Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP006881 1,666,480 G→C 17.9% Q257H (CAG→CAC)  U712_08575 → Flagellar motor switch phosphatase FliY

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068811,666,4800GC17.9% 99.0 / 3.0 51Q257H (CAG→CAC) U712_08575Flagellar motor switch phosphatase FliY
Reads supporting (aligned to +/- strand):  ref base G (16/25);  new base C (4/5);  total (21/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGAAAGATTTAATTTCAAGCCTTATGAACTCAGAAAGTGCAGAGGAAGAAGAAACGGTGCAGCCTGAAGTTACATACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGTATTGAACCGAAGCAACAGCAGCAGCCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCAAACGAAGCTGTACAAGCCCCTATTCATAATCTGGATATGCTTTTGGATATCCCG  >  CP006881/1666349‑1666618
                                                                                                                                   |                                                                                                                                          
gCGAAAGATTTAATTTCAAGCCTTATGAACTCAGAAAGTGCAGAGGAAGAAGAAACGGTGCAGCCTGAAGTTACATACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGGATTTAACCGAAGCAACagcagcagc                                                                                                                                     >  5:357464/1‑139 (MQ=255)
         ttAATTTCAAGCCTTATGAACTCAGAAAGTGCAGAGGAAGAAGAACCGGTGCAGCCTGAAGTTACATACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGTATTGAACCGAAGCAACAGCAGCAGCCGCCaaaa                                                                                                                             <  3:376065/138‑1 (MQ=255)
            aTTTCAAGCCTTATGAACTCAGAAAGTGCAGAGGAAGAAGAAACGGTGCAGCCTGAAGTTACATACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGTATTGAACCGAAGCAACAGCAGCAGCCGCCAAAAAgg                                                                                                                          <  5:144572/138‑1 (MQ=255)
             tttCAAGCCTTATGAACTCAGAAAGTGCAGAGGAAGAAGAAACGGTGCAGCCTGAAGTTACATACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGTATTGAACCGAAGCAACAGCAGCAGCCGCCAAAAAGGCa                                                                                                                        <  8:332127/139‑1 (MQ=255)
                 aaGCCTTATGAACTCAGAAAGTGCAGAGGAAGAAGAAACGGTGCAGCCTGAAGTTACATACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGGATTGCACCGAAGCAACCGCAGCAGCCGCCCAAAAGGCAGGGa                                                                                                                    >  4:376065/1‑139 (MQ=255)
                  aGCCTTATGAACTCAGAAAGTGCAGAGGAAGAAGAAACGGTGCAGCCTGAAGTTACATACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGTATTGAACCGAAGCAACAGCAGCAGCCGCCAAAAAGGCAGGGaa                                                                                                                   <  2:336544/139‑1 (MQ=255)
                       tATGAACTCAGAAAGTGCAGAGGAAGAAGAAACGGTGCAGCCTGAAGTTACATACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGGATTTAACCGAAGCCACAGCAGCAGCCGCCAAAAAGGCCGGGGACacc                                                                                                               >  1:158190/1‑136 (MQ=255)
                              tCAGAAAGTGCAGAGGAAGAAGAAACGGTGCAGCCTGAAGTTACATACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGTATTGCACCGACGCCACAGCAGCAGCCGCCAAAAAGGCAGGGAACAGCAAAAAAag                                                                                                       >  1:111587/1‑139 (MQ=255)
                              tCAGAAAGTGCAGAGGAAGAAGAAACGGTGCAGCCTGAAGTTACATACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGTATTGAACCGAAGCAACAGCAGCAGCCGCCAAAAAGGCAGGGAACAGCAAAAAAag                                                                                                       >  5:158276/1‑139 (MQ=255)
                               cAGAAAGTGGAGAGGAAGAAGAAACGGTGCAGCCTGAAGTTACATACGACCAGCCGAAAGAGCCTGTGACGCCAGCGCCGCGGATTGGACCCACGCAACAGCAGCCCCCGCCAAAAATGGCCGGAACAGCaaaaaaaa                                                                                                       >  6:92988/1‑137 (MQ=255)
                                    cgggCAGACCAACAAGAAACCGGCCAGCCTGAAGTTACATCCCAACAGCCGAAAGAGCCTGGGCCGCCAGCGCCGCGTATTGAACCGAAGCAACAGCAGCACCCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAgcgc                                                                                                 <  4:139273/136‑1 (MQ=255)
                                         agagGAAGAAGAAACGGTGCAGCCTGAAGTTACATACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGTATTGAACCGAAGCAACAGCAGCAGCCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGtt                                                                                            <  1:265770/139‑1 (MQ=255)
                                         agagCAACAACAACCGGTGCAGCCTGAAGTTACATACGAACAGCCGAAAGAGCCGGTGACGCCAGAGCCGCGTATTGAACCGAAGCAACAGCAGCAGCCGCCAAAAAGGCAGGGAACAGCAAAAAACGCAGCGCCAGtt                                                                                            <  1:193858/139‑1 (MQ=255)
                                                gaagaaACGGTGCAGCCTGAAGTTACATACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGGTTTGAACCGAAGCAACAGCAGCCGCCCCCAAAAATGCAGGGAACAGCAAAAAAAGCAGCGCCCGTTCAGGgtt                                                                                     >  4:38327/1‑139 (MQ=255)
                                                gaagaaACGGTGCAGCCTGAAGTTACATACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGGATTGAACCGAAGCAACAGCAGCCGCCGCCAAAAACGCAGGGAACAGCAAAAAAAGCAGCGCCAGGTCAGGttt                                                                                     >  1:133447/1‑139 (MQ=255)
                                                     aaCGGTGCAGCCTGAAGTTACATACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGGATTGAACCGAATCAACACCACCAGCCCCCAAAAAGGCACGGAACAGCAAAAAAACCAGCGCCAGTTAAGGTTTCCCCg                                                                                >  6:119287/1‑139 (MQ=255)
                                                       cGGTGCAGCCTGAAGTTACATACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGGTTTGTCACCCACCCACACCCCCACCCCCCCAAAAAGCAGGGAACAGCAAAAAAAGCACCGCCCCTTCAGGTTTCACCggg                                                                              >  2:364486/1‑138 (MQ=255)
                                                                  gAAGTTACATACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGTATTGAACCGCAGCAACAGCAGCAGCCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCcg                                                                   >  7:226421/1‑139 (MQ=255)
                                                                   aaGTTACATACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGTTTTGAACCGCAGCAACCGCAGCCGCCGCCCAAAAGGCAGGGTCCCGCAAAAAAAGCAGCGGCAGGTCAGGTTTCACCGGGGGCATTTTcctc                                                                  >  5:271935/1‑137 (MQ=255)
                                                                    aGTTACATACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGTTTTGAACCGAAGCCACAGCAGCCGCCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCcgcg                                                                 >  3:141477/1‑139 (MQ=255)
                                                                    aGTTACATACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGGTTTGAACCGAAGCAACACCAGCCGCCGCCAAAAAGGCAGGGAACCGCACAAAAAACACCCCCAGTTCAGGTTTGACCGGTGGAGTTTTAcgcg                                                                 >  3:237419/1‑139 (MQ=255)
                                                                     gTTACATACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGTATTGAACCGAAGCAACAGCAGCAGCCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGt                                                                <  7:15092/139‑1 (MQ=255)
                                                                         cATACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGTATTGAACCGAAGCAACAGCAGCAGCCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGa                                                            >  3:118621/1‑139 (MQ=255)
                                                                         cATACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGTATTGAACCGAAGCAACAGCAGCAGCCGCCAAAAACGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGa                                                            >  1:220896/1‑139 (MQ=255)
                                                                          atccGAACAGCGGAAAGAGCAGGTGACGCCAGAGCCGCGTATTGAACCGACGCAACAGCAGCAGCCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGAt                                                           <  7:280933/136‑1 (MQ=255)
                                                                          aTACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGTATTGAACCGAAGCAACAGCAGCAGCCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGAt                                                           <  8:382225/139‑1 (MQ=255)
                                                                               accAGCCGAAAGCGCCTGTGACGCCCGACCCGCGTATTGAACCCACGCAACACCCGCAGCCGCAAAAAAGGCAGGGAACAGAAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCaaa                                                      <  6:309535/137‑1 (MQ=255)
                                                                               aaCAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGTATTGAACCGAAGCAACAGCAGCAGCCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCaaa                                                      >  8:403707/1‑139 (MQ=255)
                                                                               aaCACCCGAAAGCGCCTGTGACGCCAGAGCCGCGTATTCAACCGACGCACCAGCCGCAGCCGCCAAAACGGCAGGGAACAGCAAAAAACGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCaaa                                                      <  5:331760/139‑1 (MQ=255)
                                                                                 cAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGTATTGAACCGAAGCAACAGCAGCAGCCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCAAACg                                                    <  3:182514/139‑1 (MQ=255)
                                                                                  cgCCGAAAGAGCCTGTGACGCCAGAGCCGCGTATTGAACCGAAGCAACAGCAGCAGCCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCAAACGa                                                   <  6:112572/138‑1 (MQ=255)
                                                                                    ccGAATCAGCCTGGGACGCCAGAGCGGCGTATGGAACCGAAGCAACAGCAGCAGCCGCCAAACCGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCAAACGAAg                                                 <  4:262387/139‑1 (MQ=255)
                                                                                    ccGAAAGAGCCTGTGACGCCAGAGCCGCGTTATGAACCGCAGCCACACCCGCCGCCGCCAAAAAGGCAGGGAACAGCCAAAAAAGCAGCGCCAGTTCCGGTTTCACCCGTGGTATTTTACTCGTTTGGTACCAACCAAg                                                 >  7:266197/1‑139 (MQ=255)
                                                                                    ccGAAAGAGCCTGTGACGCCAGAGCCGCGTATTGAACCGAAGCAACAGCAGCAGCCGCCAAAAAGGCAGGGAACCGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCAAACGAAg                                                 <  6:341727/139‑1 (MQ=255)
                                                                                    ccGAAAGAGCCTGTGACGCCAGAGCCGCGTATTGAACCGAAGCAACAGCAGCAGCCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGGTTGATCCAAACGAAg                                                 <  2:224546/139‑1 (MQ=255)
                                                                                    ccGAAAGAGCCTGTGACGCCAGAGCCGCGTATTGAACCGAAGCAACAGCAGCAGCCCCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTAAGGTTTCACCCGTGGAATTTTACGCGTTTTATCCAAACGAAg                                                 >  7:39926/1‑139 (MQ=255)
                                                                                    ccGAAAGAGCCTGTGACGCCAGAGCCGCGTATTGAACCGAAGCAACACCAGCAGCCGCCAAAAAGGCAGTGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCAAACGAAg                                                 <  5:119287/139‑1 (MQ=255)
                                                                                         agagCCTGGCACGCCAGAGCCGCGTATTGAACCGAAGCAACACCAGCAGCCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCAAACGAAGCTGTa                                            <  8:39926/139‑1 (MQ=255)
                                                                                           ccccTGTGACGCCACACCCGCTTATTCAACCGACCCAACTCCAGCACCCGCAAAAAAGGCAGGGAACAGAAAAAAACGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCAAACGAAGCTGTACa                                          <  1:321967/137‑1 (MQ=255)
                                                                                             ccggtcaCGCCACCGCCGCGTATTGACCCGACGAAACAGCAGCAGCCGCCAAAAAGGCAGGGAACAGCAAAAAACGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCAAACGAAGCTGTACAAg                                        <  2:158190/133‑1 (MQ=255)
                                                                                             ccTGTGACGCCAGAGCCGCGTATTGAACCGAAGCAACAGCAGCAGCCGCCAAAACGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCAAACGAAGCTGTACAAg                                        <  6:310297/139‑1 (MQ=255)
                                                                                             ccTGTGACGCCAGAGCCGCGTATTGAACCGAAGCAACAGCAGCAGCCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCAAACGAAGCTGTCCAAg                                        <  2:220896/139‑1 (MQ=255)
                                                                                              cTGTGACGCCAGAGCCGCGTATTGAACCGCAGCAACAACAGCCGCCGCCAAAAAGGCAGGGCACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCAAACGAAGCTGTACAAGc                                       >  2:262399/1‑139 (MQ=255)
                                                                                                 tgACGCCAGAGCCGCGTATTGAACCGAAGCAACAGCAGCAGCCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCAAACGAAGCTGTACAAGccc                                     <  7:66877/138‑1 (MQ=255)
                                                                                                 tgACGCAAGAGCCGCGTATTGAACCGAACAAAAAGCAGCAGCCGCCAAAAAGGCAGGGAAAAGCAAAAAAACCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCAAACGAAGCTGTACAAGccc                                     <  4:342830/138‑1 (MQ=255)
                                                                                                     gCCAGAGCCGCGTATTGAACCGACCCAACACCAGCAGCCGCCAAAAAGCCAGGGAACAGCAAAAAAAGCCGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCAAACGAAGCTGTACAAGCCCCTAtt                                <  1:364486/139‑1 (MQ=255)
                                                                                                       cAGAGCCGCGTATTTAACCTAAGCAACAGCAGCAGCCGCCAAAAAGGCAGGTAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCAAACGAAGCTGTACAAGCCCCTATTCa                              <  3:267150/139‑1 (MQ=255)
                                                                                                           gCCGCGTATTGAACCGAAGCAACAGCAGCAGCCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCAAACGAAGCTGTACAAGCCCCTATTCATAAt                          <  7:403707/139‑1 (MQ=255)
                                                                                                           gCCGCGTATTGAACCGAAGCAACAGCAGCACCCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCCCCGGTGGAATTTTCCGCGTTTGATCCAAACGAAGCTGTACAAGCCCCTATTCATAAt                          <  5:336019/139‑1 (MQ=255)
                                                                                                                      aaCCGAAGCAACAGCAGCAGCCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCAAACGAAGCTGTACAAGCCCCTATTCATAATCTGGATATGCt               >  3:405128/1‑139 (MQ=255)
                                                                                                                           aaGCAACAGCAGCAGCCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCAAACGAAg                                                 <  7:97833/100‑1 (MQ=255)
                                                                                                                           aaGCAACAGCAGCAGCCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCAAACGAAg                                                 >  8:97833/1‑100 (MQ=255)
                                                                                                                                 cagcagcagCCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCAAACGAAGCTGTACAAGCCCCTATTCATAATCTGGATATGCTTTTGGATATcc    >  6:90689/1‑139 (MQ=255)
                                                                                                                                   gcagcagcCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCAAACGAAGCTGTACAAGCCCCTATTCATAATCTGGATATGCTTTTGGATATCCCg  <  8:226421/139‑1 (MQ=255)
                                                                                                                                   |                                                                                                                                          
GCGAAAGATTTAATTTCAAGCCTTATGAACTCAGAAAGTGCAGAGGAAGAAGAAACGGTGCAGCCTGAAGTTACATACGAACAGCCGAAAGAGCCTGTGACGCCAGAGCCGCGTATTGAACCGAAGCAACAGCAGCAGCCGCCAAAAAGGCAGGGAACAGCAAAAAAAGCAGCGCCAGTTCAGGTTTCACCGGTGGAATTTTCCGCGTTTGATCCAAACGAAGCTGTACAAGCCCCTATTCATAATCTGGATATGCTTTTGGATATCCCG  >  CP006881/1666349‑1666618

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑