Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,728,855 G→C 9.4% A84A (GCC→GCG PP_1523 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,728,8550GC 9.4% 146.9 / 7.7 53A84A (GCC→GCGPP_1523hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (26/22);  new base C (2/3);  total (28/25)
Fisher's exact test for biased strand distribution p-value = 6.58e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.47e-01

ACGAGCAAGCCTGCCGTTTCATGATGTACGCCAGGTGATTTCCTCTTCACCGTCGGCGCTGATGCGGACCCAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTAACCAAGTGACCGGAATGTTACCGGCCTGGCATTTGAAGGTATGGCCTTTCTGC  >  NC_002947/1728711‑1729002
                                                                                                                                                |                                                                                                                                                      
aCGAGCAAGCCTGCCGTTTCATGATGTACGCCAGGTGATTTCCTCTTCACCGTCGGCGCTGATGCGGACCCAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCa                                                                                                                                                     >  6:180514/1‑148 (MQ=255)
          cTGCCGTTTCATGATGTACGCCAGGTGATTTCCTCTTCACCGTCGGCGCTGATGCGGACCCAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGcgcg                                                                                                                                         <  6:124348/149‑1 (MQ=255)
              cgggtCATGAGGCACGCCAGGGGCCTTCCTCTTCACCGTCGGCGCTCATGCGGACCCAGCGGGCAGCATCTTCTTCCCCGGCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCCGCGCCGCATTTGCCGCGCtgggt                                                                                                                                     <  8:335580/145‑3 (MQ=255)
                     tgatgTACGCCAGGTGATTTCCTCTTCACCGTCGGCGCTGATGCGGACCCAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCCGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCaa                                                                                                                              >  8:15997/1‑149 (MQ=255)
                      gatgTACGCCAGGTGATTTCCTCTTCACCGTCGGCGCTGATGCGGACCCAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAAc                                                                                                                            >  4:98979/1‑149 (MQ=255)
                      gatgTACGCCAGGTGATTTCCTCTTCACCGTCGGCGCTGATGCGGACCCAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAAc                                                                                                                            >  4:317309/1‑149 (MQ=255)
                       atgTACGCCAGGTGATTTCCTCTTCACCGTCGGCGCTGATGCGGACCCAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGGGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACg                                                                                                                           <  1:80724/149‑1 (MQ=255)
                       atgTACGCCAGGTGATTTCCTCTTCACCGTCGGCGCTGATGCGGACCCAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACg                                                                                                                           >  6:120576/1‑149 (MQ=255)
                        tgTACGCCAGGTGATTTCCTCTTCACCGTCGGCGCTGATGCGGACCCAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGt                                                                                                                          <  3:317309/149‑1 (MQ=255)
                         gTACGCCAGGTGATTTCCTCTTCACCGTCGGCGCTGATGCGGACCCAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGt                                                                                                                          >  1:318873/1‑148 (MQ=255)
                         gTACGCCAGGTGATTTCCTCTTCACCGTCGGCGCTGATGCGGACCCAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGt                                                                                                                          >  8:219861/1‑148 (MQ=255)
                         gTACGCCAGGTGATTTCCTCTTCACCGTCGGCGCTGATGCGGACCCAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACATCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGt                                                                                                                          >  7:244347/1‑148 (MQ=255)
                            cGCCAGGTGATTTCCTCTTCACCGTCGGCGCTGATGCGGACCCAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCAt                                                                                                                       <  2:318873/148‑1 (MQ=255)
                                  gTGATTTCCTCTTCACCGTCGGCGCTGATGCGGACCCAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCCGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCa                                                                                                                >  4:292712/1‑149 (MQ=255)
                                   tGATTTCCTCTTCACCGTCGGCGCTGATGCGGACCCAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCAc                                                                                                               >  3:190118/1‑149 (MQ=255)
                                   tGATTTCCTCTTCACCGTCGGCGCTGATGCGGACCCAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCAc                                                                                                               >  3:194716/1‑149 (MQ=255)
                                    gATTTCCTCTTCACCGTCGGCGCTGATGCGGACCCAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCCCTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCCCg                                                                                                              >  3:267392/1‑149 (MQ=255)
                                             ttCAACGTCGGCGCTGATGCGGACCCAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCCCGGCGTCTGGt                                                                                                     >  7:235331/1‑149 (MQ=255)
                                               cACCGGCGGCGCTGAGGCGGACCCCGCGGTCAGCATCTTCTTCCCCGTCTTCCTCCCCCCCGCCCCCCGGCGCGCCGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTgg                                                                                                      <  5:216399/146‑1 (MQ=255)
                                                aCCGTCGGCGCTGATGCGGACCCAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCg                                                                                                   <  3:98979/148‑1 (MQ=255)
                                                   gTCGGCGCTGATGCGGACCCAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCttt                                                                                               >  7:303886/1‑149 (MQ=255)
                                                      ggCGCTGATGCGGACCCAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCa                                                                                            <  8:167627/149‑1 (MQ=255)
                                                                 ggACCCAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTc                                                                                                         <  3:113418/125‑1 (MQ=255)
                                                                     ccAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCCGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATCCGGCGCGGGCGCAGGCAACGACATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGCCTGtac                                                                              >  7:327152/1‑146 (MQ=255)
                                                                       aGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCAt                                                                           <  3:292712/149‑1 (MQ=255)
                                                                           gTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTcc                                                                       <  7:219861/149‑1 (MQ=255)
                                                                                cATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTa                                                                    >  7:120919/1‑147 (MQ=255)
                                                                                         ccccGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTcc                                                                       <  8:58240/135‑1 (MQ=255)
                                                                                         ccccGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTcc                                                                       >  7:58240/1‑135 (MQ=255)
                                                                                         ccccGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTgg                                                           <  7:155994/147‑1 (MQ=255)
                                                                                           ccGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTaa                                                       <  5:120576/149‑1 (MQ=255)
                                                                                                ttCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTAACCAAg                                                  >  2:82480/1‑149 (MQ=255)
                                                                                                   cTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCtt                                                             >  3:33047/1‑135 (MQ=255)
                                                                                                   cTCGACCCAGCATCCAGGCGCGCAGCGCACTTCCTCACCCAGCGCGGCAAATGCGGCGCTGGAGCAGGCAACGTAATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGTCTGTTCCATTTCCCTACAGCCtt                                                             <  4:33047/135‑1 (MQ=255)
                                                                                                    tCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTAACCAAGTGAc                                              >  3:249469/1‑149 (MQ=255)
                                                                                                         ccAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTAACCAAGTGACCGGaa                                         >  5:233713/1‑149 (MQ=255)
                                                                                                           aGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTAACCAAGTGACCGGAAt                                        >  2:165336/1‑148 (MQ=255)
                                                                                                           aGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTAACCAAGTGACCGGAAt                                        <  1:165336/148‑1 (MQ=255)
                                                                                                           aGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTAACCAAGTGACCGGAATg                                       >  7:272897/1‑149 (MQ=255)
                                                                                                               aCCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTAACCAAGTGACCGGAATGTTAc                                   >  1:52578/1‑149 (MQ=255)
                                                                                                                cccGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTAACCAAGTGACCGGAATGTTAcc                                  <  1:82480/149‑1 (MQ=255)
                                                                                                                    gcgcgcAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTAACCAAGTGACCGGAATGTTACCGGcc                              >  2:57666/1‑149 (MQ=255)
                                                                                                                     cgcgcAGCGCTCTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTAACCAAGTGACCGGAATGTTACCGGCCt                             <  1:57666/149‑1 (MQ=255)
                                                                                                                      gcgcagcgcaCTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTAAc                                                      >  7:158431/1‑123 (MQ=255)
                                                                                                                      gcgcagcgcaCTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTAAc                                                      <  8:158431/123‑1 (MQ=255)
                                                                                                                        gctccgcaCTTCCACTCCCAGCGCGGCAATTGCGGCGCGGGCGCAGGCAACGTCATCGGCGCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTGCATTTCCCTACAGCCTTGGGTAACCAAGTGTCCGGAATGTTACCGGCCTGGc                          <  8:327152/145‑1 (MQ=255)
                                                                                                                               aCTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTAACCAAGTGACCGGAATGTTACCGGCCTGGCATTTGaa                  <  8:303886/149‑1 (MQ=255)
                                                                                                                                cTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTAACCAAGTGACCGGAATGTTACCGGCCTGGCATTTGAAg                 <  4:249469/149‑1 (MQ=255)
                                                                                                                                       acCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGTCTGTTCCATTTCCCTACAGCCTTGGGTAACCAAGTGACCGGAATGTTACCGGCCTGGCATTTGAAGGTATGGc          <  8:120919/149‑1 (MQ=255)
                                                                                                                                        gcccgcgcCGCATTTGCCGCGCTGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTAACCAAGTGACCGGAAt                                        <  4:284781/116‑1 (MQ=255)
                                                                                                                                        gcccgcgcCGCATTTGCCGCGCTGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTAACCAAGTGACCGGAAt                                        <  4:121111/116‑1 (MQ=255)
                                                                                                                                        gcccgcgcCGCATTTGCCGCGCTGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTAACCAAGTGACCGGAAt                                        >  3:284781/5‑120 (MQ=255)
                                                                                                                                        gcccgcgcCGCATTTGCCGCGCTGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTAACCAAGTGACCGGAAt                                        >  3:121111/5‑120 (MQ=255)
                                                                                                                                             cgcgGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTAACCAAGTGACCGGAATGTTACCGGCCTGGCATTTGAAGGTATGGCCTTTCt    <  6:73156/149‑1 (MQ=255)
                                                                                                                                               cgGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTAACCAAGTGACCGGAATGTTACCGGCCTGGCATTTGAAGGTATGGCCTTTCTGc  <  7:103373/149‑1 (MQ=255)
                                                                                                                                               cgGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTAACCAAGTGACCGGAATGTTACCGGCCTGGCATTTGAAGGTATGGCCTTTCTGc  >  8:103373/1‑149 (MQ=255)
                                                                                                                                                ggCAAATGCGGCGCGGGCGCAGGCAAGCGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTGCATTTCCCTACAGCCTTGGGAAACCAAGTGCCCGTAAAGTAACCGCCGGGCAATTTGAAGGTAGGGCGttagtgc  >  1:3448/1‑144 (MQ=255)
                                                                                                                                                |                                                                                                                                                      
ACGAGCAAGCCTGCCGTTTCATGATGTACGCCAGGTGATTTCCTCTTCACCGTCGGCGCTGATGCGGACCCAGCGGTCAGCATCTTCTTCCCCGTCTTCCTCGACCCAGCCACCCGGCGCGCAGCGCACTTCCACACCCAGCGCGGCAAATGCGGCGCGGGCGCAGGCAACGTCATCGGCCCACGGCGTCTGGTCGCTTTCCAGATACAGGCTGTTCCATTTCCCTACAGCCTTGGGTAACCAAGTGACCGGAATGTTACCGGCCTGGCATTTGAAGGTATGGCCTTTCTGC  >  NC_002947/1728711‑1729002

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: