Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 714,958 G→A 9.4% intergenic (+24/+53) ispH → / ← PP_0607 4‑hydroxy‑3‑methylbut‑2‑enyl diphosphate reductase/type IV pili biogenesis protein FimT

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947714,9580GA 9.4% 146.8 / 5.0 53intergenic (+24/+53)ispH/PP_06074‑hydroxy‑3‑methylbut‑2‑enyl diphosphate reductase/type IV pili biogenesis protein FimT
Reads supporting (aligned to +/- strand):  ref base G (23/25);  new base A (3/2);  total (26/27)
Fisher's exact test for biased strand distribution p-value = 6.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.68e-01

GTGCGTGGCGTGATCGAACAGCTCAAGGCCTGGGGCGCCACTGGCGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCGGTCATTGCTCAGGTCCTCCGTAAGCAACCTGACTCTGCCGCTTGATGCCAGCACCACCTGATATCGGCTGCGAGCAGCGGCGCG  >  NC_002947/714812‑715103
                                                                                                                                                  |                                                                                                                                                  
gTGCGTGGCGTGATCGAACAGCTCAAGGCCTGGGGCGCCACTGGCGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAggg                                                                                                                                                  >  4:279052/1‑149 (MQ=255)
gTGCGTGGCGTGATCGAACAGCTCAAGGCCTGGGGCGCCACTGGCGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAg                                                                                                                                                    <  5:324601/147‑1 (MQ=255)
    gtggcgtgATCGAACAGCTCAAGGCCTGGGGCGCCACTGGCGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGgctg                                                                                                                                              <  7:230579/149‑1 (MQ=255)
       gggtgATCGAACAGCTCAAGGGCTGGTGCTCCACTGGGGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCtt                                                                                                                                           <  3:20763/147‑1 (MQ=255)
            aTCGAACAGCTCAAGGCCTGGGGCGCCACTGGCGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCa                                                                                                                                       <  4:103428/148‑1 (MQ=255)
            aTCGAACAGCTCAAGGCCTGGGGCGCCACTGGCGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCa                                                                                                                                       <  6:243200/148‑1 (MQ=255)
               gAACAGCTCAAGGCCTGGGGCGCCACTGGCGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAAGGGCTGCAAAGCAGccc                                                                                                                                   <  8:20716/149‑1 (MQ=255)
                 aCAGCTCAAGGCCTGGGGCGCCACTGGCGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCtt                                                                                                                                 >  6:213234/1‑149 (MQ=255)
                    gCTCAAGGCCTGGGGCGCCACTGGCGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAAGGGCTGCAAAGCAGCCCCTgca                                                                                                                              <  7:295463/149‑2 (MQ=255)
                     cTCAAGGCCTGGGGCGTCACTGGCGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGACAGTACCGCCGCCAATGCAg                                                                                                                                                    <  5:327158/126‑1 (MQ=255)
                     cTCAAGGCCTGGGGCGTCACTGGCGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGACAGTACCGCCGCCAATGCAg                                                                                                                                                    >  6:327158/1‑126 (MQ=255)
                      tCAAGGCCTGGGGCGCCACTGGCGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTgcgc                                                                                                                             >  5:96819/1‑148 (MQ=255)
                       cAAGGCCTGGGGCGCCACTGGCGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGa                                                                                                                           >  4:77177/1‑149 (MQ=255)
                        aaGGCCTGGGGCGCCACTGGCGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCttt                                                                                                                                          <  7:302862/133‑1 (MQ=255)
                        aaGGCCTGGGGCGCCACTGGCGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCttt                                                                                                                                          >  8:302862/1‑133 (MQ=255)
                        aaGGCCTGGGGCGCCACTGGCGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGa                                                                                                                           <  3:279052/148‑1 (MQ=255)
                            ccTGGGGCGCCACTGGCGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACaa                                                                                                                      <  6:96819/149‑1 (MQ=255)
                                  gcgcCACTGGCGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTgcgc                                                                                                                             >  2:165362/1‑136 (MQ=255)
                                  gcgcCACTGGCGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTgcgc                                                                                                                             <  1:165362/136‑1 (MQ=255)
                                     ccACTGGCGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTcc                                                                                                             >  3:369310/1‑149 (MQ=255)
                                       aCTGGCGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTg                                                                                                           >  2:350248/1‑149 (MQ=255)
                                        cTGGCGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGTGACACAAGACCGCTCCTGc                                                                                                          <  8:254235/149‑1 (MQ=255)
                                           gcgcTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCaa                                                                                                        <  5:213234/148‑1 (MQ=255)
                                             gcTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGa                                                                                                     <  3:77177/149‑1 (MQ=255)
                                                 aaGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACcg                                                                                                  <  7:119224/148‑1 (MQ=255)
                                                         gACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTagcag                                                                                        >  3:284526/1‑149 (MQ=255)
                                                            gggCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTa                                                                                            >  6:76203/1‑142 (MQ=255)
                                                            gggCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTa                                                                                            <  5:76203/142‑1 (MQ=255)
                                                            gggCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCgg                                                                                     <  1:350248/149‑1 (MQ=255)
                                                                   aaGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCTGCTAGCGCGGTCATTGc                                                                              <  5:124303/149‑1 (MQ=255)
                                                                    agagAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCGGTCATTGc                                                                              >  1:327583/1‑148 (MQ=255)
                                                                     gagaACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCGGTCATTGCTc                                                                            <  2:327583/149‑1 (MQ=255)
                                                                           aTCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCGGTCATTGCTCAGGtcc                                                                      >  1:345830/1‑149 (MQ=255)
                                                                             cACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCGGTCATTGCTCAg                                                                          >  7:77051/1‑143 (MQ=255)
                                                                             cACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCGGTCATTGCTCAg                                                                          <  8:77051/143‑1 (MQ=255)
                                                                              aCCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCGGTCATTGCTCAGGtcctcc                                                                   >  5:224093/1‑149 (MQ=255)
                                                                                           ccAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCgcgc                                                                                              <  2:138643/109‑1 (MQ=255)
                                                                                           ccAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCgcgc                                                                                              >  1:138643/1‑109 (MQ=255)
                                                                                            cAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCg                                                                                      <  6:158712/116‑1 (MQ=255)
                                                                                            cAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCg                                                                                      >  5:158712/1‑116 (MQ=255)
                                                                                            cAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCGGTCATTGCTCAGGTCCTCCGTAAGCAACCTGAc                                                     >  8:133681/1‑149 (MQ=255)
                                                                                             aaaGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCGGTCATTGCTCAGGTCCTCCGTAAGCAACCTGAc                                                     >  8:32232/1‑148 (MQ=255)
                                                                                                       gggTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCGGTCATTGCTCAGGTCCTCCGTAAGCAACCTGACCCTGCCGCTTg                                          <  7:133681/149‑1 (MQ=255)
                                                                                                         gTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCGGTCATTGCTCAGGTCCTCCGTAAGCAACCTGACTCTGCCGCTTGAt                                        <  4:284526/149‑1 (MQ=255)
                                                                                                             gctcgctGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCGGTCATTGCTCAGGTCCTCCGTAAGCAACCTGACTCTGCCGCTTGATGc                                      >  3:261174/1‑147 (MQ=255)
                                                                                                                 gctGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCACTCCTGCAATGACCGCGCTAGCAGCGGTCATTGCTCAGGTCCTCCGTAAGCAACCTGACTCTGCCGCTTGATGCCAGcac                                >  3:237288/1‑149 (MQ=255)
                                                                                                                           cGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCGGTCATTGCTCAGGTCCTCCGTAAGCAACCTGACTCTGCCGCTTGATGCCAGCACCACCTGatat                      <  6:224093/149‑1 (MQ=255)
                                                                                                                            gggCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCGGTCATTGCTCAGGTCCTCCGTAAGCAACCTGACTCTGCCGCTTGATGCCAGCACCACCTGATATc                     >  1:284784/1‑149 (MQ=255)
                                                                                                                               cAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCGGTCATTGCTCAGGTCCTCCGTAAGCAACCTGACTCTGCCGCTTGATGCCAGCACCACCTGATATCGGc                  <  7:32232/149‑1 (MQ=255)
                                                                                                                                 gTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCGGTCATTGCTCAGGTCCTCCGTAAGCAACCTGACTCTGCCGCTTGATGCCAGCACCACCTGATATCGGCTg                <  4:261174/149‑1 (MQ=255)
                                                                                                                                 gTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTACTGAAATGACCGAGCTAGCAGCGGTCAATGCTCATGTCATCCGTAAGCAACCTTACTCTGCCGCTTTATGCCCGCACAACCTGATATCGGCTg                >  6:366801/1‑149 (MQ=255)
                                                                                                                                        cgccAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCGGTCATTGCTCAGGTCCTCCGTAAGCAACCTGACTCTGCCGCTTGATGCCAGCACCACCTGATATCGGCTGCGagcag         >  2:21340/1‑149 (MQ=255)
                                                                                                                                         gccAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCGGTCATTGCTCAGGTCCTCCGTAAGCAACCTGActc                                                   <  3:82348/106‑1 (MQ=255)
                                                                                                                                         gccAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCGGTCATTGCTCAGGTCCTCCGTAAGCAACCTGActc                                                   >  4:82348/1‑106 (MQ=255)
                                                                                                                                           tcgcgCAAGGGCTGCAAAGCAGCCCCTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCGGTCATTGCTCAGGTCCTCCGTAAGCAACCTGACTCTGCCGCTTGATGCCAGCACCACCTGATATCGGCTGCGAGCAgcgg      >  8:349180/5‑149 (MQ=255)
                                                                                                                                               gCAAGGGCTGCAAAGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCGGTCATTGCTCAGGTCCTCCGTAAGCAACCTGACTCTGCCGCTTGATGCCAGCACCACCTGATATCGGCTGCGAGCAGCGGcgcg  >  6:327969/1‑149 (MQ=255)
                                                                                                                                               gCAAGGGCTGCAAAGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCGGTCATTGCTCAGGTCCTCCGTAAGCAACCTGACTCTGCCGCTTGATGCCAGCACCACCTGATATCGGCTGCGAGCAGCGGcgcg  >  3:209281/1‑149 (MQ=255)
                                                                                                                                                  |                                                                                                                                                  
GTGCGTGGCGTGATCGAACAGCTCAAGGCCTGGGGCGCCACTGGCGCTGAAGAGCTGGACGGGCGCGAAGAGAACATCACCTTTTCAATGCCCAAAGAGCTGCGGGTTCGCTCGCTGATCTGACGGGCAGTACCGCCGCCAATGCAGGGGCTGCTTTGCAGCCCTTGCGCGACACAAGACCGCTCCTGCAATGACCGCGCTAGCAGCGGTCATTGCTCAGGTCCTCCGTAAGCAACCTGACTCTGCCGCTTGATGCCAGCACCACCTGATATCGGCTGCGAGCAGCGGCGCG  >  NC_002947/714812‑715103

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: