Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,561,206 A→T 8.8% intergenic (+308/‑162) yffL → / → yffM CPZ‑55 prophage; uncharacterized protein YffL/CPZ‑55 prophage; uncharacterized protein YffM

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,561,2060AT 8.8% 122.0 / 4.0 49intergenic (+308/‑162)yffL/yffMCPZ‑55 prophage; uncharacterized protein YffL/CPZ‑55 prophage; uncharacterized protein YffM
Reads supporting (aligned to +/- strand):  ref base A (22/20);  new base T (2/2);  total (25/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.44e-01

CTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGCATTCGTTCATGGGGAGCGCGGTATATCTCAAAGGGTGATTTCTTATTGGTGGGCCTTCGGAAGGCTTCGAGCAATTGCCA  >  NC_000913/2561068‑2561346
                                                                                                                                          |                                                                                                                                            
cTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTg                                                                                                                                          <  1:714051/143‑1 (MQ=255)
    gCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGaaa                                                                                                                                      <  1:267253/143‑1 (MQ=255)
    gCGACGGGAGTGGTTTAGCCTCCCGGGGGGTCATAGAGAGGCGCCTGTTGTTAAACAGAAGGATTATGTCGCCGGCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCTTGCTGGaaa                                                                                                                                      <  2:141795/143‑1 (MQ=255)
      gACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGCTAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACg                                                                                                                                    >  2:199639/1‑143 (MQ=255)
      gACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTGGGGCAATCACTTGCACCAAGCTGGAAACg                                                                                                                                    >  2:615958/1‑143 (MQ=255)
       gcGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATGTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATGAGCGCAATCATTTCCAGCAAGCTGGAAACGc                                                                                                                                   <  2:393704/142‑1 (MQ=255)
       aCGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCTTGCTGGaaatga                                                                                                                                   <  2:85996/143‑4 (MQ=255)
                               ctgtcATAGAGATTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATCGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGaa                                                                                                           <  1:454417/141‑1 (MQ=255)
                               cggtcATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCACAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGaa                                                                                                           <  1:622633/143‑1 (MQ=255)
                                  tcATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATAAGTAAAAACATTTCCAGCCAGCTGGAAACGCCCATTCACTCACGCACAACCTGAAcag                                                                                                        >  2:100884/1‑143 (MQ=255)
                                  gtcgggggagTCGCCGGGATTGACACAGAAGAATGATTGCGCCGCCCGATAGCTCGGCTGGTAGCGATCAGTAACCGTGCTGAGTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATGCACTCACGCACAACCTGAAcag                                                                                                        <  2:348444/136‑1 (MQ=255)
                                       gagagTCGCCTAGAGTGAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGAc                                                                                                   <  1:475856/143‑1 (MQ=255)
                                         gagTCGCCTAGAGTTAAACAGGAGAATTATTTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACca                                                                                                 <  2:465195/143‑1 (MQ=255)
                                          agTCGCCTAGAGGTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCAGTAACCATGCTGATTAGCGCCCTAATCTCCTGCTAGTTGGAACGGCCGGTGCACTCACGCGCAAACTGGACAGGCGACcac                                                                                                >  1:404227/1‑142 (MQ=255)
                                            tCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACaaaca                                                                                              >  2:107768/1‑143 (MQ=255)
                                              gacTAGAGTGAAACAGCAGAATTAGTTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGACTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACaaa                                                                                            <  2:75668/141‑1 (MQ=255)
                                               cgtAGAGTGAGACAGACGAGTCAGTCCGGCGCCTGATAGGTCGGCTGGTTGCGAGCATCAACCAGGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACTCCCATTCACTCACGCACAACCTGAACAGTAGACCAACAAAc                                                                                           <  2:243781/141‑1 (MQ=255)
                                               ccTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCACTCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACATGCACAGCAGACcaacaacc                                                                                           >  2:804923/1‑141 (MQ=255)
                                                cTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGAACAACAAAcc                                                                                          >  1:673230/1‑143 (MQ=255)
                                                    ggTTAAACAGAAGACTTATTTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCCCTCACGCACAACCTGAACAGCAGACCAACAAACcatca                                                                                      <  2:511693/142‑1 (MQ=255)
                                                      ttAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCCTTTCCAGCACGCTGGACACGCCCATTCACTCACGCACCACCTGAACAGCAAACCAACAAACCATCATg                                                                                    >  2:334832/1‑143 (MQ=255)
                                                      ttAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGCAGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACGTGAACAGCAGACCCACAAACaatcaag                                                                                    >  2:529096/1‑141 (MQ=255)
                                                       tAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATgg                                                                                   >  1:253648/1‑143 (MQ=255)
                                                        aaaCAGAAGAATTATTTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACCACCTGAACCGCAGACCAACCAACCATCCTGGc                                                                                  >  2:378326/1‑143 (MQ=255)
                                                        aaaCAGAAGAATTATTTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCACTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGc                                                                                  >  1:213668/1‑143 (MQ=255)
                                                              acggatttttCCGCCGCCGGATAGGTCGGCTGGTTGCGAGCATTATCCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGCATTCGt                                                                            <  2:554499/139‑1 (MQ=255)
                                                                 aaTTATTTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGCATTCGTTCa                                                                         >  1:137629/1‑143 (MQ=255)
                                                                     attTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGCATTCGTTCATggg                                                                     <  2:5744/143‑1 (MQ=255)
                                                                           ccgccTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGCATTCGTTCATGGGGAgcgc                                                               >  1:819035/1‑143 (MQ=255)
                                                                                  attgatCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGCATTCGTTCATGGGGAGCGCGGTatat                                                        <  1:232292/138‑1 (MQ=255)
                                                                                  aTAGGTCGGCTGGTTTGTAGCATGAACCATGGTGCTTAGCGCAAGGATTTCCAGTAGTCTGGAAACTGCCATTGACTCACGCACAAACTGCACAGCAGACCAACAAACCTTCGTGGCATTCTTTCATGGGGAGCGCGGTatat                                                        <  2:40682/143‑1 (MQ=255)
                                                                                     ggTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGCATTCGTTCATGGGGAGCGCGGTATAtctc                                                     <  1:251503/143‑1 (MQ=255)
                                                                                     ggTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGCATTCGTTCATGGGGAGCGCGGTATAtctc                                                     >  1:107216/1‑143 (MQ=255)
                                                                                       tCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCCTCATCGCATTCGTTCATGGGGCGCGCGGTATATCTCaa                                                   >  1:759037/1‑143 (MQ=255)
                                                                                                       aTTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACCACCTGAACAGCAGACCAACAAACCATCATGGCATTCGTTCATGGGGAGCGCGGTATATCTCACAGGGTGATTCCTTAtt                                   >  1:407107/1‑143 (MQ=255)
                                                                                                        ttAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGCATTCGTTCATGGGGAGCGCGGTATATCTCAAAGGGTGATTTCTTACtg                                  >  1:50132/1‑143 (MQ=255)
                                                                                                                 cTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGCATTCGTTCATGGGGAGCGCGGTATATCTCAAAGGGTGCTTTCTTATTGGTGGGCCtt                         >  1:612849/1‑143 (MQ=255)
                                                                                                                          gcAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTAACGCACAACCTGAACAGCAAACCAACAAACCATCATGGCATTCGTTCATGGGGAGCGCGGTATCTCTCAAGGGGTGACTTCTCCTTCGTGGGCCTTCGGGCGGCt                >  1:237010/1‑143 (MQ=255)
                                                                                                                            aaTCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGCATTCGTTCATGGGGAGCGCGCCAGATCTCAAAGCGTGCATTCTTATTGGGGGGCCTTCGGAAGGCTTc              >  2:303751/1‑143 (MQ=255)
                                                                                                                              tCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGCATTCGTTCATGGGGAGCGCGGTATATCTCAAAGGGTGATTTCTTATTGGTGGGCCTTCGGAAGGCTTCGa            >  1:459963/1‑143 (MQ=255)
                                                                                                                              gcATTTCCAGCAGGCTGGAAACGCCCATGCCCTCACGCACAAGCTGAACAGCAGACCAACAAACCATCTTGGCTTTTGTTCATGGGGAGCGCGGTATATCTCAAAGGGTGATTTCTTATTGGTGGGCCTTCGGAAGGCTTCGa            <  2:578129/142‑1 (MQ=255)
                                                                                                                                gtttCCAGCTTGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGCATTCGTTCACGAGGAGCGCGGTATATCCCCACGGGAGGTGTCTTAGTGGTCGGCCTTCGGAAGGCTTCGAGc          >  2:387157/2‑143 (MQ=255)
                                                                                                                                 tttCCAGCTTGCTGGAAACGCCCATTCACTCACGCACAACCTGAACCGCAGACCCACAAACCATCATGGCATTCGATCATGGGGAGCGCGGTAAATCTCAAAGGGGGATTTCTTATTGGTGGGCCTACGGAAGGCTTCGacga         >  2:50101/1‑140 (MQ=255)
                                                                                                                                  ttCCCGCAAGCTGGAATCGCCCAATCACCCACGCCCAACCTGAAACGCATGCCGTCAAGCCATCACGGCGCGCGTTCACGGGGAGCGCGGTATATCTCACAGCGTGATTTCTTATTGGTGGGCCTTCGGAAGGCTTCGAGCaa        <  2:57961/143‑1 (MQ=255)
                                                                                                                                   tCCAGCGAGGTGGAAACGACCAGTCGCCCAGGCACAACCTGAACAGCAGACCAACAAACCATCATGGCATTCGTTCTTGGGGAGCGCGGTATATCTCAGAGGGTGATTTCTTATTGGTGGGCATTCGGAAGGCTTCGAGCAAt       <  2:34146/143‑1 (MQ=255)
                                                                                                                                   tCCAGCAAGCTGGAGACGCCCATTCACTCACGGACAACCTGAACACGAATAATACAACCCATCATGGCATTCGTTCATGGGGAGCGCGGTATATCTCAAAGGGTGATTTCTTATTGGTGGGCCTTCGGAAGGCTTCGAGCAAt       <  1:200429/143‑1 (MQ=255)
                                                                                                                                     cAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGCATTCGTTCATGGGGAGCGCGGTATATCTCAAAGGGTGATTTCTTATTGGTGGGCCCTCGGAAGGCTTCGAGCAATTg     >  1:67530/1‑143 (MQ=255)
                                                                                                                                      aGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGCATTCGTTCATGGGGAGCGCGGTATATCTCAAAGGGTGATTTCTTATTGGTGGGCCTTCGGAAGGCTTCGAGCAATTGc    <  1:551804/143‑1 (MQ=255)
                                                                                                                                        cAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGGAGACCAACAAACCATCATGGCATTCGTTCATGGGGAGCGCGGTATATCTCAAAGGGTGATTTCTTATTGGTGGGCCTTCGGAAGGCTTCGAGCAATTGCCa  <  2:790326/143‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                            
CTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAGAAGAATTATTTCGCCGCCTGATAGGTCGGCTGGTTGCGAGCATTAACCATGCTGATTAGCGCAATCATTTCCAGCAAGCTGGAAACGCCCATTCACTCACGCACAACCTGAACAGCAGACCAACAAACCATCATGGCATTCGTTCATGGGGAGCGCGGTATATCTCAAAGGGTGATTTCTTATTGGTGGGCCTTCGGAAGGCTTCGAGCAATTGCCA  >  NC_000913/2561068‑2561346

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑