Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 4,407,546 G→A 8.3% L100F (CTC→TTC)  PP_3889 ← putative Phage integrase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029474,407,5460GA 8.3% 133.5 / 2.2 48L100F (CTC→TTC) PP_3889putative Phage integrase
Reads supporting (aligned to +/- strand):  ref base G (23/21);  new base A (2/2);  total (25/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.20e-01

GCTTATCAATCAGCTCGGCGGTGATGTACTTGATCGGCAGATCGCCTAAGCACGGCCGCACATGCTGCCCAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGACGCAGCGCGGGCAGCTCGGCCAGCACCGCCGCCACGCTCAACTCAGGCCAGCGGGCGATCGGTACCCATTTCTTGCC  >  NC_002947/4407399‑4407690
                                                                                                                                                   |                                                                                                                                                
gCTTATCAATCAGCTCGGCGGTGATGTACTTGCTCGGCAGATCGCCTAAGCACCGCCGCACATGCTGCCCAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGc                                                                                                                                                 <  2:352462/149‑1 (MQ=255)
    atcaatcaGCTCGGCGGTGATGTACTTGATCGGCAGATCGCCTAAGCACGGCCGCACATGCTGCCCAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGt                                                                                                                                              <  8:220223/148‑1 (MQ=255)
        atcaGCTTGGCGGTGATGTACTTGATCGGCAGATCGCCTAAGCACGGCCGCACATGCTGCCCAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGcc                                                                                                                                         >  4:102966/1‑149 (MQ=255)
        atcaGCTTGGCGGAGATGTAATTGATCGGCAGATCGCCTAAGCACGGCCGCACATGCTGCCGAATTCCTGCGCGGCTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTggac                                                                                                                                         >  4:194320/1‑147 (MQ=255)
              tCGGCGGTGATGTACTTGATCGGCAGATCGCCTAAGCACGGCCGCACATGCTGCCCAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCACACGGt                                                                                                                                   >  8:393730/1‑149 (MQ=255)
                 gcggTGATGTACTTGATCGGCAGATCGCCTAAGCACGGCCGCACATGCTGCCCAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGc                                                                                                                                >  2:140906/1‑149 (MQ=255)
                        tGTACTTGATCGGCAGATCGCCTAAGCACGGCCGCACATGCTGCCCGATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGccc                                                                                                                         >  3:70184/1‑149 (MQ=255)
                          tACTTGATCGGCAGATCGCCTAAGCACGGCCGCACATGCTGCCCAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGa                                                                                                                       <  4:296551/149‑1 (MQ=255)
                               gATCGGCAGATCGCCTAAGCACGGCCGCACATGCTGCCCAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTa                                                                                                                  >  6:46976/1‑149 (MQ=255)
                                aTCGGCAGATCGCCTAAGCACGGCCGCACATGCTGCCCAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGcc                                                                                                                               <  4:69638/135‑1 (MQ=255)
                                aTCGGCAGATCGCCTAAGCACGGCCGCACATGCTGCCCAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGcc                                                                                                                               >  3:69638/1‑135 (MQ=255)
                                 tCGGCAGATCGCCTAAGCACGGCCGCACATGCTGCCCAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCCCGGTGGCCATGCCCGACCCTAcc                                                                                                                >  3:297981/1‑149 (MQ=255)
                                     cAGATCGCCTAAGCACGGCCGCACATGCTGCCCAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACcggtg                                                                                                            <  5:171509/149‑1 (MQ=255)
                                        aTCGCCTAAGCACGGCCGCACATGCTGCCCAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGGCACTACcggtgcgg                                                                                                         <  3:219685/149‑1 (MQ=255)
                                                aGCACGGCCGCACATGCTGCCCAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCg                                                                                                   <  6:393853/147‑1 (MQ=255)
                                                 gCACGGCCGCACATGCTGCCCAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGt                                                                                                <  2:311468/149‑1 (MQ=255)
                                                     ggCCGCACATGCTGCCCAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAg                                                                                                                                                  >  8:203300/1‑95 (MQ=255)
                                                     ggCCGCACATGCTGCCCAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAg                                                                                                                                                  <  7:203300/95‑1 (MQ=255)
                                                         gCACATGCTGCCCAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCAt                                                                                         >  1:114297/1‑148 (MQ=255)
                                                                   cccAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGAc                                                                              >  1:369816/1‑149 (MQ=255)
                                                                    ccAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAACAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGgc                                                                                             <  7:50119/133‑1 (MQ=255)
                                                                    ccAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAACAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGgc                                                                                             >  4:129934/1‑133 (MQ=255)
                                                                    ccAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAACAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGgc                                                                                             >  8:50119/1‑133 (MQ=255)
                                                                    ccAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAACAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGgc                                                                                             <  3:129934/133‑1 (MQ=255)
                                                                     cAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGACGc                                                                            <  2:369816/149‑1 (MQ=255)
                                                                     cAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGAGGCGCATCGGGCGCGGCCGc                                                                            >  8:377098/1‑149 (MQ=255)
                                                                                  ggTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGACGCAGCGCGGGCAGCt                                                               <  2:114297/149‑1 (MQ=255)
                                                                                    tGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGACGCAGCGCGGGCAGCTCg                                                             <  7:393730/149‑1 (MQ=255)
                                                                                     ggCAGCCTTACGCTTTGCAGACAACGAGCGATCATGCCTAATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGACGCAGCGCGGGCAGCTCgg                                                            >  5:93996/1‑149 (MQ=255)
                                                                                         gCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGACGCAGCGCGGGCAGCTCGGCCAg                                                        <  7:377098/149‑1 (MQ=255)
                                                                                                 cTTTGCAGACAACGAGCGATCATGGCTCATGCGTGCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGACGCAGCGCGGGCAGCTCGGCCAGCAccgccg                                                <  3:194320/149‑1 (MQ=255)
                                                                                                 cTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGACGCAGCGCGGGCAGCTCGGCCAGCAccgccg                                                <  3:102966/149‑1 (MQ=255)
                                                                                                       aGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGACGCAGCGCGGGCAGCTCGGCCAGCACCGCCGCCACGc                                          >  5:395702/1‑149 (MQ=255)
                                                                                                           aaCGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCGTCAGGCGCTGACGCAGCGCGGGCAGCTCGGCCAGCACCGCCGCCACGCTCaa                                      >  1:114630/1‑149 (MQ=255)
                                                                                                           aaCGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGCCGCAGCGCGGGCAGCTCGGCCAGCACCGCCGCCACGCGCac                                      >  8:183224/1‑148 (MQ=255)
                                                                                                            aCGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGACGCAGCGCGGGc                                                                   <  7:386793/119‑1 (MQ=255)
                                                                                                            aCGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGACGCAGCGCGGGc                                                                   >  8:386793/1‑119 (MQ=255)
                                                                                                              gAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTAc                                                                                                                 >  4:394708/1‑71 (MQ=255)
                                                                                                              gAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTAc                                                                                                                 <  3:394708/71‑1 (MQ=255)
                                                                                                                gCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCTTCAGGCGCTGACGCAGCGCGGGCAGCTCGGCCAGCACCGCCGCCACGCTCAACTCAg                                 <  2:114630/149‑1 (MQ=255)
                                                                                                                             aTGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGACGCAGCGCggg                                                                    <  2:339923/101‑1 (MQ=255)
                                                                                                                             aTGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGACGCAGCGCggg                                                                    >  1:339923/1‑101 (MQ=255)
                                                                                                                                   tCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGACGCAGCGCGGGCAGCTCGGCCAGCACCGCCGCCACGCTCAACTCAGGCCAGCGGGCGATCGGTAc              <  7:379335/149‑1 (MQ=255)
                                                                                                                                     gACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGACGCAGCGCGGGCAGCTCGGCCAGCACCGCCGCCACGCTCAACTCAGGCCAGCGGGCGATCGGTAcc             >  5:250193/1‑148 (MQ=255)
                                                                                                                                     gACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGACGCAGCGCGGGCAGCTCGGCCAGCACCGCCGCCACGCTCAACTCAGGCCAGCGGGCGATCGGTAcc             >  3:107461/1‑148 (MQ=255)
                                                                                                                                          aCCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGACGCAGCGCGGGCAGCTCGGCCAGCACCGCCGCCACGCTCAACTCAGGCCAGCGGGCGATCGGTACCCATTTc       >  7:63690/1‑149 (MQ=255)
                                                                                                                                          aCCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGACGCAGCGCGGGCAGCTCGGCCAGCACCGCCGCCACGCTCAACTCAGGCCAGCGGGCGATCGGTACCCATTTc       >  1:43467/1‑149 (MQ=255)
                                                                                                                                            cAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGACGCAGCGCGGGCAGCTCGGCCAGCACCGCCGCCACGCTCAACTCAGGCCAGCGGGCGATCGGTACCCATTTCtt     >  5:91184/1‑149 (MQ=255)
                                                                                                                                             aGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGACGCAGCGCGGGCAGCTCGGCCAGCACCGCCGCCACGCTCAACTCAGGCCAGCGGGCGATCGGTAGCCATTTCTTg    <  6:93996/149‑1 (MQ=255)
                                                                                                                                               tCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGACGCAGCGCGGGCAGCTCGGCCAGCACCGCCGCCACGCTCAACTCAGGCCAGCGGGCGATCGGTACCCATTTCTTGcc  <  6:395702/149‑1 (MQ=255)
                                                                                                                                                   |                                                                                                                                                
GCTTATCAATCAGCTCGGCGGTGATGTACTTGATCGGCAGATCGCCTAAGCACGGCCGCACATGCTGCCCAATTGCTGCGCGGGTGGCAGCCTTACGCTTTGCAGACAACGAGCGATCATGGCTCATGCGGTCGACATACCAGTCGAGCAGTTGGCCCACGGTGGCCATGCCCGACACTACCGGTGCGGTGGCCGGGTGGCGCATCAGGCGCTGACGCAGCGCGGGCAGCTCGGCCAGCACCGCCGCCACGCTCAACTCAGGCCAGCGGGCGATCGGTACCCATTTCTTGCC  >  NC_002947/4407399‑4407690

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: ‑