Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,414,456 C→G 7.8% T489S (ACT→AGT)  PP_3026 → recombinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,414,4560CG 7.8% 151.4 / 2.8 51T489S (ACT→AGT) PP_3026recombinase
Reads supporting (aligned to +/- strand):  ref base C (24/23);  new base G (2/2);  total (26/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.49e-01

AAGCTGCATCAGGAAGAGCGAGAACTGGCCGGCATCGCCTCCAGGCAAAGGCCCGCGGATGCTAGGGCATGGTTGGATCTGGCTGCTGGTGTCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTC  >  NC_002947/3414311‑3414601
                                                                                                                                                 |                                                                                                                                                 
aagcTGCATCAGGAAGAGCGAGAACTGGCCGGCATCGCCTCCAGGCAAAGGCCCGCGGATGCTAGGGCATGGTTGGATCTGGCTGCTGGTGTCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACttt                                                                                                                                                <  3:163447/149‑1 (MQ=255)
   cTGCATCAGGAAGAGCGAGAACTGGCCGGCATCGCCTCCAGGCAAAGGCCCGCGGATGCTAGGGCATGGTTGGATCTGGCTGCTGGTGTCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGAAAGTATCGa                                                                                                                                             >  1:113669/1‑149 (MQ=255)
      cATCAGGAAGAGCGAGAACTGGCCGGCATCGCCTCCAGGCAAAGGCCCGCGGATGCTAGGGCATGGTTGGATCTGGCTGCTGGTGTCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCg                                                                                                                                          >  4:80798/1‑149 (MQ=255)
        tCAGGAAGAGCGAGAACTGGCCGGCATCGCCTCCAGGCAAAGGCCCGCGGATGCTAGGGCATGGTTGGATCTGGCTGCTGGTGTCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCa                                                                                                                                        <  6:262078/149‑1 (MQ=255)
        tCAGGAAGAGCGAGAACTGGCCGGCATCGCCTCCAGGCAAAGGCCCGCGGATGCTAGGGCATGGTTGGATCTGGCTGCTGGTGTCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGAAAGTATCGATcatc                                                                                                                                        <  2:113669/149‑4 (MQ=255)
          aGGAAGAGCGAGAACTGGCCGGCATCGCCTCCAGGCAAAGGCCCGCGGATGCTAGGGCATGGTTGGATCTGGCTGCTGGTGTCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATc                                                                                                                                      <  4:105902/149‑1 (MQ=255)
          aGGAAGAGCGAGAACTGGCCGGCATCGCCTCCAGGCAAAGGCCCGCGGATGCTAGGGCATGGTTGGATCTGGCTGCTGGTGTCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATc                                                                                                                                      >  1:157102/1‑149 (MQ=255)
                              ggCATCGCCTCCAGGCAAAGGCCCGCGGATGCTAGGGCATGGTTGGATCTGGCTGCTGGTGTCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCgtggtg                                                                                                                   >  4:239866/1‑148 (MQ=255)
                                  tCGCCTCCAGGCAAAGGCCCGCGGATGCTAGGGCATGGTTGGATCTGGCTGCTGGTGTCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTg                                                                                                              >  2:244646/1‑149 (MQ=255)
                                         cAGGCAAAGGCCCGCGGATGCTAGGGCATGGTTGGATCTGGCTGCTGGTGTCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCg                                                                                                        <  3:11883/148‑1 (MQ=255)
                                           ggCAAAGGCCGGCGGATGCTAGGGCATGGTTGGATCTGGCTTCTGGTGTCGAGGCGCTAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCgggg                                                                                                     <  7:93627/149‑1 (MQ=255)
                                           ggCAAAGGCCCGCGGATGCTAGGGCATGGTTGGATCTGGCTGCTGGTGTCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCgggg                                                                                                     <  2:157102/149‑1 (MQ=255)
                                              aaaGGCCCGCGGATGCTAGGGCATGGTTGGATCTGGCTGCTGGTGTCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGt                                                                                                                                    <  4:215004/115‑1 (MQ=255)
                                              aaaGGCCCGCGGATGCTAGGGCATGGTTGGATCTGGCTGCTGGTGTCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGt                                                                                                                                    >  3:215004/1‑115 (MQ=255)
                                                aGGCCCGCGGATGCTAGGGCATGGTTGGATCTGGCTGCTGGTGTCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTa                                                                                                                 >  8:220429/1‑132 (MQ=255)
                                                aGGCCCGCGGATGCTAGGGCATGGTTGGATCTGGCTGCTGGTGTCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTa                                                                                                                 <  7:220429/132‑1 (MQ=255)
                                                       cgGATGCTAGGGCATGGTTGGATCTGGCTGCTGGTGTCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAgg                                                                                         <  1:244646/149‑1 (MQ=255)
                                                                     tGGTTGGATCTGGCTGCTGGTGTCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCtt                                                                           <  3:239866/149‑1 (MQ=255)
                                                                        ttGGATCTGGCTGCTGGTGTCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACttt                                                                                                                                                >  5:150812/1‑77 (MQ=255)
                                                                        ttGGATCTGGCTGCTGGTGTCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACttt                                                                                                                                                <  6:150812/77‑1 (MQ=255)
                                                                                      tgGTGTCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAg                                                          >  6:202601/1‑149 (MQ=255)
                                                                                       ggTGTCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAg                                                          >  6:34906/1‑148 (MQ=255)
                                                                                           tCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACa                                                      <  5:202601/148‑1 (MQ=255)
                                                                                             gAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTAGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAgcg                                                   >  4:147562/1‑149 (MQ=255)
                                                                                              aGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGc                                                                                             >  1:139577/1‑106 (MQ=255)
                                                                                              aGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGc                                                                                             <  2:139577/106‑1 (MQ=255)
                                                                                                    aagaagTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATgg                                            >  2:174584/1‑149 (MQ=255)
                                                                                                    aagaagTCGAGGCGCGGGAGAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGTGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACTGCGGCGATg                                             >  5:243753/1‑148 (MQ=255)
                                                                                                     agaagTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTc                                                                  >  4:52328/1‑126 (MQ=255)
                                                                                                     agaagTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTc                                                                  <  3:52328/126‑1 (MQ=255)
                                                                                                        agTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCa                                        <  5:34906/149‑1 (MQ=255)
                                                                                                         gTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAgcgg                                                  <  3:141061/138‑1 (MQ=255)
                                                                                                         gTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAgcgg                                                  >  4:141061/1‑138 (MQ=255)
                                                                                                         gTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAg                                       >  5:230483/1‑149 (MQ=255)
                                                                                                          tCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTATATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCa                                        <  1:59090/147‑1 (MQ=255)
                                                                                                          tCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCa                                        >  2:59090/1‑147 (MQ=255)
                                                                                                          tCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAgg                                      <  3:80798/149‑1 (MQ=255)
                                                                                                          tCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAgg                                      >  1:189943/1‑149 (MQ=255)
                                                                                                            gAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAggg                                     >  7:67377/1‑148 (MQ=255)
                                                                                                            gAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAggg                                     >  5:172193/1‑148 (MQ=255)
                                                                                                                 gcgGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGaaa                               <  6:172193/149‑1 (MQ=255)
                                                                                                                   gggATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAgg                                                                                         >  2:52881/1‑89 (MQ=255)
                                                                                                                   gggATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAgg                                                                                         <  1:52881/89‑1 (MQ=255)
                                                                                                                     gATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAgg                             >  6:172463/1‑147 (MQ=255)
                                                                                                                       tAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGa                         >  3:214852/1‑149 (MQ=255)
                                                                                                                         aGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCa                                                                <  6:134964/108‑1 (MQ=255)
                                                                                                                         aGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCa                                                                >  5:134964/1‑108 (MQ=255)
                                                                                                                         aGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTTGAAAGGAAGAc                        <  8:67377/148‑1 (MQ=255)
                                                                                                                                    gatgcgatCGAAAGTATCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGga                    >  7:247122/6‑141 (MQ=255)
                                                                                                                                    gatgcgatCGAAAGTATCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGga                    <  8:247122/136‑1 (MQ=255)
                                                                                                                                               tACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTc  <  6:230483/148‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                                 
AAGCTGCATCAGGAAGAGCGAGAACTGGCCGGCATCGCCTCCAGGCAAAGGCCCGCGGATGCTAGGGCATGGTTGGATCTGGCTGCTGGTGTCGAGGCGCAAGAAGTCGAGGCGCGGGATAAGGTTCGCCAGTTGATGATCGATACTTTCGATCGCATCGTGATTTACATGCGTGGTGTAGTGCCAGCGGGGCGCAGGGCCAGGTACATCGATGTCTTGCTGATTTCCAAGGCAGGACAGCGGCGATGGCTCAGGGTAGAAAGGAAGACCGGAGAGTGGGCGGCCGGCGTC  >  NC_002947/3414311‑3414601

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: ‑