Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,502,143 A→T 9.5% N163Y (AAT→TAT)  PP_5568 → membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,502,1430AT 9.5% 122.6 / 5.2 42N163Y (AAT→TAT) PP_5568membrane protein
Reads supporting (aligned to +/- strand):  ref base A (19/19);  new base T (2/2);  total (21/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.86e-01

CCTATGGGCATCGAAGCAAGGCGAGTTCATTCCTGTTACGCGGTGAGCGGGTAGAAGTATTCGAACCCGAGCAGGCCAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGTCTTCTATAATCGCACCAATATCGCTTCGTTAAGGGCGTTAAAAGAACGCGAGCGTCGTGAGGCGCGTCAATACACATTTCTTGAGATCGAATAT  >  NC_002947/3501997‑3502292
                                                                                                                                                  |                                                                                                                                                     
ccTATGGGCATCGAAGCAAGGCGAGTTCATTCCTGTTACGCGGTGAGCGGGTAGAAGTATTCGAACCCGAGCAGGCCAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTataata                                                                                                                                                    <  1:20292/150‑1 (MQ=255)
 cTATGGGCATCGAAGCAAGGCGAGTTCATTCCTGTTACGCGGTGAGCGGGTAGAAGTATTCGAACCCGAGCAGGCCAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAg                                                                                                                                                   >  2:48236/1‑150 (MQ=255)
         aTCGAAGCAAGGCGAGTTCATTCCTGTTACGCGGTGAGCGGGTAGAAGTATTCGAACCCGAGCAGGCCAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATgg                                                                                                                                           >  1:996992/1‑150 (MQ=255)
              aGCAAGGCGAGTTCATTCCTGTTACGCGGTGAGCGGGTAGAAGTATTCGAACCCGAGCAGGCCAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCgtg                                                                                                                                      <  1:739819/150‑1 (MQ=255)
                cAAGGCGAGTTCATTCCTGTTACGCGGTGAGCGGGTAGAAGTATTCGAACCCGAGCAGGCCAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCgtggt                                                                                                                                    <  2:421619/150‑1 (MQ=255)
                            aTTCCTGTTACGCGGTGAGCGGGTAGAAGTATTCGAACCCGAGCAGGCCAATTCGTGGGTTGTGGGCGGGCTTGGTACAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATTATAGTTCtttatc                                                                                                                                          >  2:206382/1‑127 (MQ=255)
                            aTTCCTGTTACGCGGTGAGCGGGTAGAAGTATTCGAACCCGAGCAGGCCAATTCGTGGGTTGTGGGCGGGCTTGGTACAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATTATAGTTCtttatc                                                                                                                                          <  1:206382/132‑6 (MQ=255)
                                cTGTTACGCGGTGAGCGGGTAGAAGTATTCGAACCCGAGCAGGCCAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGCGATGGtt                                                                                                                    >  1:588226/1‑150 (MQ=255)
                                          gTGAGCGGGTAGAAGTATTCGAACCCGAGCAGGCCAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGc                                                                                                          <  2:892609/150‑1 (MQ=255)
                                                 ggTAGAAGTATTCGAACCCGAGCAGGCCAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTAttt                                                                                                   <  1:48236/150‑1 (MQ=255)
                                                 gatAGAAGTATTCGAACCCGAGCAGGCCAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACAATAATAGTTCTATGGCCGTGTTGCTGTGTGTGCTGGTGTGTTGTTGGCTGTAttt                                                                                                   <  2:595840/148‑1 (MQ=255)
                                                  gTAGAAGTATTCGAACCCGAGCAGGCCAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTg                                                                                                  <  1:775260/150‑1 (MQ=255)
                                                  gTAGAAGTATTCGAACCCGAGCAGGCCAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGCGATGGTTTTCATTTCGCTGTATTTg                                                                                                  <  2:588226/150‑1 (MQ=255)
                                                       aGTATTCGAACCCGAGCAGGCCAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGtctt                                                                                             <  1:396597/150‑1 (MQ=255)
                                                       aGTATTCGAACCCGAGCAGGCCAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGtctt                                                                                             >  2:101128/1‑150 (MQ=255)
                                                           ttCGAACCCGAGCAGGCCAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGTCTTCtat                                                                                         >  1:1026406/1‑150 (MQ=255)
                                                              gAACCCGAGCAGGCCAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGTCTTCTATAAt                                                                                      >  2:885829/1‑150 (MQ=255)
                                                               aaCCCGAGCAGGCCAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGTCTTCTATAATc                                                                                     >  2:1091848/1‑150 (MQ=255)
                                                                 cccGAGCAGGCCAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGc                                                                                                          >  1:856408/1‑127 (MQ=255)
                                                                 cccGAGCAGGCCAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGc                                                                                                          <  2:856408/127‑1 (MQ=255)
                                                                          gCCAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGTCTTCTATAATCGCACCAATATc                                                                          >  1:789073/1‑150 (MQ=255)
                                                                          gCCAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGTCTTCTATAATCGCACCAATATc                                                                          >  2:873164/1‑150 (MQ=255)
                                                                            cAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGttt                                                                                                                   >  1:1040363/1‑107 (MQ=255)
                                                                            cAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGttt                                                                                                                   <  2:1040363/107‑1 (MQ=255)
                                                                                  gTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGTCTTCTATAAt                                                                                      >  1:961166/1‑130 (MQ=255)
                                                                                  gTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGTCTTCTATAAt                                                                                      <  2:961166/130‑1 (MQ=255)
                                                                                       ttGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGTCTTCTATAATCGCACCAATATCGCTTCGTTAAggg                                                             <  2:996992/150‑1 (MQ=255)
                                                                                            ggcgggcTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGTCTTCTATAATCGCACCAATATCGCTTCGTTAAGGGCGTTa                                                        >  1:603291/1‑150 (MQ=255)
                                                                                                  cTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGTCTTCTATAATCGCACCAATATCGCTTCGTTAAGGGCGTTAAAAGaa                                                  <  1:885829/150‑1 (MQ=255)
                                                                                                       tGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCtgt                                                                                                                               <  1:1019041/68‑1 (MQ=255)
                                                                                                       tGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCtgt                                                                                                                               >  2:1019041/1‑68 (MQ=255)
                                                                                                       tGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGTCTTCTATAATCGCACCAATATCGCTTCGTTAAGGGCGTTAAAAGAACGCGa                                             <  1:101128/150‑1 (MQ=255)
                                                                                                            ggTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGtcttc                                                                                            <  2:244161/98‑1 (MQ=255)
                                                                                                            ggTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGtcttc                                                                                            >  1:244161/1‑98 (MQ=255)
                                                                                                            ggTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGTCTTCTATAATCGCACCAATATCGCTTCGTTAAGGGCGTTAAAAGAACGCGAGcgtc                                        >  2:178063/1‑150 (MQ=255)
                                                                                                              ttGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTg                                                                                                  <  1:820319/90‑1 (MQ=255)
                                                                                                              ttGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTg                                                                                                  >  2:820319/1‑90 (MQ=255)
                                                                                                                gAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGTCTTCTATAATCGCACCAATATCGCTTCGTTAAGGGCGTTAAAAGAACGCGAGCGTCGTGa                                    <  1:1091848/150‑1 (MQ=255)
                                                                                                                        tgctgTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGTCTTCTATAATCGCACCAATATCGCTTCGTTAAGGGCGTTAAAAGAACGCGAGCGTCGTGAGGCGCGTc                            >  1:1143566/1‑150 (MQ=255)
                                                                                                                           tgTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGTCTTCTATAATCGCACCAATATCGCTTCGTTAAGGGCGTTAAAAGAACGCGAGCGTCGTGAGGCGCGTCAAt                         >  2:448444/1‑150 (MQ=255)
                                                                                                                                      ccataGAACTATTATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGTCTTCTATAATCGCACCAATATCGCTTCGTTAAGGGCGTTaaaa                                                     <  2:509041/107‑1 (MQ=255)
                                                                                                                                      ccataGAACTATTATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGTCTTCTATAATCGCACCAATATCGCTTCGTTAAGGGCGTTaaaa                                                     >  1:509041/5‑111 (MQ=255)
                                                                                                                                      aTAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGTCTTCTATAATCGCACCAATATCGCTTCGTTAAGGGCGTTAAAAGAACGCGAGCGTCGTGAGGCGCGTCAATACACATTTCtt              <  2:1026406/150‑1 (MQ=255)
                                                                                                                                                  aataGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGTCTTCTATAATCGCACCAATATCGCTTCGTTAAGGGCGTTAAAAGAACGCGAGCGTCGTGAGGCGCGTCAATACACATTTCTTGAGATCGAatat  <  2:789073/150‑1 (MQ=255)
                                                                                                                                                  |                                                                                                                                                     
CCTATGGGCATCGAAGCAAGGCGAGTTCATTCCTGTTACGCGGTGAGCGGGTAGAAGTATTCGAACCCGAGCAGGCCAATTCGTGGGTTGTGGGCGGGCTTGGTGCAGGGTTGAGTAGTCTGCTGTATCCGACGATAAAGAACTATAATAGTTCTATGGCCGTGGTGCTGTGTGTGATGGTTTTCATTTCGCTGTATTTGGTCTTCTATAATCGCACCAATATCGCTTCGTTAAGGGCGTTAAAAGAACGCGAGCGTCGTGAGGCGCGTCAATACACATTTCTTGAGATCGAATAT  >  NC_002947/3501997‑3502292

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑