Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 75,986 T→C T456A (ACC→GCC)  leuC ← 3‑isopropylmalate dehydratase large subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP00927375,9860TC82.9% 93.7 / 13.1 41T456A (ACC→GCC) leuC3‑isopropylmalate dehydratase large subunit
Reads supporting (aligned to +/- strand):  ref base T (4/3);  new base C (16/18);  total (20/21)
Fisher's exact test for biased strand distribution p-value = 6.97e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01

TCGGGATGATTGCATCGGTATCGACATTGGCGGCATCCAGCGGAACCACCAGGCCTGTGTGTTTGATAAATTTCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGTCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTGCTGGTGGAGGCACAACGTTCGCCCGGATTCAGACGGTCGTTGTTCATCGC  >  NZ_CP009273/75859‑76118
                                                                                                                               |                                                                                                                                    
tCGGGATGATTGCATCGGTATCGACATTGGCGGCATCCAGCGGAACCACCAGGCCTGTGTGTTTGATAAATTTCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGCCAcagcagca                                                                                                                            <  2:151578/138‑1 (MQ=255)
              tCGGTATCGACATTGGCGGCATCCAGCGGAACCACCAGGCCTGTGTGTTTGATAAATTTCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGcc                                                                                                             >  1:644807/1‑139 (MQ=255)
                 gTATCGACATTGGCGGCATCCAGCGGAACCACCAGGCCTGTGTGTTTGATAAATTTCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCggg                                                                                                          <  2:764099/139‑1 (MQ=255)
                 gTATCGACATTGGCGGCATCCAGCGGAACCACCAGGCCTGTGTGTTTGATAAATTTCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCggg                                                                                                          <  2:650171/139‑1 (MQ=255)
                          ttGGCGGCATCCAGCGGAACCACCAGGCCTGTGTGTTTGATAAATTTCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGa                                                                                                 <  2:164158/139‑1 (MQ=255)
                            ggcggcATCCAGCGGAACCACCAGGCCTGTGTGTTTGATAAATTTCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGt                                                                                                                                      <  2:622610/100‑1 (MQ=255)
                            ggcggcATCCAGCGGAACCACCAGGCCTGTGTGTTTGATAAATTTCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGt                                                                                                                                      >  1:622610/1‑100 (MQ=255)
                            ggcggcATCCAGCGGAACCACCAGGCCTGTGTGTTTGATAAATTTCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGTCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGAtg                                                                                               >  2:205384/1‑139 (MQ=255)
                                         ggACCCACCAGGCCTGTGTGTTTGATAAATTTCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCccgccg                                                                                  <  2:442792/139‑1 (MQ=255)
                                                ccaGGCCTGTGTGTTTGATAAATTTCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCt                                                                           >  2:654268/1‑139 (MQ=255)
                                                   ggCCTGTGTGTTTGATAAATTTCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTggc                                                                        <  1:65154/139‑1 (MQ=255)
                                                         tgtgtTTGATAAATTTCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGc                                                                                                                    <  2:321612/89‑1 (MQ=255)
                                                         tgtgtTTGATAAATTTCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGc                                                                                                                    >  1:321612/1‑89 (MQ=255)
                                                         tgtgtTTGATAAATTTCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCtt                                                                  >  1:652792/1‑139 (MQ=255)
                                                         tgtgtTTGATAAATTTCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCtt                                                                  >  2:116495/1‑139 (MQ=255)
                                                         tgtgtTTGATAAATTTCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCtt                                                                  >  1:300215/1‑139 (MQ=255)
                                                              ttGATAAATTTCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAg                                                             >  1:621046/1‑139 (MQ=255)
                                                                gATAAATTTCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGt                                                            >  2:740175/1‑138 (MQ=255)
                                                                 aTAAATTTCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTa                                                          <  2:621046/139‑1 (MQ=255)
                                                                    aaTTTCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACg                                                        <  2:112051/138‑1 (MQ=255)
                                                                        tctcTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTg                                                    <  1:654268/138‑1 (MQ=255)
                                                                              ccATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGTCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTGCtggt                                               <  2:335913/137‑1 (MQ=255)
                                                                               cagggTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTGCTGGTGGa                                            <  2:557426/136‑1 (MQ=255)
                                                                                              aTTTAATGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTGCTGGTGGAGGCACAACGTTCGcc                             >  2:135949/1‑139 (MQ=255)
                                                                                              aTTTAATGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTGCTGGTGGAGGCACAACGTTCGcc                             >  1:449416/1‑139 (MQ=255)
                                                                                               tttAATGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTGCTGGTGGAGGCACAACGTTCGcc                             <  1:116495/138‑1 (MQ=255)
                                                                                                ttAATGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTGCTGGTGGAGGCACAACGTTCGCCCg                           >  2:581129/1‑139 (MQ=255)
                                                                                                ttAATGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTGCTGGTGGAGGCACAACGTTCGCCCg                           >  1:446041/1‑139 (MQ=255)
                                                                                                   aTGTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTGCTGGTGGAGGCACAACGTTCGCCCGGAt                        >  2:858000/1‑139 (MQ=255)
                                                                                                     gTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCgg                                                                                                                        >  2:86811/1‑41 (MQ=255)
                                                                                                     gTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCgg                                                                                                                        <  1:86811/41‑1 (MQ=255)
                                                                                                     gTTGCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTGCTGGTGGAGGCACAACGTTCGCCCGGAtt                       >  1:755094/1‑138 (MQ=255)
                                                                                                       tGCGAATGTCGGCGAAATGTCCGGTCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTGCTGGTGGAGGCACAACGTTCGCCCGGAtt                       >  1:779620/1‑136 (MQ=255)
                                                                                                       tGCGAATGTCGGCGAAATGTCCGGTCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTGCTGGTGGAGGCACAACGTTCGCCCGGAtt                       >  1:44817/1‑136 (MQ=255)
                                                                                                        gCGAATGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTGCTGGTGGAGGCACAACGTTCGCCCGGATTCAGa                   >  2:361373/1‑139 (MQ=255)
                                                                                                           aaTGTCGGCGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTGCTGGTGGAGGCACAACGTTCGCCCGGATTCAGACgg                <  1:740175/139‑1 (MQ=255)
                                                                                                                 ggCGAAATGTCCGGTCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTGCTGGTGGAGGCACAACGTTCGCCCGGAt                        >  2:61048/1‑125 (MQ=255)
                                                                                                                 ggCGAAATGTCCGGTCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTGCTGGTGGAGGCACAACGTTCGCCCGGAt                        <  1:61048/125‑1 (MQ=255)
                                                                                                                   cGAAATGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTGCTGGTGGAGGCACAACGTTCGCCCGGATTCAGACGGTCgttgtt        <  2:309730/139‑1 (MQ=255)
                                                                                                                   cGAAATGCCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTGCTGGTGGAGGCACAACGTTCGCCCGGATTCAGACGGTCgttgtt        <  1:450400/139‑1 (MQ=255)
                                                                                                                     aaaTGTCCGGCCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTGCTGGTGGAGGCACAACGTTCGCCCGGATTCAGACGGTCGTTGTTCa      <  1:581129/139‑1 (MQ=255)
                                                                                                                       ttGTCCGGCCACAGCAGAAGCGGCAGCCATGGCCGGGCTGACCAGTTGCGTGCGTCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTGCTGGTGGAGGCACAACGTTCGCCCGGATTCAGACGGTCGTTGTTCATc    <  2:802642/138‑1 (MQ=255)
                                                                                                                          tCCGGTCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTGCTGGTGGAGGCACAACGTTCGCCCGGATTCAGACGGTCGTTGTTCATCGc  <  2:393490/138‑1 (MQ=255)
                                                                                                                               |                                                                                                                                    
TCGGGATGATTGCATCGGTATCGACATTGGCGGCATCCAGCGGAACCACCAGGCCTGTGTGTTTGATAAATTTCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCGGTCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTTCAAAGTTACGGTTGCTGGTGGAGGCACAACGTTCGCCCGGATTCAGACGGTCGTTGTTCATCGC  >  NZ_CP009273/75859‑76118

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑