Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 2,724,005 G→A 6.9% S196L (TCG→TTG)  azlC ← branched‑chain amino acid transport protein AzlC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029472,724,0050GA 6.9% 170.6 / 2.5 58S196L (TCG→TTG) azlCbranched‑chain amino acid transport protein AzlC
Reads supporting (aligned to +/- strand):  ref base G (30/24);  new base A (2/2);  total (32/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.38e-01

AGAAACACGATGGCGCCCATGGCGAAAATCAGGATCCAGGTCATGCGCGGGCTCCGGCGAATTTCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATGGAGAAATCCAGACCGAACTGGTCCAGGTGTGGAATGTTCTGGCCCAGCAGTATGCCGGC  >  NC_002947/2723859‑2724150
                                                                                                                                                  |                                                                                                                                                  
agaAACACGATGGCGCCCATGGCGAAAATCAGGATCCAGGTCATGCGCGGGCTCCGGCGAATTTCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCgaa                                                                                                                                                  <  6:294951/149‑1 (MQ=255)
     cacGATGGCGCCCATGGCGAAAATCAGGATCCAGGTCATGCGCGGGCTCCGGCGAATTTCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCgaacagaa                                                                                                                                             <  5:70869/149‑1 (MQ=255)
        gATGGCGGCGATGGCGAAAATCAGGATCCAGGTCATGCGCGGGCTCCGGCGAATTTCTGGCTGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCATGGCGGTTTCCCAGTGCCAGTAGCTTAACAGCACCGaacagaacag                                                                                                                                          <  3:363822/149‑1 (MQ=255)
        gATGGCGCCCATGGCGAAAATCAGGATCCAGGTCATGCGCGGGCTCCGGCGAATTTCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGaacagaacag                                                                                                                                          >  5:199912/1‑149 (MQ=255)
                    ggCGAAAATCAGGATCCAGGTCATGCGCGGGCTCCGGCGAATTTCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTAc                                                                                                                              >  1:6407/1‑149 (MQ=255)
                     tcGAAAATCAGGATCCAGTTCATGCGCGGGCTCCGGCGAATTTCTGGCAGATGAACCCGGCTCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACg                                                                                                                             <  7:4168/148‑1 (MQ=255)
                     gCGAAAATCAGGATCCAGGTCATGCGCGGGCTCCGGCGAATTTCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACg                                                                                                                             <  8:57241/149‑1 (MQ=255)
                     gCGAAAATCAGGATCCAGGTCATGCGCGGGCTCCGGCGAATTTCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACg                                                                                                                             >  6:53803/1‑149 (MQ=255)
                     gCGAAAATCAGGATCCAGGTCATGCGCGGGCTCCGGCGAATTTCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCAAACAGAACAGCGACACGGCTACg                                                                                                                             >  4:194741/1‑149 (MQ=255)
                        aaaaTCAGGATCCAGGTCATGCGCGGGCTCCGGCGAATTTCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGcac                                                                                                                          <  5:53803/149‑1 (MQ=255)
                                         cATGCGCGGGCTCCGGCGAATTTCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGCACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGtt                                                                                                         >  3:34451/1‑149 (MQ=255)
                                          aTGCGCGGGCTCCGGCGAATTTCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTg                                                                                                       >  5:343734/1‑149 (MQ=255)
                                             cgcgGGCTCCGGCGAATTTCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTgcg                                                                                                     <  2:6407/148‑1 (MQ=255)
                                                      cGGCGAATTTCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCt                                                                                                                                >  2:332711/1‑113 (MQ=255)
                                                      cGGCGAATTTCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCt                                                                                                                                <  1:332711/113‑1 (MQ=255)
                                                      cGGCGAATTTCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAgggg                                                                                            <  6:357422/148‑1 (MQ=255)
                                                      cGGCGAATTTCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAggg                                                                                             <  4:34451/147‑1 (MQ=255)
                                                       ggCGAATTTCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGc                                                                                                                            <  8:187971/116‑1 (MQ=255)
                                                       ggCGAATTTCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGc                                                                                                                            >  7:187971/1‑116 (MQ=255)
                                                       ggCGAATTTCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGgcg                                                                                          <  6:199912/149‑1 (MQ=255)
                                                        gCGAATTTCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACg                                                                                                                             >  4:257530/1‑114 (MQ=255)
                                                        gCGAATTTCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACg                                                                                                                             <  3:257530/114‑1 (MQ=255)
                                                            aTTTCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGAt                                                                                      >  5:99096/1‑148 (MQ=255)
                                                               tCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAgg                                                                                  >  2:240985/1‑149 (MQ=255)
                                                                 tGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGc                                                                                >  2:181083/1‑149 (MQ=255)
                                                                   gCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGc                                                                                <  6:343734/147‑1 (MQ=255)
                                                                       aTGAACCCGGCGCTCATGCCCAGTAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACaa                                                                           >  7:304229/1‑148 (MQ=255)
                                                                             ccGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGc                                                                    >  3:190163/1‑149 (MQ=255)
                                                                             ccGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCAAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGc                                                                    <  3:194741/149‑1 (MQ=255)
                                                                                    tCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATg                                                             >  1:288203/1‑149 (MQ=255)
                                                                                     cATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGTCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATg                                                             >  8:302853/1‑148 (MQ=255)
                                                                                        gCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGgc                                                                                           >  7:294486/1‑115 (MQ=255)
                                                                                        gCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGgc                                                                                           <  8:294486/115‑1 (MQ=255)
                                                                                         cccAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATGGAGaa                                                        <  8:82527/149‑1 (MQ=255)
                                                                                             gcagGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGc                                                                    >  3:93079/1‑133 (MQ=255)
                                                                                             gcagGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGc                                                                    <  4:93079/133‑1 (MQ=255)
                                                                                                 gCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGc                                                                                >  8:286052/1‑117 (MQ=255)
                                                                                                 gCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGc                                                                                <  7:286052/117‑1 (MQ=255)
                                                                                                       gACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCAAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATGGAGAAATCCAGACCGAACt                                          >  3:34727/1‑149 (MQ=255)
                                                                                                        accaccAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATGGAGAAATCCAGACCGAACTg                                         >  7:276249/1‑149 (MQ=255)
                                                                                                          caccaGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATGGAGAAATCCAGACCGAACTGGt                                       >  6:211545/1‑149 (MQ=255)
                                                                                                            ccaGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATGga                                                           >  6:228941/1‑127 (MQ=255)
                                                                                                            ccaGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATGga                                                           <  5:228941/127‑1 (MQ=255)
                                                                                                               gggCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATGGAGAAATCCAGACCGAACTGGTCCAgg                                  <  6:99096/149‑1 (MQ=255)
                                                                                                                ggCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATGGAGAAATCCAGACCGAACTGGTCCAGgt                                 <  4:190163/149‑1 (MQ=255)
                                                                                                                   ggTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATGGAGAAATCCAGACCGAACTGGTCCAGGtgtg                              <  1:240985/149‑1 (MQ=255)
                                                                                                                     tttCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGgcgc                                                                                         <  5:369528/88‑1 (MQ=255)
                                                                                                                         ccAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCACGGGCGCGATCAGTGCGACAAAAGTGGCGACAATGGAGAAATCCAGACCGAACTGCTCCAGGTGTGGAAtct                        >  6:253009/1‑147 (MQ=255)
                                                                                                                           aGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGTTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATGGAGAAATCCATACCGAAc                                           <  7:249620/128‑1 (MQ=255)
                                                                                                                           aGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATGGAGAAATCCAGACCGAAc                                           >  8:249620/1‑128 (MQ=255)
                                                                                                                           aGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATGGAGAAATCCAGACCGAACTGGTCCAGGTGTGGAATGTTc                      >  5:253120/1‑149 (MQ=255)
                                                                                                                                  gTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATGGAGAAATCCAGACCGAACTGGTCCAg                                   <  2:91647/129‑1 (MQ=255)
                                                                                                                                  gTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATGGAGAAATCCAGACCGAACTGGTCCAg                                   >  1:91647/1‑129 (MQ=255)
                                                                                                                                  gTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATGGAGAAATCCAGACCGAACTGGTCCAGGTGTGGAATGTTCTGGCCca               <  2:288203/149‑1 (MQ=255)
                                                                                                                                     gCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATGGAGAAATCCAGACCGAACTGGTCCAGGTGTGGAATGTTCTGGCCcag              >  5:125768/1‑147 (MQ=255)
                                                                                                                                      cTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATGGAGAAATCCAGACCGAACTGGTCCAGGTGTGGAATGTTCTGGCCcagcag           >  5:318261/1‑149 (MQ=255)
                                                                                                                                       tGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATGGAGAAATCCAGACCGAACTGGTCCAGGTGTGGAATGTTCTGGCCcagcag           >  8:271937/1‑148 (MQ=255)
                                                                                                                                              cACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATGGAGAAATCCAGACCGAACTGGTCCAGGTGTGGAATGTTCTGGCCCAGCAGTATGCCg    >  1:280213/1‑149 (MQ=255)
                                                                                                                                               aCCAAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATGGAGAAATCCAGACCGAACTGGTCCAGGTGTGGAATGTTCTGGCCCAGCAGTATGCCGGc  <  4:34727/149‑1 (MQ=255)
                                                                                                                                                 cGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATGGAGAAATCCAGACCGAACTGGTCCAGGTGTGGAATGTTCTGGCCCAGCAGTATGCCGGc  >  8:29334/1‑147 (MQ=255)
                                                                                                                                                  |                                                                                                                                                  
AGAAACACGATGGCGCCCATGGCGAAAATCAGGATCCAGGTCATGCGCGGGCTCCGGCGAATTTCTGGCAGATGAACCCGGCGCTCATGCCCAGCAGGCCTGCGACCACCAGGGCGGTTTCCCAGTGCCAGTAGCTGAACAGCACCGAACAGAACAGCGACACGGCTACGCACACCACGGTGGCCAGGTTGCGCACCAGGGGCGCGATCAGGGCGACAAAAGTGGCGACAATGGAGAAATCCAGACCGAACTGGTCCAGGTGTGGAATGTTCTGGCCCAGCAGTATGCCGGC  >  NC_002947/2723859‑2724150

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: