Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 2,848,623 T→C 7.8% Q8Q (CAA→CAG)  PP_2501 ← integrase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029472,848,6230TC 7.8% 144.7 / 3.0 51Q8Q (CAA→CAG) PP_2501integrase
Reads supporting (aligned to +/- strand):  ref base T (23/24);  new base C (2/2);  total (25/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01

AAGCGCTTCCTAGTTCGCGCTCCATCCAGCTTGAATTCATAGCTGAACTGAACTGTGATCCCGCGGACTCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTTGGCTGGTGGTGGACGGTATCGGATGCTATTGGATGAAAGAGTAGCCTCTAAGGCA  >  NC_002947/2848477‑2848766
                                                                                                                                                  |                                                                                                                                               
aaGCGCTTCCTAGTTCGCGCTCCATCCAGCTTGAATTCATAGCTGAACTGAACTGTGATCCCGCGGACTCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTg                                                                                                                                               >  2:162619/1‑149 (MQ=255)
         cTAGTTCGCGCTCCATCCAGCTTGAATTCATAGCTGAACTGAACTGTGATCCCGCGGACTCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGt                                                                                                                                      <  5:193810/149‑1 (MQ=255)
         cTAGTTCGCGCTCCATCCAGCTTGAATTCATAGCTGAACTGAACTGTGATCCCGCGGACTCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGt                                                                                                                                      >  3:263480/1‑149 (MQ=255)
             ttCGCGCTCCATCCAGCTTGAATTCATAGCTGAACTGAACTGTGATCCCGCGGACTCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTAcc                                                                                                                                  <  3:128659/149‑1 (MQ=255)
             ttCGCGCTCCATCCAGCTTGAATTCATAGCTGAACTGAACTGTGATCCCGCGGACTCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTAcc                                                                                                                                  >  3:100407/1‑149 (MQ=255)
                 cgcTCCATCCAGCTTGAATTCATAGCTGAACTGAACTGTGATCCCGCGGACTCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCt                                                                                                                                 <  1:188500/146‑1 (MQ=255)
                 cgcTCCATCCAGCTTGAATTCATAGCTGAACTGAACTGTGATCCCGCGGACTCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCt                                                                                                                                 >  2:188500/1‑146 (MQ=255)
                            gCTTGAATTCATAGCTGAACTGAACTGTGATCCCGCGGACTCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTAc                                                                                                                   >  7:218847/1‑149 (MQ=255)
                            gCTTGAATTCATAGCTGAACTGAACTGTGATCCCGCGGACTCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTAc                                                                                                                   >  3:120510/1‑149 (MQ=255)
                             cTTGAATTCATAGCTGAACTGAACTGTGATCACGCGGACTCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTAcc                                                                                                                  >  3:165929/1‑149 (MQ=255)
                                   ttCATAGCTGAACTGAACTGTGATCCCGCGGACTCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAACTGCTTGATCGTTACCTTGGACACTCTCTAcccc                                                                                                                >  5:63105/1‑145 (MQ=255)
                                   ttCATAGCTGAACTGAACTGTGATCCCGCGGACTCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAACTGCTTGATCGTTACCTTGGACACTCTCTAcccc                                                                                                                <  4:123109/145‑1 (MQ=255)
                                   ttCATAGCTGAACTGAACTGTGATCCCGCGGACTCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAACTGCTTGATCGTTACCTTGGACACTCTCTAcccc                                                                                                                <  6:63105/145‑1 (MQ=255)
                                   ttCATAGCTGAACTGAACTGTGATCCCGCGGACTCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAACTGCTTGATCGTTACCTTGGACACTCTCTAcccc                                                                                                                >  3:123109/1‑145 (MQ=255)
                                     cATAGCTGAACTGAACTGTGATCCCGCGGACTCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTa                                                                                                           <  8:228541/148‑1 (MQ=255)
                                     cATAGCGGAACTGCACGTTGATCCCGCGGACTCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTa                                                                                                           <  8:224975/148‑1 (MQ=255)
                                           tgaactgaacTGTGATCCCGCGGACTCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTcc                                                                                                    >  1:130396/1‑149 (MQ=255)
                                             aactgaactgTGATCCCGCGGACTCCGACACGCACCTCAGCATCCAGTCCTCCATCCTCACTTAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCTATTGCTTGTTCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTcc                                                                                                    <  2:204253/147‑1 (MQ=255)
                                             aactgaactgTGATCCCGCGGACTCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTc                                                                                                     <  2:56974/146‑1 (MQ=255)
                                             aactgaactgTGATCCCGCGGACTCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTc                                                                                                  <  2:136968/149‑1 (MQ=255)
                                                  aactgTGATCCCGCGGACTCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCAcc                                                                                             >  1:81727/1‑149 (MQ=255)
                                                            ccGCGGACTCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAAttttgt                                                                                   <  8:218847/149‑1 (MQ=255)
                                                                    tCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAAttttgtgccacttt                                                                           >  3:111109/1‑149 (MQ=255)
                                                                       gACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTAAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAAttttgtgccacttttgt                                                                        >  7:173816/1‑149 (MQ=255)
                                                                          acGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAAttttgtgccacttttgtgc                                                                      >  2:86854/1‑148 (MQ=255)
                                                                             cACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGccacc                                                                  <  8:173816/149‑1 (MQ=255)
                                                                              aCCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGccacc                                                                  >  7:28441/1‑148 (MQ=255)
                                                                                 tCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCaaaa                                                              >  1:256893/1‑149 (MQ=255)
                                                                                      aaCCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCtt                                                         <  7:11388/149‑1 (MQ=255)
                                                                                         cAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTTGGc                                                      <  2:81727/149‑1 (MQ=255)
                                                                                          aGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTTGGCt                                                     >  3:60152/1‑149 (MQ=255)
                                                                                              ctccATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTTGGCtggt                                                  <  1:162619/148‑1 (MQ=255)
                                                                                                ccATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTTGGCtggtggt                                               >  1:109284/1‑149 (MQ=255)
                                                                                                     cTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTTGGCTGGTGGTGGAc                                           <  2:109284/148‑1 (MQ=255)
                                                                                                     cTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTTGGCTGGTGGTGGACg                                          <  2:130396/149‑1 (MQ=255)
                                                                                                     cTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTCGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTTGGCTGGTGGTGGACg                                          <  4:100407/149‑1 (MQ=255)
                                                                                                          ggAAGACGTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTTGGCTGGTGGTGGACGGTATc                                     <  2:256893/149‑1 (MQ=255)
                                                                                                          ggAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTTGGCTGGTGGTGGACGGTATc                                     >  6:71005/1‑149 (MQ=255)
                                                                                                          gcaaGACCTTTCCTTCATCTTGCGCTGTCAGTGACTCCAATTGCTTGATCGTTACATTGGACACTCGATACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTTGGCTGGTGGTGGACGGTATc                                     <  4:165929/147‑1 (MQ=255)
                                                                                                                      cGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTTGGCTGGTGGTGGACGGTATCGGATGCTATTgg                         <  4:111109/149‑1 (MQ=255)
                                                                                                                      cGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTTGGCTGGTGGTGGACGGTATCGGATGCTATTg                          >  1:169426/1‑148 (MQ=255)
                                                                                                                       gTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTTGGCTGGTGGTGGACGGTATCGGATGCTATTGGa                        <  7:84325/149‑1 (MQ=255)
                                                                                                                           tCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTTGGCTGGTGGTGGACGGTATCGGATGCTATTGGATGa                     >  8:95897/1‑148 (MQ=255)
                                                                                                                           tCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTTGGCTGGTGGTGGACGGTATCGGATGCTATTGGATGa                     >  8:145368/1‑148 (MQ=255)
                                                                                                                              tGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTAGGCTGGTGGTGGACGGTATCGGATGCTATTGGATGaaa                   >  6:248797/1‑147 (MQ=255)
                                                                                                                               gcgcTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTGTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTTGGCTGGTGGTGGACGGTATCGGATGCTATTGGATGaaa                   <  4:263480/146‑1 (MQ=255)
                                                                                                                               gcgcTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTTGGCTGGTGGTGGACGGTATCGGATGCTATTGGATGaaa                   <  8:28441/146‑1 (MQ=255)
                                                                                                                               gcgcTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTTGGCTGGTGGTGGACGGTATCGGATGCTATTGGATGaaa                   <  4:60152/146‑1 (MQ=255)
                                                                                                                                     tCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTTGGCTGGTGGTGGACGGTATCGGATGCTATTGGATGAAAGAGTAGCct          <  1:22964/149‑1 (MQ=255)
                                                                                                                                            cTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTTGGCTGGTGGTGGACGGTATCGGATGCTATTGGATGAAAGAGTAGCCTCTAAgg    >  4:80028/1‑148 (MQ=255)
                                                                                                                                             tCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTTGGCTGGTGGTGGACGGTATCGGATGCTATTGGATGAAAGAGTAGCCTCTAAGGCa  >  8:35283/1‑149 (MQ=255)
                                                                                                                                                  |                                                                                                                                               
AAGCGCTTCCTAGTTCGCGCTCCATCCAGCTTGAATTCATAGCTGAACTGAACTGTGATCCCGCGGACTCCGACACGCACCTCAGCAACCAGTCCTCCATCCTCACGGAAGACCTTGCCGTCATCTTGCGCTGTCAGTGCCTCCAATTGCTTGATCGTTACCTTGGACACTCTCTACCCCTAGTAAAATTCCTCGCACCCGAATTTTGTGCCACTTTTGTGCCACCAAAATGCTTGGCTGGTGGTGGACGGTATCGGATGCTATTGGATGAAAGAGTAGCCTCTAAGGCA  >  NC_002947/2848477‑2848766

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: ‑