Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,359,494 G→A 100% S259L (TCG→TTG)  nusA ← transcription termination/antitermination factor L

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,359,4940GA98.3% 187.7 / ‑4.6 58S259L (TCG→TTG) nusAtranscription termination/antitermination factor L
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base A (29/28);  total (30/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.17e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GGCATCTTCATCAACGATGATCGCCGCGACTTCAGCCGGCGACATGGCGTTGATGACGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCGAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCAGCCATGACTTCGATGAGGCCCTCGGCAATTTCCGGCACTTCAATGCGG  >  NC_002947/5359358‑5359637
                                                                                                                                         |                                                                                                                                                
ggCATCTTCATCAACGATGATCGCCGCGACTTCAGCCGGCGACATGGCGTTGATGACGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGc                                                                                                                                      <  7:199770/149‑1 (MQ=255)
     cTTCATCAACGATGATCGCCGCGACTTCAGCCGGCGACATGGCGTGTGATGACGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGAt                                                                                                                                  >  1:268711/1‑149 (MQ=255)
         atcaACGATGATCGCCGCGACTTCAGCCGGCGACATGGCGTTGATGACGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAg                                                                                                                              <  7:169693/148‑1 (MQ=255)
         atcaACGATGATCGCCGCGACTTCAGCCGGCGACATGGCGTTGATGACGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAg                                                                                                                              <  3:333027/148‑1 (MQ=255)
         atcaACGATGATCGCCGCGACTTCAGCCGGCGACATGGCGTTGATGACGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCAGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAgg                                                                                                                             >  1:103259/1‑149 (MQ=255)
          tcaACGATGATCGCCGCGACTTCAGCCGGCGACATGGCGTTGATGACGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGc                                                                                                                            >  5:244283/1‑149 (MQ=255)
           caACGATGATCGCCGCGACTTCAGCCGGCGACATGGCGTTGATGACGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGc                                                                                                                                >  6:324215/1‑144 (MQ=255)
           caACGATGATCGCCGCGACTTCAGCCGGCGACATGGCGTTGATGACGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGc                                                                                                                                <  5:324215/144‑1 (MQ=255)
            aaCGATGATCGCCGCGACTTCAGCCGGCGACAAGGCGTTGATGACGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCAc                                                                                                                          >  1:46667/1‑149 (MQ=255)
                   atCGCCGCGACTTCAGCCGGCGACATGGCGTTGATGACGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCgg                                                                                                                   <  3:183293/149‑1 (MQ=255)
                    tCGCCGCGACTTCAGCCGGCGACATGGCGTTGATGACGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCggg                                                                                                                  >  5:84244/1‑149 (MQ=255)
                    tCGCCGCGACTTCAGCCGGCGACATGGCGTTGATGACGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCgg                                                                                                                   <  7:182276/148‑1 (MQ=255)
                         gcgACTTCAGCCGGCGACATGGCGTTGATGACGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGa                                                                                                              >  6:323545/1‑148 (MQ=255)
                             cgtCAGCCGGCGACATGGCGTTGATGACGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGc                                                                                                         <  4:103563/147‑1 (MQ=255)
                             cTTCAGCCGGCGACATGGCGTTGATGACGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGc                                                                                                         <  4:199376/149‑1 (MQ=255)
                              ttCAGCCGGCGACATGGCGTTGATGACGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCt                                                                                                        >  6:352950/1‑149 (MQ=255)
                                  cgtgccGACATGGCGTTGATGACGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTc                                                                                                    <  2:153870/144‑1 (MQ=255)
                                         aCATGGCGTTGATGACGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAg                                                                                             <  7:45801/149‑1 (MQ=255)
                                                 ttGATGACGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACgg                                                                                      >  8:69858/1‑148 (MQ=255)
                                                       gaCGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCt                                                                                >  6:274282/1‑149 (MQ=255)
                                                        aCGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCtt                                                                               <  2:219078/149‑1 (MQ=255)
                                                         cGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTg                                                                              <  2:180705/149‑1 (MQ=255)
                                                            aCTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCt                                                                           >  6:202670/1‑149 (MQ=255)
                                                              tGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTcg                                                                         >  3:79585/1‑149 (MQ=255)
                                                                 gcCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTcgcg                                                                       >  7:322185/1‑148 (MQ=255)
                                                                    gggTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAAcc                                                                  <  7:23344/149‑1 (MQ=255)
                                                                          tCGTCCCAAAGGACGATATCCCCACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGGATGCCGATGCAGGCACCTTGCGGGTCGATACCCTTGCCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGAt                                                             >  2:310336/1‑148 (MQ=255)
                                                                             tCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACg                                                         >  1:232755/1‑149 (MQ=255)
                                                                                 aaaGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACggg                                                       >  5:175455/1‑147 (MQ=255)
                                                                                 aaaGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGaa                                                     <  2:268711/149‑1 (MQ=255)
                                                                                  aaGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAag                                                    >  5:237312/1‑149 (MQ=255)
                                                                                    ggACTATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAATCCACGCATGCCGATGAAGGCACGTTGCGGTTCTATACGCTTGTCCGTGGATCGGACGGCAATCTTGGCTCTCGAACCCGGCTGACGTGAag                                                    >  8:192331/1‑147 (MQ=255)
                                                                                     gACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAagcag                                                 >  8:202706/1‑149 (MQ=255)
                                                                                     gACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAagcag                                                 >  5:333102/1‑149 (MQ=255)
                                                                                       cGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCAGcc                                               <  3:166251/149‑1 (MQ=255)
                                                                                         atatCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCAGCCAt                                             <  2:114621/149‑1 (MQ=255)
                                                                                            tCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCAGCCATGAc                                          <  6:84244/149‑1 (MQ=255)
                                                                                             ccACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCGAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCAGCCATGACt                                         >  5:94877/1‑149 (MQ=255)
                                                                                                  cGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCAGCCATGACTTCGAt                                    <  2:103259/149‑1 (MQ=255)
                                                                                                   gCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCAGCCATGACTTCGAt                                    >  4:245738/1‑148 (MQ=255)
                                                                                                   gCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCAGCCATGACTTCGAt                                    <  3:245738/148‑1 (MQ=255)
                                                                                                   gCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCAGCCATGACTTCGATg                                   <  5:323545/149‑1 (MQ=255)
                                                                                                    cTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCAGCCATGACTTCGATGa                                  <  5:274282/149‑1 (MQ=255)
                                                                                                       accaccCAGCTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCAGCCATGACTTCGATGAg                                 <  5:202670/147‑1 (MQ=255)
                                                                                                                cTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCCGGATCACGGGAAGCAGCCATGACTTCGAt                                    <  1:225907/136‑1 (MQ=255)
                                                                                                                cTCCCCGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCAGCCATGACTTCGAt                                    >  2:225907/1‑135 (MQ=255)
                                                                                                                   cccGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCAGCCATGACTTCGATGAGGCCCTCGGCAAttt                   >  3:223703/1‑149 (MQ=255)
                                                                                                                     cGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCAGCCATGACTTCGATGAGGCCCTCGGCAATTTcc                 <  5:352950/149‑1 (MQ=255)
                                                                                                                     cGGATACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCAGCCATGACTTCGATGAGGCCCTCGGCAATTTcc                 <  8:322185/149‑1 (MQ=255)
                                                                                                                        aTACGGCCTGGTCGCGCAATCCACGCATGCCGATGCAGGCTCCTTGCGGGGCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCTGCCATGACt                                         <  4:93251/122‑1 (MQ=255)
                                                                                                                        aTACGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCAGCCATGACt                                         >  3:93251/1‑122 (MQ=255)
                                                                                                                          aCGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCAGCCATGACTTCGATGAGGCCCTCGGCAATTTCCGGCAc            >  6:341207/1‑149 (MQ=255)
                                                                                                                          aCGGCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCAGCCATGACTTCGATGAGGCCCTCGGCAATTTCCGGCAc            >  2:316675/1‑149 (MQ=255)
                                                                                                                            ggCCTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCAGCCATGACTTCGATGAGGCCCTCGGCAATTTCCGGCACt           >  6:52609/1‑148 (MQ=255)
                                                                                                                               cTGGACGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCAGCCATGACTTCGATGAGGCCCTCGGCAATTTCCGGCACTTCaa       >  1:339131/1‑149 (MQ=255)
                                                                                                                                 ggACGCGCAAACCACGCATGCCGAGGCAGGCACCTTCCGGGTCGATACGGTAGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGCACCCGGATCCCGGGAAGCAGGCATGACTTGGATGAGGCCCTCGGCAATTTCCGGCCCTTCACTg     >  8:222876/1‑149 (MQ=255)
                                                                                                                                  gACGCGCAAACCACGCATGCAGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTTGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACTGGAAGCAGCCATGACTTCGATGAGGCCCTCGGCAATTTCCGGCACTTCAATGc    <  4:233313/149‑1 (MQ=255)
                                                                                                                                   aCGCGCAAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCAGCCATGACTTCGATGAGGCCCTCGGCAATTTCCGGCACTTCAATGCg   <  2:46667/149‑1 (MQ=255)
                                                                                                                                    cgcgcaAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCAGCCATGACTTCGATGAGGCCCTCGGCAATTTCCGGCACTTCAATGCgg  <  6:175455/149‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                                
GGCATCTTCATCAACGATGATCGCCGCGACTTCAGCCGGCGACATGGCGTTGATGACGAACTGCGCCGGGTTATCGTCCCAAAGGACGATATCCACACGCTCACCACCCAGCTCCCCGGATACGGCCTGGACGCGCGAACCACGCATGCCGATGCAGGCACCTTGCGGGTCGATACGCTTGTCCTTGGAGCGGACGGCAATCTTGGCTCGCGAACCCGGATCACGGGAAGCAGCCATGACTTCGATGAGGCCCTCGGCAATTTCCGGCACTTCAATGCGG  >  NC_002947/5359358‑5359637

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: