipopolysaccharide core biosynthesis protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,832,7840TC 7.3% 181.2 / 6.7 68C156R (TGC→CGC) rfaQlipopolysaccharide core biosynthesis protein
Reads supporting (aligned to +/- strand):  ref base T (23/40);  new base C (3/2);  total (26/42)
Fisher's exact test for biased strand distribution p-value = 3.63e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.79e-01

TTTATCGGTCCTTGAGCCATTAGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAATTAGATGCCCTGGGCGTAAAAGATCATTATGTTGTCATCCAACCGA  >  W3110S.gb/3832714‑3832853
                                                                      |                                                                     
tttATCGGTCCTTGAGCCATTAGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGAtt                                                                       >  1:861933/1‑71 (MQ=255)
tttATCGGTCCTTGAGCCATTAGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGAtt                                                                       <  1:4021299/71‑1 (MQ=255)
  tATCGGTCCTTGAGCCATTAGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGc                                                                     >  1:79320/1‑71 (MQ=255)
  tATCGGTCCTTGAGCCATTAGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATCGc                                                                     >  1:37217/1‑71 (MQ=255)
         ccTTGAGCCATTAGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATCGCTGgaag                                                               >  1:724913/1‑70 (MQ=255)
          cTTGAGCCATTAGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGgaagaa                                                             <  1:352502/71‑1 (MQ=255)
          cTTGAGCCATTAGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGgaagaa                                                             <  1:4131249/71‑1 (MQ=255)
          cTTGAGCCATTAGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGgaaga                                                              <  1:477428/70‑1 (MQ=255)
          cTTGAGCCATTAGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGgaag                                                               >  1:3439562/1‑69 (MQ=255)
             gAGCCATTAGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGaagaag                                                            <  1:1125466/69‑1 (MQ=255)
             gAGCCATTAGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGaagaag                                                            <  1:1248163/69‑1 (MQ=255)
             gAGCCATTAGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGaagaag                                                            <  1:4220315/69‑1 (MQ=255)
             gAGCCATTAGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAagaaga                                                           <  1:250394/70‑1 (MQ=255)
             gAGCCATTAGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAagaaga                                                           <  1:4019098/70‑1 (MQ=255)
             gAGCCATTAGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAagaaga                                                           <  1:1151777/70‑1 (MQ=255)
             gAGCCATTAGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGAt                                                          >  1:4036878/1‑71 (MQ=255)
              aGCCATTAGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGAt                                                          <  1:2185573/70‑1 (MQ=255)
                  aTTAGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGcc                                                     <  1:2118419/71‑1 (MQ=255)
                   ttAGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCg                                                    >  1:1307951/1‑71 (MQ=255)
                     aGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCgg                                                   >  1:4241173/1‑70 (MQ=255)
                     aGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCgg                                                   >  1:4245961/1‑70 (MQ=255)
                     aGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCgg                                                   >  1:1502274/1‑70 (MQ=255)
                     aGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCgg                                                   >  1:608185/1‑70 (MQ=255)
                       gTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCggg                                                  <  1:400676/69‑1 (MQ=255)
                        tATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTTGAAGAAGATGCGCCGGGAAt                                               <  1:1126971/71‑1 (MQ=255)
                        tATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAAt                                               <  1:1525354/71‑1 (MQ=255)
                        tATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAAt                                               <  1:251905/71‑1 (MQ=255)
                          ttACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAAtt                                              <  1:3936974/70‑1 (MQ=255)
                          ttACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAAt                                               <  1:3669358/69‑1 (MQ=255)
                          ttACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATCGCTGGAAGAAGATGCGCCGGGa                                                 <  1:56967/67‑1 (MQ=255)
                            aCCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGaagaag                                                            >  1:2183654/1‑54 (MQ=255)
                              cGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGgaa                                                                >  1:2701807/1‑48 (MQ=255)
                              cGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGgaa                                                                >  1:1281907/1‑48 (MQ=255)
                              cGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGAt                                                          >  1:1574445/1‑54 (MQ=255)
                              cGAATTCTACACCGACACAACAATGAGTTACGCAGAAGATTGCTGgaa                                                                >  1:1561898/1‑48 (MQ=255)
                                aTTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAATTAGa                                           >  1:2856863/1‑67 (MQ=255)
                                  ttCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAagaaga                                                           >  1:2834769/1‑49 (MQ=255)
                                  ttCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCg                                                    >  1:3194012/1‑56 (MQ=255)
                                  ttCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAAt                                               >  1:2840564/1‑61 (MQ=255)
                                  ttCTACACCGACACAACAATGAGTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAATTAGATGCCCt                                     <  1:4071895/70‑1 (MQ=255)
                                   tCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGaa                                                >  1:3669987/1‑59 (MQ=255)
                                       cacCGAAACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCAGGGAATTAGATGCCCTGGGc                                 <  1:1568072/70‑1 (MQ=255)
                                        acCGACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCgg                                                   >  1:1214036/1‑51 (MQ=255)
                                        acCGACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAAtt                                              <  1:2364069/56‑1 (MQ=255)
                                         ccGACACAACAATGAGTTACGCCGAAGATTGCTGgaagaa                                                             <  1:4245559/40‑1 (MQ=255)
                                          cGACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAATTAGATGCCCTGGGCGTaa                             <  1:3531673/71‑1 (MQ=255)
                                          cGACACAACAAAGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAATTAGATGCCCTGGGCGTaa                             <  1:476567/71‑1 (MQ=255)
                                           gACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAATTAGATGCCCTGGGCGTaaa                            <  1:2102668/71‑1 (MQ=255)
                                              acaacaATGAGTTACGCCGAAGATTGCTGgaagaa                                                             <  1:48470/35‑1 (MQ=255)
                                              acaacaATGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAATTa                                             <  1:3320266/51‑1 (MQ=255)
                                               caacaaTGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAATTa                                             <  1:2414775/50‑1 (MQ=255)
                                               caacaaTGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAATTa                                             <  1:2657154/50‑1 (MQ=255)
                                               caacaaTGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAATTAGATGCCCTGGGCGTAAAAGAt                        <  1:1267464/71‑1 (MQ=255)
                                                 acaaTGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAATTAGATGCCCTGGGCGTAAAAGATCa                      <  1:2899058/71‑1 (MQ=255)
                                                  caaTGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAATTAGATGCCCTGGGCGTAAAAGATCAt                     <  1:3489435/71‑1 (MQ=255)
                                                  caaTGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAATTAGATGCCCTGGGCGTAAAAGATCAt                     >  1:542606/1‑71 (MQ=255)
                                                  caaTGAGTTACGCCGAAGATTGCTGGAAGAAGATGCCCCGGGAATTAGATGCCCTGGGCGTAAAAGATCAt                     >  1:1659197/1‑71 (MQ=255)
                                                   aaTGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAATTAGGTGCCCTGGGCGTAAAAg                          <  1:4267999/65‑1 (MQ=255)
                                                   aaTGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAATTAGATGCCCTGGGCGTAAAAg                          <  1:806475/65‑1 (MQ=255)
                                                   aaTGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAATTAGATGCCCTGGGCGTAAAAGATCAt                     >  1:776357/1‑70 (MQ=255)
                                                       aGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAATTa                                             <  1:430946/42‑1 (MQ=255)
                                                       aGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAATTAGATGCCCTGGGCGTAAAAGATGATTAtg                 <  1:546895/70‑1 (MQ=255)
                                                         ttACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAATTAGa                                           <  1:3901314/42‑1 (MQ=255)
                                                         ttACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAATTAGATGCCCt                                     <  1:789152/48‑1 (MQ=255)
                                                             gCCGAAGATTGCTGGAAGAAGATGCGCCGGGAATTAGATGCCCTGGGCGTAAAAGATCATTATGTTGTCAt          <  1:3191065/71‑1 (MQ=255)
                                                               cGAAGATTGCTGGAAGAAGATGCGCCGGGAATTAGATGCCCTGGGCGTAAAAGATCATTATGTTGTCATcc        <  1:11946/71‑1 (MQ=255)
                                                                gAAGATCGCTGGAAGAAGATGCGCCGGGAATTAGATGCCCTGGGCGTaaaa                           >  1:1163799/1‑51 (MQ=255)
                                                                 aaGATTGCTGGAAGAAGATGCGCCGGGAATTAGATGCCCTGGGCGTaaaa                           >  1:2400701/1‑50 (MQ=255)
                                                                   gATTGCTGGAAGAAGATGCGCCGGGAATTAGATGCCCTGGGCGTAAAAGATCATTATGTTGTCATCCAAcc    <  1:3424258/71‑1 (MQ=255)
                                                                   gATCGCTGGAAGAAGATGCGCCGGGAATTAGATGCCCTGGGCGTAAAAGATCATTATGTTGTCATCCAAcc    <  1:428931/71‑1 (MQ=255)
                                                                      tGCTGGAAGAAGATGCGCCGGGAATTAGATGCCCTGGGCGTAAAAGATCATTATGTTGTCATCCaa      <  1:2251612/66‑1 (MQ=255)
                                                                      tGCTGGAAGAAGATGCGCCGGGAATTAGATGCCCTGGGCGTAAAAGATCATTATGTTGTCATCCAACCGa  >  1:1722706/1‑70 (MQ=255)
                                                                      tGCTGGAAGAAGATGCGCCGGGAATTAGATGCCCTGGGCGTAAAAGATCATTATGTTGTCATCCAACCGa  <  1:2512275/70‑1 (MQ=255)
                                                                      |                                                                     
TTTATCGGTCCTTGAGCCATTAGGTATTACCGATTTCTACACCGACACAACAATGAGTTACGCCGAAGATTGCTGGAAGAAGATGCGCCGGGAATTAGATGCCCTGGGCGTAAAAGATCATTATGTTGTCATCCAACCGA  >  W3110S.gb/3832714‑3832853

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: