Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 2,506,454 C→T 17.3% intergenic (‑269/‑67) mntH ← / → nupC manganese/divalent cation transporter/nucleoside (except guanosine) transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092732,506,4540CT17.3% 70.3 / 9.6 37intergenic (‑269/‑67)mntH/nupCmanganese/divalent cation transporter/nucleoside (except guanosine) transporter
Reads supporting (aligned to +/- strand):  ref base C (14/16);  new base T (2/4);  total (16/21)
Fisher's exact test for biased strand distribution p-value = 6.72e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.70e-01

AAGATTGATGACTTGAATGTTATGGTTATGTTTAATGTTAGCACATTTACATAACTTTCAGCTTCCATACACAACATAGCAGAAATGTATGACAGATCACTATTTTTGAAGCCTGTCACAGGACGTCATTATAGTGTGTGTCAGATCTCGTTTTCCTTAACCATGTTACATAGAATGTGCACGGAAATTTAACCTGCCTCATATTTGGAGCAAATATGGACCGCGTCCTTCATTTTGTACTGGCACTTGCCGTTGTTGCGATTCTCGCACTGCTGGTAAGCAGCGACCGCAAA  >  CP009273/2506306‑2506598
                                                                                                                                                    |                                                                                                                                                
aaGATTGATGACTTGAATGTTATGGTTATGTTTAATGTTAGCACATTTACATAACTTTCAGCTTCCATACACAACATAGCAGAAATGTATGACAGATCACTATTTTTGAAGCCTGTCACAGGACGTCATTATAGTGTGTGTCAGAtctc                                                                                                                                                  <  2:439408/149‑1 (MQ=255)
   catgatgaAATGAGTGTTATGGGTATGTTTAATGTTAGCACATTTACATAACTTTCAGCTTCCATACACAACATAGCAGAAAGGTATGACAGATCACTATTTTTGAAGCCTGTCACAGGACGTCATTATAGTGTGTGTCAGATCTCGtt                                                                                                                                               <  2:519514/147‑1 (MQ=255)
            ttGAATGTTATGGTTATGTTTAATGTTAGCACATTTACATAACTTTCAGCTTCCATACACAACATAGCAGAAGTTTATGACAGATCACTATTTTTGAAGCCTGTCACAGGACGTCATGATAGTGTGGGTCAGATATCGTTTTCCTTAAc                                                                                                                                      >  2:381027/1‑149 (MQ=255)
            tcgAATGTTATGGTTATGTTTAATGTTATCACATTTACATAACTTTCAGCTTCCATACACAACATAGCAGAAATGTATGACAGATCACTATTTTTGAAGCCTGTCACAGGACGTCATTATAGTGTGTGTCAGATCTCGTTTTCCTTAAc                                                                                                                                      <  2:137124/147‑1 (MQ=255)
                ctGTTATGGTTATGTTTAATGTTAGCACATTTACATAACTTTCAGCTTCCATACACAACATAGCAGAAATGTATGACAGATCACTATTTTTGAAGCCTGTCACAGGACGTCATTATAGTGTGTGTCAGATCTCGTTTTCCTTa                                                                                                                                        <  1:448654/142‑1 (MQ=255)
                   ttatggttatgTTTAATGTTAGCACATTTACATAACTTTCAGCTTCCATACACAACATGGCAGAAATGTGGGACAGATCACTATTTTTAAAGCCAGTCACAGGAAGTCATAAAAGAGGGTGTCAGAGGTCGTTTTCCTTAACGATGttg                                                                                                                               >  2:371559/1‑148 (MQ=255)
                                tAATGTTAGCACATTGACATAACTTTCAGCTTCCATACACAACATAGCAGAAATGTATGACAGATCACTATTTTTGAAGCCTGTCACAGGACGTCATTATAGTGTGTGGCAGATCTCGTTTTCCTTAACCATGTTACATAGAATGTGCa                                                                                                                  <  2:152500/149‑1 (MQ=255)
                                     ttAGCACATTTACATAACTTTCAGCTTCCATACACAACATAGCAGAAATGTATGACAGATCACTATTTTTGAAGCCTGTCACAGGACGTCATTATAGTGTGTGTCAGATCTCGTTTTCCTTAACCATGTTACATAGAATGTGc                                                                                                                   >  1:55933/1‑143 (MQ=255)
                                     ttAGCACATTTACATAACTTTCAGCTTCCATACACAACATAGCAGAAATGTATGACAGATCACTATTTTTGAAGCCTGGCACAGGACGTCATTATAGTGTGTGTCAGATCTCGTTTTCCTTAACCATGTTACATAGAATGTGCACGGaa                                                                                                             <  2:309351/149‑1 (MQ=255)
                                            aTTTACATAACTTTCAGCTTCCATACACAACATAGCAGAAATGTATGACAGATCACTATTTTTGAAGCCTGTCACAGGACGTCATTATAGTGTGTGTCAGATCTCGTTTTCCTTAACCATGTTACATAGAATGTGCACGGAAATTTAAc                                                                                                      <  2:509163/149‑1 (MQ=255)
                                                   tAACTTTCAGCTTCCATACACAACATAGCAGAAATGTATGACAGATCACTATTTTTGAAGCCTGTCACAGGACGTCATTATAGTGTGTGTCAGATCTCGTTTTCCTTAACCACGTTACATAGAATGTGCACGGAAATTTAAcc                                                                                                     <  1:60702/143‑1 (MQ=255)
                                                    aaCTTTCAGCTTCCATACACAACATAGCAGAAAGGTATGACAGATCACTATTTTTGAAGCCTGTCACAGGACGTCATTATAGTGTGTGTCAGATCTCGTTTTCCTTAACCATGTTAGATAGAATGTGCACGGAAATTTGACCTGCCTCa                                                                                              >  2:504799/1‑149 (MQ=255)
                                                       tttCAGCTTCCATACACAACATAGCAGAAATGTATGACAGATCACTATTTTTGAAGCCTGTCACAGGACGTCATTATAGTGTGTGTCAGATCTCGTTTTCCTTAACCATGTTACATAGAATGTGCACGGAAATTTAACCTGcc                                                                                                 >  1:292208/1‑143 (MQ=255)
                                                       tttCAGCTTCCATACACAACATAGCAGAAATGTATGACAGATCACTATTTTTGAAGCCTGTCACAGGACGTCATTATAGTGTGTGTCAGATCTCGTTTTCCTTAACCATGTTACATAGAATGTGCACGGAAATTTAACCTGCCTCatat                                                                                           >  2:254670/1‑149 (MQ=255)
                                                           aGCTTCCATACACAACATAGCAGAAATGTATGACAGATCACTATTTTTGAAGCCTGTCACAGGACGTCATTATAGTGTGTGTCAGATCTCGTTTTCCTTAACCATGTTACATAGAATGTGCACGGAAATTTAACCTGCCTCATATTTgg                                                                                       >  2:233828/1‑149 (MQ=255)
                                                            gCTTCCATACACAACATAGCAGAAATGTATGACAGATCACTATTTTTGAAGCCTGTCACAGGCCGTCATTATAGTGTGTGTCAGATCTTTTTTTCCTTCACCATGTTACTTAGAATGTGCACGGAAATTTAACCTGCCTCata                                                                                            <  1:408769/143‑1 (MQ=255)
                                                                ccAGACACAACATAGTAGAAATGTATGTCAGAGCACTATTTTTGAAGCCTGTCAGAGGACGTCAGTATAGTGTGTGTCAGATCTTGTTTTCCTTAACCATGTTACATAGAATGTGCACGGAAATTTAACCTGCCTCATATTTGGAGCaa                                                                                  <  2:446422/149‑1 (MQ=255)
                                                                  aTACACAACATAGCAGAAATGTATGACAGATCACTATTTTTGAAGCCTGTCACAGGACGTCATTATAGTGTGTGTCAGATCTCGTTTTCCTTAACCATGTTACATAGAATGTGCACGGAAATTTAACCTGCCTCATATTTGGAGCAAat                                                                                <  2:210551/149‑1 (MQ=255)
                                                                   tACACAACATAGCAGAAATGTATGACAGATCACTATTTTTGAAGCCTGTCACAGGACGTCATTATAGTGTGTGTCAGATCTCGTTTTCCTTAACCATGTTACATAGAATGTGCACGGAAATTTAACCTGCCTCCTATTTGGAg                                                                                     >  1:222058/1‑143 (MQ=255)
                                                                    acacAACATAGCAGAAATGTATGACAGATCACTATTTTTGAAGCCTGTCACAGTACGTCATTATAGTGTGTGTCAGATCTTGTTTTCCTTAACCATGTTACATAGAATGTGCACGGAAATTTAACCTGCCTCATATTTgctcc                                                                                    <  1:128191/143‑5 (MQ=255)
                                                                     cacaACATAGCAGAAATGTATGACAGATCACTATTTTTGAAGCCGGTCACAGGACGTCATTATAGTGTGTGTCAGATCTCGTTTTCCTTAACCATGTTACATAGAATTGGCACGGAACTTTAACCTGCCTCATATTTGGCGCAACTATg                                                                             >  2:175171/1‑149 (MQ=255)
                                                                        aacaTAGCAGAAATGTATGACAGATCACTATTTTTGAAGCCTGTCACAGGACGTCATTATAGTGTGTGTCAGATCTCGTTTTCCTTAACCATGTTACATAGAATGTGCACGGAAATTTAACCTGCCTCATATTTGGAGCAAATATGGAc                                                                          >  2:204697/1‑149 (MQ=255)
                                                                        aacaTAGCAGAAATGTATGACAGATCACTATTTTTGAAGCCTGTCACAGGACGTCATTATAGTGTGTGTCAGATCCCGTTTTCCCTGACCATGTTAAAAAGAATGTGAACGGACATTTAACCTGCCTCATATTTGGACCaaaa                                                                                >  1:4977/1‑142 (MQ=255)
                                                                           aTAGCAGAAATGTATTACAGATCACTATTTTTGAAGCCTGTCACAGGACGTCATTATAGTGTGTGTCAGATCTCGTTTTCCTTAACCATGTTACATAGAATGTGCACGGAAATTTAACCTGCCTCATATTTGGAGCAAATATg                                                                             <  1:427547/143‑1 (MQ=255)
                                                                             agaaGAAATGTATTACAGATCACTATTTTTGAAGCTTGTCACAGGACGTCATTATAGTGTGTGTCAGATCTGGTTTTCCTTACCCATGTTACATAGAATGTGCACGGAAATTTAACCTGCCTCATATTTGGAGCAAATATGGa                                                                           <  1:121751/140‑1 (MQ=255)
                                                                             aGCAGAAATGTATGACAGATCACTATTTTTGAAGCCTGTCACAGGACGTCATTATAGTGTGTGTCAGATCTCGTTTTCCTTAACCATGTTACATAGAATGTGCACGGAAATTTAACCTGCCTCATATTTGGAGCAAATATGGa                                                                           <  1:79111/143‑1 (MQ=255)
                                                                                            cAGATCACTATTTTTGAAGCCTGTCACAGGACGTCATTATAGTGTGTGTCAGATCTTGTTTTCCTTAACCATGTTACATAGAATGTGCACGGAAATTTAACCTGCCTCATATTTGGAGCAAATATGGACCGCGTCCTTCAttt                                                            >  1:364776/1‑143 (MQ=255)
                                                                                               aTCACTATTTTTGAAGCCTGTCAGCGGACGTCATTATAGTGTGTGTCAGATCTCGTTGTCCTTAACCATGTTACATAGAATGTGCACGGAAATTTAACCTGCCTCATATTTGGAGCAAATATGGACCGCGTCCTTCATTTTGt                                                         <  1:414202/143‑1 (MQ=255)
                                                                                                   cTATTTTTTTAGTTTTTCACAGGACGTCATTATAGTGTGTGTCAGATCTTGTTTTCCTTAACCATGTTACATAGAATGTGCACGGAAATTTAACCTGCCTCATATTTGGAGCAAATATGGACCGCGTCCTTCATTTTGTTCTg                                                     >  1:27839/1‑143 (MQ=255)
                                                                                                      tttttGAAGCCTGTCACAGGACGTCATTATAGTGTGTGTCAGATCTCGTTTTCCTTAACCATGTTACATAGAATGTGCACGGAAATTTAACCTGCCTCATATTTGGAGCAAATATGGACCGCGTCCTTCATTTTGTACTGGCACTTGcc                                            >  2:78412/1‑149 (MQ=255)
                                                                                                                              cATTATAGTGTGTGTCAGATCTCGTTTTCCCTAACCATGTTACATAGAATGTGCACGGAAATTTAACCTGCCTCATATTTGGAGCAAATATGGACCGCGTCCTTCATTTTGTACTGGCACTTGCCGTTGTTGCGATTCTCGCa                          <  1:302590/143‑1 (MQ=255)
                                                                                                                                      tgtgtgtCAGATCTTGTTTTCCTTAACCATGTTACATAGTATGTGCCCGGAAATTTCACCTTCCTCATCTTTGGTGCAAATATGGACCGCGTCCTTCATTTTGTAATGTCACTTGCCGTTGTTGCGATTCTCGCACTGCTGGt                  <  1:157891/143‑1 (MQ=255)
                                                                                                                                         tgtttaGATCGCGTTTTCCTTAACCATGTTACATATAATGTGCACGGAAATTTAACCTGCCTCATATTTGGAGCAAATCTGGACCGCGGCCTTCATTTTTTACTGGCACTTGCCGTTGTTGCGATTCTCGCACTGCTGGTAag               <  1:233872/138‑1 (MQ=255)
                                                                                                                                         gtgtCAGATCTCGTTTTCCTTAACCATGTTACATAGAATGTGCACGGAAATTTAACCTGCCTCATATTTGGAGCAAATATGGACCGCGTCCTTCATTTTGTACTGGCACTTGCCGTTGTTGCGATTCTCGCACTGCTGGTAAGCAGCGa         <  2:323729/149‑1 (MQ=255)
                                                                                                                                          tgtCAGATCTCGTTTTCCTTAACCATGTTACATAGAATGTGCACGGAAATTTAACCTGCCTCATATTTGGAGCAAATATGGACCGCGTCCTTCATTTTGTACTGGCACTTGCCGTTGTTGCGATTCTCGAACTGCTGGTAagc              >  1:326475/1‑143 (MQ=255)
                                                                                                                                           gcgataTCTCGTTTTCCTTAACAATGTTACATAAAATGTGCACGGAAATTTAACCTGCCCCAGATTTGGAGCAAATATGGCCCGCGTCCTTCATTTTGTACTGCCACTAACAGCTGTTGCGATGCTCGCACTGCTGGTAAGCAGCGAcc       <  2:311756/144‑1 (MQ=255)
                                                                                                                                              aGATCTCGTTTTCCTTAACCATGTTACATAGAATGTGCACGGAAATTTAACCTGCCTCATATTTGGAGCAAATATGGACCGCGTCCTTCATTTTGTACTGGCACTTGCCGTTGTTGCGATTCTCGCACTGCTGGTAAGCAGCGACCGCa    >  2:514641/1‑149 (MQ=255)
                                                                                                                                                aTCTCGTTTTCCTTAACCATGTTACATAGAATGTGCACGGAAATTTAACCTGCCTCATATTTGGAGCAAATATGGACCGCGTCCTTCATTTTGTACTGGCACTTGCCGTTGTTGCGATTCTCGCACTGCTGGTAAGCAGCGACCGCaaa  <  2:182857/149‑1 (MQ=255)
                                                                                                                                                   tcGTTTTCCTTAACCATGTTACATAGAATGTGCACGGAAATTTAACCTGCCTCATATTTGGAGCAAATATGGACCGCGTCCTTCATTTTGTACTGGCACTTGCCGTTGTTGCGATTCTCGCACTGCTGGTAAGCAGCGACCGc     >  1:432930/1‑143 (MQ=255)
                                                                                                                                                    |                                                                                                                                                
AAGATTGATGACTTGAATGTTATGGTTATGTTTAATGTTAGCACATTTACATAACTTTCAGCTTCCATACACAACATAGCAGAAATGTATGACAGATCACTATTTTTGAAGCCTGTCACAGGACGTCATTATAGTGTGTGTCAGATCTCGTTTTCCTTAACCATGTTACATAGAATGTGCACGGAAATTTAACCTGCCTCATATTTGGAGCAAATATGGACCGCGTCCTTCATTTTGTACTGGCACTTGCCGTTGTTGCGATTCTCGCACTGCTGGTAAGCAGCGACCGCAAA  >  CP009273/2506306‑2506598

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑