Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 2,635,440 C→A 12.5% intergenic (+30/+87) PP_2304 → / ← PP_2305 peptidyl‑prolyl cis‑trans isomerase D/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029472,635,4400CA12.5% 135.3 / 8.7 48intergenic (+30/+87)PP_2304/PP_2305peptidyl‑prolyl cis‑trans isomerase D/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (21/21);  new base A (3/3);  total (24/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01

CGCCACCGACGAAGAGAAGCAGCAGATTCGCCGCTACCTCGCGTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGTGCAATCTCTCGCCCCAGGGC  >  NC_002947/2635293‑2635586
                                                                                                                                                   |                                                                                                                                                     
cgccACCGACGAAGAGAAGCAGCAGATTCGCCGCTACCTCGCGTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCt                                                                                                                                                      <  6:8938/149‑1 (MQ=255)
  ccACCGACGAAGAGAAGCAGCAGATTCGCCGCTACCTCGCGTCACGTGCTGGCCAGCAGGACTTAGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATCAAGAAACAGGCCGCCTCg                                                                                                                                                    >  7:75397/1‑149 (MQ=255)
   cACCGACGAAGAGAAGCAGCAGATTCGCCGCTACCTCGCGTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGt                                                                                                                                                   <  6:132568/149‑1 (MQ=255)
               gaAGCAGCAGATTCGCCGCTACCTCGCGTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCACGAGGCGGCCTGT‑‑TTc                                                                                                                                     <  7:99138/149‑1 (MQ=255)
                aaGCAGCAGATTCGCCGCTACCTCGCGTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCt                                                                                                                                            <  3:268180/143‑1 (MQ=255)
                aaGCAGCAGATTCGCCGCTACCTCGCGTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCt                                                                                                                                            >  4:268180/1‑143 (MQ=255)
                aaGCAGCAGATTCGCCGCTACCTCGCGTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCg                                                                                                                                    >  6:4500/1‑149 (MQ=255)
                 agcagcAGATTCGCCGCTACCTCGCGTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGt                                                                                                                                   <  6:167625/149‑1 (MQ=255)
                     gcagATTCGCCGCTACCTCGCGTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTc                                                                                                                              <  6:132591/149‑1 (MQ=255)
                     gcagATTCGCCGCTACCTCGCGTCACGTGATGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGATGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTAGTTTTc                                                                                                                              >  4:249346/1‑149 (MQ=255)
                        gATTCGCCGCTACCTCGCGTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCTATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGc                                                                                                                            >  6:245180/1‑148 (MQ=255)
                                gcTACCTCGCGTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGa                                                                                                                   <  7:119978/149‑1 (MQ=255)
                                        gcgTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTc                                                                                                           <  5:102941/149‑1 (MQ=255)
                                          gTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCAt                                                                                                         >  2:100794/1‑149 (MQ=255)
                                               gTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTc                                                                                                                              >  6:58355/1‑123 (MQ=255)
                                               gTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTc                                                                                                                              <  5:58355/123‑1 (MQ=255)
                                                    ggCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGt                                                                                               >  2:2978/1‑149 (MQ=255)
                                                      ccAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGGAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTca                                                                                             <  6:299059/149‑1 (MQ=255)
                                                      ccAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTca                                                                                             >  3:148796/1‑149 (MQ=255)
                                                            ggACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACgg                                                                                                             <  7:94502/127‑1 (MQ=255)
                                                            ggACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACgg                                                                                                             >  8:94502/1‑127 (MQ=255)
                                                            ggACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGc                                                                                       <  1:287429/149‑1 (MQ=255)
                                                             gACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCAACCGTTACTTAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGA‑‑CACCTGTTTCTCCAGCCGCTAGCACGGTCATTGTCTAAGTTCAAAGTga                                                                                       >  1:108390/1‑148 (MQ=255)
                                                             gACTTTGCAGCTTACCTCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGt                                                                                         <  2:108390/146‑1 (MQ=255)
                                                                          aCCGCAAGCAGCTGGAAGCCTATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTgg                                                                           <  5:245180/147‑1 (MQ=255)
                                                                                      tGGAAGCCAATGCAGACATCACGCGTTACTAAGGTGTTCGTTGAATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGGCAGCCGAGAGCACGGTCATTGTCGATGGTCAAAGAGCCTTCAGCGGTGGGGCTAACCAGGTGc                                                             >  8:61568/1‑149 (MQ=255)
                                                                                      tGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGTCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGc                                                             >  1:256117/1‑149 (MQ=255)
                                                                                        taaGCCAATGCAGACATCACCGGTTAATAAGGTGTTCGTTGCATGAATAAACAGGCCGCCTCGTGCGGCCTGTTCTTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTg                                                              <  1:100794/147‑1 (MQ=255)
                                                                                              aaTGGAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGGCAGCCGCGAGCACGGTCATTGTCGCAGGTCACAGTGCCTTCAGGGGTGGCGCTACCCAGGTGCTACCGCtt                                                     >  8:81777/1‑149 (MQ=255)
                                                                                              aaTGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCtt                                                     <  4:148796/149‑1 (MQ=255)
                                                                                                   aGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCAccc                                                >  3:268721/1‑149 (MQ=255)
                                                                                                    gACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCAcccc                                               >  5:323839/1‑149 (MQ=255)
                                                                                                       aTCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCtt                                             >  2:138869/1‑148 (MQ=255)
                                                                                                          aCCCGTTTCTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCGGCGAGCACGGTGATTGTCGAAGGTCACAGTGCCTTCAGGTGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCAt                                          <  8:252350/148‑1 (MQ=255)
                                                                                                             cGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACt                                      <  3:249346/149‑1 (MQ=255)
                                                                                                             cGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACt                                      <  1:138869/149‑1 (MQ=255)
                                                                                                                             gTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGt                      >  7:98972/1‑149 (MQ=255)
                                                                                                                                 cATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATa                                         <  8:56171/126‑1 (MQ=255)
                                                                                                                                 cATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATa                                         >  7:56171/1‑126 (MQ=255)
                                                                                                                                  aTGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGATACCGCTTCACCCATTCATAACTGTCCAGCGTATCGCGTGCaa                  >  2:134399/1‑148 (MQ=255)
                                                                                                                                      cgaaACAGGCCGCACGAGGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGACGGTCACAGTGCCTTCAGGGGTGGCGCTAAGCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGt                      <  7:57819/139‑1 (MQ=255)
                                                                                                                                      cgaaACAGGCCGCACGAGGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCAATCGTATCGCGt                      >  8:57819/2‑140 (MQ=255)
                                                                                                                                      agaaACAGGCCGGCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGTGCAAtctct             <  2:256117/149‑1 (MQ=255)
                                                                                                                                       gaaACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGTGCAAtctctc            >  7:195967/1‑149 (MQ=255)
                                                                                                                                       gaaACAGGCCGCACGAGGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATaa                                        <  6:321821/121‑1 (MQ=255)
                                                                                                                                       gaaACAGGCCGCACGAGGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATaa                                        >  5:321821/1‑121 (MQ=255)
                                                                                                                                       gaaACAGGCCGCACGAGGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGTGCAAtctctc            >  7:175268/1‑149 (MQ=255)
                                                                                                                                           cAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGTGCAATCTCTCGccc        <  4:268721/149‑1 (MQ=255)
                                                                                                                                               ccgccTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGTGCAATCTCTCGCCCCAgg    >  5:265903/1‑149 (MQ=255)
                                                                                                                                                cgccTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTGACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGTGCAATCTCTCGCCCCAggg   <  8:75397/149‑1 (MQ=255)
                                                                                                                                                cgccTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACt                                      >  3:246929/1‑114 (MQ=255)
                                                                                                                                                cgccTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACt                                      <  4:246929/114‑1 (MQ=255)
                                                                                                                                                cgccTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGTGCAATCTCTCGCCCCAggg   <  6:265903/149‑1 (MQ=255)
                                                                                                                                                 gccTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGTGCAATCTCTCGCCCCAGGGc  >  5:207550/1‑149 (MQ=255)
                                                                                                                                                  ccTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGTGCAATCTCTCGCCCCAGGGc  >  4:82149/1‑148 (MQ=255)
                                                                                                                                                   |                                                                                                                                                     
CGCCACCGACGAAGAGAAGCAGCAGATTCGCCGCTACCTCGCGTCACGTGCTGGCCAGCAGGACTTTGCCGCTTACCGCAAGCAGCTGGAAGCCAATGCAGACATCACCCGTTACTAAGGTGTTCGTTGCATGAAGAAACAGGCCGCCTCGTGCGGCCTGT‑‑TTCGTTTTCGCCAGCCGCGAGCACGGTCATTGTCGAAGGTCACAGTGCCTTCAGGGGTGGCGCTAACCAGGTGCTACCGCTTCACCCCTTCATAACTGTCCAGCGTATCGCGTGCAATCTCTCGCCCCAGGGC  >  NC_002947/2635293‑2635586

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: