Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,006,814 C→A 8.9% L1056I (CTC→ATC)  PP_4410 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,006,8140CA 8.9% 131.2 / 3.5 45L1056I (CTC→ATC) PP_4410hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (18/22);  new base A (2/2);  total (20/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.93e-01

CACCTATCCAGACTCCATGTCGAGGGAGTTTGAGTACAAGATTGATCGTGC‑AACTCGCCTCCTCATGATTAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAGGCTGGGAGCAAGCATTACTCACTTATAAGCCGACCAAGTCGACGTCTGATGGCTCGCCCTAAATTCAAAATCCAG  >  NC_002947/5006672‑5006961
                                                                                                                                               |                                                                                                                                                   
cACCTATCCAGACTCCATGTCGAGGGAGTTTGAGTACAAGATTGATCGTGC‑AACTCGCCTCCTCATGATTAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGa                                                                                                                                                <  6:49491/148‑1 (MQ=255)
   cTATCCAGACTCCATGTCGAGGGAGTTTGAGTACAAGATTGATCGTGC‑AACTCGCCTCCTCATGATTAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGatcat                                                                                                                                            >  4:295151/1‑149 (MQ=255)
     aTCCAGACTCCATGTCGAGGGAGTTTGAGTACAAGATTGATCGTGC‑AACTCGCCTCCTCATGATTAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATcc                                                                                                                                          <  8:152018/149‑1 (MQ=255)
        cAGACTCCATGTCGAGGGAGTTTGAGTACAAGATTGATCGTGC‑AACTCGCCTCCTCATGATTAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCt                                                                                                                                        >  8:143351/1‑148 (MQ=255)
            cTCCATTTCGAGGGAGTTTGAGTTCAATATTGATCGTGCTAACTCGCCTCCTCATGATTAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGATCGGAGCATCCCtacaa                                                                                                                                    <  1:272069/149‑5 (MQ=255)
                aTGTCGAGGGAGTTTGAGTACAAGATTGATCGTGC‑AACTCGCCTCCTCATGATTAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTg                                                                                                                                >  8:125037/1‑148 (MQ=255)
                aTGTCGAGGGAGTTTGAGTACAAGATTGATCGTGC‑AACTCGCCTCCTCATGATTAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGa                                                                                                                               <  7:91947/149‑1 (MQ=255)
                aTGTCGAGGGAGTTTGAGTACAAGATTGATCGTGC‑AACTCGCCTCCTCATGATTAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGa                                                                                                                               >  7:220875/1‑149 (MQ=255)
                aTGTCGAGGGAGTTTGAGTACAAGATTGATCGTGC‑AACTCGCCTCCTCATGATTAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGa                                                                                                                               <  8:220875/149‑1 (MQ=255)
                       gggAGTTTGAGTACAAGATTGATCGTGC‑AACTCGCCTCCTCATGATTAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGAc                                                                                                                              >  5:157419/1‑143 (MQ=255)
                        ggAGTTTGAGTACAAGATTGATCGTGC‑AACTCGCCTCCTCATGATTAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATc                                                                                                                        >  6:320254/1‑148 (MQ=255)
                          aGTTTGAGTACAAGATTGATCGTGC‑AACTCGCCTCCTCATGATTAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGAc                                                                                                                     <  4:296234/149‑1 (MQ=255)
                              tGAGTACAAGATTGATCTTGC‑AACTCGCCTCCTCATGATAAACGACGGAAATACGCTTGGCGCAGCACTTATGCCATCAAATTTCCCTAGCGCATTAAAACTAGTAGGGATGCTCCCATCATCCCTGAACTTTGACAAGATCGACAtt                                                                                                                  <  1:200544/148‑1 (MQ=255)
                              tGAGTACAAGATTGATCGTGC‑AACTCGCCTCCTCATGATTAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGACAtt                                                                                                                  <  7:125037/148‑1 (MQ=255)
                                aGTACAAGATTGATCGTGC‑AACTCGCCTCCTCATGATTAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAAGTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTaa                                                                                                                <  1:248560/148‑1 (MQ=255)
                                      aGATTGATCGTGC‑AACTCGCCTCCTCATGATTAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGATCGGAGCATCCCtacaagt                                                                                                                                  <  7:267136/124‑7 (MQ=255)
                                      aGATTGATCGTGC‑AACTCGCCTCCTCATGATTAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGATCGGAGCATCCCtacaagt                                                                                                                                  >  8:267136/1‑118 (MQ=255)
                                           gATCGTGC‑AACTCGCCTCCTCATGATTAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTcc                                                                                                     <  3:186030/148‑1 (MQ=255)
                                            aTCGTGC‑AACTCGCCTCCTCATGATTAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCa                                                                                                    <  7:143351/148‑1 (MQ=255)
                                                    aaCTCGCCTCCTCATGATTAACGACGGAAATACGCTTGGCGCCGCACTTATGCGATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTACGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCa                                                                                            <  2:84658/149‑1 (MQ=255)
                                                         tcctgctCATGATTAAAGACGGAAATAGGCTTGGCTCCGGACTTATGCGATCAAATTTGGCTCGCGCATTCTAACTTGTAGGGATGGTCCGTTCATCGCTGAACTTTGACAAGATCGAGATTATTGTTTTTGTCGACCTTCTCAAtctc                                                                                       <  6:145397/148‑1 (MQ=255)
                                                                   gATTAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAg                                                                             >  6:69510/1‑149 (MQ=255)
                                                                   gATTAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAg                                                                             >  7:116239/1‑149 (MQ=255)
                                                                    aTTAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAg                                                                             <  8:116239/148‑1 (MQ=255)
                                                                      tAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAGGCt                                                                          >  8:134665/1‑149 (MQ=255)
                                                                          gacgGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAGGCTgg                                                                        >  1:44247/1‑147 (MQ=255)
                                                                              gAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCAACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAGGCTGGGagcaa                                                                  <  1:96246/149‑1 (MQ=255)
                                                                                aaTACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAGGCTGGGagcaagc                                                                <  2:44247/149‑1 (MQ=255)
                                                                                  tACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCTCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAGGCTGGGAGCAAGCAt                                                              <  5:69510/149‑1 (MQ=255)
                                                                                     gCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAGGCTGGGAGCAAGCATTAc                                                           >  3:301225/1‑149 (MQ=255)
                                                                                            gccgcACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTcgac                                                                                    <  6:57101/117‑1 (MQ=255)
                                                                                                         cATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAGGCTGGGAGCAAGCATTACTCACTTATAAGCCGACCAAg                                       >  2:291606/1‑149 (MQ=255)
                                                                                                          aTCAAATTTCCCTAGCTCATTCAAACTTGTAGGGATGCTACGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGCCGATAAAGGCTGGGAGCAAGCATTACTCACTTATAAGCCGACCAAGt                                      <  1:72921/149‑1 (MQ=255)
                                                                                                          aTCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAACATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAGGCTGGGAGCAAGCATTACTCACTTATAAGCCGACCAAGt                                      >  8:70934/1‑149 (MQ=255)
                                                                                                           tCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAGGCTGGGAGCAAGCATTACTCACTTATAAGCCGACCAAGTc                                     >  4:280836/1‑149 (MQ=255)
                                                                                                              aaTTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAGGCTGGGAGCAAGCATTACTCACTTATAAGCCGACCAAGTCGAc                                  <  3:295151/149‑1 (MQ=255)
                                                                                                                      tAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAGGCTGGGAGCAAGCATTACTCACTTATAAGCCGACCAAGTCGACGTCTGATg                          >  2:104596/1‑149 (MQ=255)
                                                                                                                       aGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAGGCTGGGAGCAAGCATTACTCACTTATAAGCCGACCAAGTCGACGTCTGATgg                         >  1:77020/1‑149 (MQ=255)
                                                                                                                          gcATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGCCAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAGGCTGGGAGCAAGCATTACTCACTTATAAGCCGACCAAGTCGACGTCTGATGGCTc                      >  8:242510/1‑149 (MQ=255)
                                                                                                                           cATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAGGCTGGGAGCAAGCATTACTCACTTATAAGCCGACCAAGTCGACGTCTGATGGCTCg                     <  6:157419/149‑1 (MQ=255)
                                                                                                                             ttCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAGGCTGGGAGCAAGCATTACTCACTTATAAGCCGACCAAGTCGACGTCTGATGGCTCGcc                   <  5:320254/149‑1 (MQ=255)
                                                                                                                             ttCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAGGCTGGGAGCAAGCATTACTCACTTATAAGCCGACCAAGTCGACGTCTGATGGCTCGcc                   <  1:104596/149‑1 (MQ=255)
                                                                                                                                        aGGGATGATCGGAGCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAGGCTGGGAGCAAGCATTACTCACTTATAAGCCGACCAAGTCGACGTCTGATGGCTCGCCCTAAATTCaa         >  4:184473/1‑148 (MQ=255)
                                                                                                                                           gATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAGGCTGGGAGCAAGCATTACTCACTTATAAGCCGACCAAGTCGACGTCTGATGGCTCGCCCTaaa              >  4:5612/1‑140 (MQ=255)
                                                                                                                                           gATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAGGCTGGGAGCAAGCATTACTCACTTATAAGCCGACCAAGTCGACGTCTGATGGCTCGCCCTaaa              <  3:5612/140‑1 (MQ=255)
                                                                                                                                               cTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAGGCTGGGAGCAAGCATTACTCACTTATAAGCCGACCAAGTCGACGTCTGATGGCTCGCCCTAAATTCAAAATCCAg  <  7:144603/148‑1 (MQ=255)
                                                                                                                                               cTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAGGCTGGGAGCAAGCATTACTCACTTATAAGCCGACCAAGTCGACGTCTGATGGCTCGCCCTAAATTCAAAATCCAg  >  1:146645/1‑148 (MQ=255)
                                                                                                                                               |                                                                                                                                                   
CACCTATCCAGACTCCATGTCGAGGGAGTTTGAGTACAAGATTGATCGTGC‑AACTCGCCTCCTCATGATTAACGACGGAAATACGCTTGGCGCCGCACTTATGCCATCAAATTTCCCTAGCGCATTCAAACTTGTAGGGATGCTCCGATCATCCCTGAACTTTGACAAGATCGACATTAAGGATTTTGTCCACCTTCTCAATCTCGACGATAAAGGCTGGGAGCAAGCATTACTCACTTATAAGCCGACCAAGTCGACGTCTGATGGCTCGCCCTAAATTCAAAATCCAG  >  NC_002947/5006672‑5006961

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: ‑