Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NZ_CP034943 1,968,182 C→A 16.4% L85I (CTA→ATA)  EO946_RS09780 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0349431,968,1820CA16.4% 106.2 / 2.2 54L85I (CTA→ATA) EO946_RS09780hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (23/20);  new base A (9/2);  total (32/22)
Fisher's exact test for biased strand distribution p-value = 1.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGAATGTAAATATCTTTCTCAATTCAGCTGTAGAAAATTTGAACCCTGATGACGTTAAACAAACCCTAAAGACAATTAAAGAGTCGATTATCTTAAAAAACGGTGAATATTCATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTAGAGCAATTCTACAATCTTAAAGATAGTGAAATTGAAACAGGCTCAGAGCAATTACAAGGAGATTTTAG  >  NZ_CP034943/1968045‑1968306
                                                                                                                                         |                                                                                                                            
cGAATGTAAATATCTTTCTCAATTCAGCTGTAGAAAATTTGAACCCTGATGACGTTAAACAAACCCTAAAGACAATTAAAGAGTCGATTATCTTAAAAAACGGTGAATATTCATTTGATGAATCGAAAGCAATAAAACTa                                                                                                                            <  2:1205028/140‑1 (MQ=255)
  aaTGTAAATATCTTTCTCAATTCAGCTGTAGAAAATTTGAACCCTGATGACGTTAAACAAACCCTAAAGACAATTAAATAGTCGAGTATCATAAAAAACGGTGAATAATGATTTGATGTAACGAAAGCAATAAAACTAgg                                                                                                                          >  2:1787874/1‑140 (MQ=255)
  aaTGTAAATATCTTTCTCAATTCAGCTGTAGAAAATTTGAACCCTGATGACGTTAAACAAACCCTAAAGACAATTAAAGAGTCGATTATCTTAAAAAACCGTGAATATTGATTTGATGAAACGAAAGCAATAAAACTatg                                                                                                                          >  2:2198123/1‑138 (MQ=255)
  aaTGTAAATATCTTTCTCAATTCAGCTGTAGAAAATTTGAACCCTGATGACGTTAAACAAACCCTAAAGACAATTAAAGAGTCGATTATCTTAAAAAAAGGTGAATATTCATGTGAGGAATAGAAACGACTAAAACGAgg                                                                                                                          >  1:298917/1‑140 (MQ=255)
  aaTGTAAATATCTTTCTCAATTCAGCTGTAGAAAATTTGAACCCTGATGACGTTAAACAAACCCTAAAGACAATTAAAGAGTCGATTATATTAAAAAAAGGTGAATATTAATTTTATTAATGGAAAGCAAAAAAAATAgg                                                                                                                          >  2:105091/1‑140 (MQ=255)
  aaTGTAAATATCTTTCTCAATTCAGCTGTAGAAAATTTGAACCCTGATGACGTTAAACAAACCCTAAAGACAATTAAAGAGTCGAGTATCTTAAAAAAAGGTGAATATTAATTTTATGAATCGAAAGCAATAAAACTatg                                                                                                                          >  2:308363/1‑138 (MQ=255)
         atatCTTTCTCAATTCAGCTGTAGAAAATTTGAACCCTGATGACGTTAAACAAACCCTAAAGACAATTAAAGAGTCGATTATCTTAAAAAACGGTGAATATTCATTTGATGAATCGAAAGCAATAAAACTAGGGCTTgag                                                                                                                   <  1:2312953/140‑1 (MQ=255)
             cTTTCTCAATTCAGCGGTAGAAAATTTCAACCCTGAGGACGGTAAACAAACCCTAAAGACAATTAAAGAGTCGAGTATCTTAAAAAACGGTGGATATTCATTTTATGGATCGAGAGGCATAAAAAGAGGGCGTGTGGAAg                                                                                                               >  1:338662/1‑140 (MQ=255)
              tttCTCAATTCAGCTGTAGAAAATTTGAACCCTGATGACGTTAAACAAACCCTAAAGACAATTAAAGAGTCGATTATCTTAAAAAACGGTGAATATTCATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGa                                                                                                              <  1:670227/140‑1 (MQ=255)
              tttCTCAATTCAGCTGTAGAAAATTTGAACCCTGATGACGTTAAACAAACCCTAAAGACAATTAAAGAGTCGATTATCTTAAAAAACGGTGAATATTCATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGa                                                                                                              <  1:1203619/140‑1 (MQ=255)
               ttCTCAATTCAGCTGTAGAAAATTTGAACCCTGATGACGTTAAACAAACCCTACAGACAATTAAAGAGTCGAGTATCTTAAAAAACCGTTAAAATTAATTTTATGAATCGAAAGCAATAAAACTAGGGGGTGAGAAACAt                                                                                                             >  2:306977/1‑140 (MQ=255)
               ttCTCAATTCAGCTGTAGAAAATTTGAACCCTGATGACGTTAAACAAACCCTAAAGACAATTAAAGAGTCGCTTATCTTAAAAAACGGGGAATAATAATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGAt                                                                                                             >  2:722775/1‑140 (MQ=255)
               ttCTCAATTCAGCTGTAGAAAATTTGAACCCTGATGACGTTAAACAAACCCTAAAGACAATTAAAGAGTCGATTATCTTAAAAAACGGTGAATATTCATTTGCTGAATCGAAAGCCATAAAACGAGGGGGTGTGGAAGAt                                                                                                             >  2:1056204/1‑140 (MQ=255)
               ttCTCAATTCAGCTGTAGAAAATTTGAACCCTGATGACGTTAAACAAACCCTAAAGACAATTAAAGAGTCGATTATCTTAAAAAAAGGTGAAAATTCATTTGATGAATATAAAGAAAAAAAAATAGGGCTTTAGAAatat                                                                                                             >  2:1690130/1‑140 (MQ=255)
                tctcAATTCAGCTGTAGAAAATTTGAACCCTGATGACGTTAAACAAACCCTAAAGACAATTAAAGAGTCGATTATGTTAAAAAAAGGTGAATATTAATTTGATGAATCGAAAGCAATAAAAATAGGGCTTGAGAAAGAtt                                                                                                            >  2:1451930/1‑139 (MQ=255)
                                     tttGAACCCTGATGACGTTAAACAAACCCTAAAGACAATTAAAGAGTCGATTGTGTTAAAAAAAGGTGTATATTCATTTTATGAATCGAAAGCAATAAAAATAGGGCGTGAGAAAGATGTAATTGAGAACCTTAAGAAcc                                                                                       >  2:1482336/1‑140 (MQ=255)
                                               gatgaCGTTAAACAAACCCTAAAGACAATTAAAGAGTCGATTATCTTAAAAAACGGTGAATATTCATTTGATGAATCGAAAGCAATAAAAATAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTaa                                                                             <  2:419352/140‑1 (MQ=255)
                                                       tAAACAAACCCTAAAGACAATTACAGAGTCGATTATCTTAAAAAACGGTGAATATTCATTTGATGAATCGAAAGCAATAACACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTag                                                                     <  2:1100166/140‑1 (MQ=255)
                                                        aaacaaacCCTAAAGACAATTAAAGAGTCGATTATCTTAAAAAAAGGTGAATATTCATTTTATGAAACGAAAGCAATAAAAATAGGGCGTGAGAAAGATTTAATTGATAAACTTAATAACCAAGAAAAAAATGTCTTata                                                                    >  1:1039632/1‑138 (MQ=255)
                                                         aacacacCCTAACCACCATTAAAGAGTCGATTATCTTAAAAAACGGTGAATCTTCATTTGATGAATCGAAAGCCATACAACGAGGGCTTGAGAAAGATGTAATTGATCACGTTAAGAACCTAGAATCTAATGTCTTagag                                                                   <  2:1378135/140‑1 (MQ=255)
                                                         aacaaacCCTAAAGACAATTAAAGACTCGATTATCTTAAAAAACGGTGAATATTCATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTagag                                                                   <  2:1378161/140‑1 (MQ=255)
                                                             aacCCTACAGACAATTAAACAGTCGATTAGCTTAAAAAACCGTGACTATTCATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAATATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTAGAGCAAt                                                               <  1:1779362/140‑1 (MQ=255)
                                                              acCCTAAAGACAATTAAAGAGTCGATTATCTTAAAAAACGGTGAATATTCATTTGATGAATGGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTTATAACCTTAAGAAACAAGAATATAATGTCTTATAGCAAtt                                                              >  2:1672139/1‑140 (MQ=255)
                                                              acCCTAAAGACAATTAAAGAGTCGAGTATCTTAAAAAACGGTGAAAATTCATTTTATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATTTAATTTGTAACGTTAAGAAACTATAATATAATTTGTTAGAGCAAtt                                                              >  2:495708/1‑140 (MQ=255)
                                                                 cgaaaGACAATTAAAGAGTCGATTATCTTAAAAAACGGTGAATATTCATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTAGAGCAATTCTa                                                           <  1:308363/138‑1 (MQ=255)
                                                                 cTAAAGACAATTAAAGAGTCGATTATCTTAAAAAACGGTGAATATTCATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTAGAGCAATTCTa                                                           <  1:2198123/140‑1 (MQ=255)
                                                                   aaaGACAATTAAAGAGTCGATTATCTTAAAAAACGGTGAATATTCATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTAGAGCAATTCTACa                                                         <  1:1601107/140‑1 (MQ=255)
                                                                    aaGACAATTAAAGAGTCGATTATCTTAAAAAACGGTGAATATTCATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTAGAGCAATTCTACaa                                                        <  1:1548569/140‑1 (MQ=255)
                                                                    aaGACAATTAAAGAGTCGATTATCTTAAAAAACGGTGAATAGTCATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTAGAGCAATTCTACaa                                                        <  1:2427858/140‑1 (MQ=255)
                                                                          aTTAAAGAGTCGATTATCTTAAAAAACCGTGAAAATTAATTTGATGAATCGAAAGCAATAAAACTAGGGGGTGAGAAAGATGTAATTGATAACGTTAAGAAACTAGAATCTAATGTCTTATAGCAATTCTAAAAAATTaa                                                  >  2:828828/1‑140 (MQ=255)
                                                                          aTTAAAGAGTCGATTATCTTAAAAAAAGCTGAATAATCAGTTGCTGAATCCAAACCAAAAAAACAAGGGGAGGTGAAAGATGTAATTGTTAACCTTAAGAACCTAGAATCTAATTGATTAGAGCAAATATAAAATCTTaa                                                  >  2:466252/1‑140 (MQ=255)
                                                                           ttAAAGAGTCGAGTATCTTAAAAAACGGTGAATATTCATTTGATGAATAGAAAGCAATAAAACTAGGGCTTGAGTAAGATGTAATTGATAACGTTAAGAACCTAGAATATAATGTCTTAGAGCAATTCTACAATCTTaaa                                                 >  2:1245591/1‑140 (MQ=255)
                                                                                   tCGATTATCTTAAAAAAAGGTGTAAATTAATTTGATTAATCGAAAGCAATAAAACTATGGGTTGAGAAAGATGTAATTTTTAAAGTTAATAAACTAGAATATTATGTATTATAGCAATTATAAAATCTTAAATATAGtta                                         >  1:1736702/1‑138 (MQ=255)
                                                                                     gagtATCATAAAAAAAGGTGAATATTCATTTGATGAATAGAAAGCAATAAAAAGAGGGCTTGAGAAAAATTTAAATTATAACCTTAAGAACCTAGAAACTAATGTCTTAGAGCAAATAAAAAATATTAAAGAAAGTTaaa                                       >  2:2233110/4‑140 (MQ=255)
                                                                                     gATTATCTTAAAAAACGGGTAATATTGCTTTGATGAATAGAAATCAAAAAAAATAGGGCTTGAGAAAGATGTAATTTATAAACTTAAAAAACAAGAATCTAATTTCTTATAGCAATTATAAAAAATTAAATATAGTGaaa                                       >  1:1299213/1‑140 (MQ=255)
                                                                                     gATTATCTTAAAAAACCGTGAATATTAAATTTATGAATCGAAAGCAATAAAACTATGGCTTGAGAAAGATGTTATTGATAACCTTAATAAACTAGAATATAATGTATTAGAGCAATTCTAAAAAATTAAAAATATTTaaa                                       >  1:1299063/1‑140 (MQ=255)
                                                                                           cTTAAAAAACGGTGAAAATTAATTTTATTAATCGAAAGCAAGAAAAATAGGGCGTGAGAAAGATGTAATTGATAACGTTAATAAACTAGAATATAATGTGTTAGAGCAAATATACAATCTTAAAGATAGTTAAATTTaaa                                 >  2:745848/1‑140 (MQ=255)
                                                                                             tAAAAAACGGTGAATATTCATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTATAATCTAATGTCTTAGAGCAATTCTACAATCTTAAAGATAGTGAAATTGAAACa                               >  1:1090681/1‑140 (MQ=255)
                                                                                             tAAAAAACGGTGAATATTCATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTCATGTCTTAGAGCAATTCTACAATCTTACAGATAGTGAAATTGAAACa                               >  2:1962854/1‑140 (MQ=255)
                                                                                             tAAAAAACGGTGAATATTCATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTAGAGCAATTCTACAATCTTAAAGATAGTGAAATTGAAACa                               >  1:1268323/1‑140 (MQ=255)
                                                                                             tAAAAAACGGTGAATATTCATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTAGAGCAATTCTACAATCTTAAAGATAGTGAAATTGAAACa                               >  2:442435/1‑140 (MQ=255)
                                                                                               aaaaaCGGTGAATATTCATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTAGAGCAATTCTACAATCTTAAAGATAGTGAAATTGAAACAgg                             >  2:2196239/1‑140 (MQ=255)
                                                                                                 aaaCGGTGAATATTCATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTAGAGCAATTCTACAATCTTAAAGATAGTGAAATTGAAACAGGCt                           <  2:1296552/140‑1 (MQ=255)
                                                                                                 aaaCGGTGAATATTCATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTAGAGCAATTCTACAATCTTAAAGATAGTGAAATTGAAACAGGCt                           <  1:1034314/140‑1 (MQ=255)
                                                                                                 aaaCGGTGAATATTCATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTAGAGCAATTCTACAATCTTAAAGATAGTGAAATTGAAACAGGCt                           <  2:421081/140‑1 (MQ=255)
                                                                                                 aaaCGGTGAATATTCATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTAGAGCAATTCTACAATCTTAAAGATAGTGAAATTGAAACAGGCt                           <  2:203304/140‑1 (MQ=255)
                                                                                                    ctgTGAATATTCATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTAGAGCAATTCTACAATCTTAAAGATAGTGAAATTGAAACAGGCTCag                        <  2:1424848/138‑1 (MQ=255)
                                                                                                    cGGTGAATATTCATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTAGAGCAATTCTACAATCTTAAAGATAGTGAAATTGAAACAGGCTCag                        <  2:1942027/140‑1 (MQ=255)
                                                                                                               cATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTAGAGCAATTCTACAATCTTAAAGATAGTGAAATTGAAACAGGCTCAGAGCAATTACaa             >  2:717399/1‑140 (MQ=255)
                                                                                                                 tttGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTAGAGCAATTCTACAATCTTAAAGATAGTGAAATTGAAACAGGCTCAGAGCAATTACAAgg           <  2:1039632/140‑1 (MQ=255)
                                                                                                                 tttGAAGAATCGAAAGCAATAAAAATAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAAAATAGAATCTAATTTCTTAGATAAATTCTACAATCTTAAATATAGTGAAATTTAAACAGGCTCAGAGCAATTACAAgg           <  1:745848/140‑1 (MQ=255)
                                                                                                                      tgaATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTATAGCAATTCTAAAATCTTAAAGATAGTGAAATTGAAACAGGCTCAGAGCAATTACAAGGAGAtt      >  1:766644/1‑140 (MQ=255)
                                                                                                                      tgaATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTAGAGCAATTCTACAATCTTAAAGATAGTGAAATTGAAACAGGATCAGAGCAATTACAAGGAGAtt      >  1:1389440/1‑140 (MQ=255)
                                                                                                                          tCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTAGAGCAATTCTACAATCTTAAAGATAGTTAAATTTAAACAGGCTCAGAGCAATTACAAGGAGATTTTat  >  2:539819/1‑139 (MQ=255)
                                                                                                                                         |                                                                                                                            
CGAATGTAAATATCTTTCTCAATTCAGCTGTAGAAAATTTGAACCCTGATGACGTTAAACAAACCCTAAAGACAATTAAAGAGTCGATTATCTTAAAAAACGGTGAATATTCATTTGATGAATCGAAAGCAATAAAACTAGGGCTTGAGAAAGATGTAATTGATAACGTTAAGAACCTAGAATCTAATGTCTTAGAGCAATTCTACAATCTTAAAGATAGTGAAATTGAAACAGGCTCAGAGCAATTACAAGGAGATTTTAG  >  NZ_CP034943/1968045‑1968306

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑