Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,376,387 G→A 8.0% A77T (GCC→ACC)  PP_2975 → insertion element ISR1 protein A3

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,376,3870GA 8.0% 138.2 / 2.8 50A77T (GCC→ACC) PP_2975insertion element ISR1 protein A3
Reads supporting (aligned to +/- strand):  ref base G (26/20);  new base A (2/2);  total (28/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.00e-01

CGCGAGCATGGCATCAGTTCGGCGACCTTCTACAAGTGGCGTGCCAAGTTCGGCGGCATGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCC  >  NC_002947/3376243‑3376530
                                                                                                                                                |                                                                                                                                               
cgcgAGCATGGCATCAGTTCGGCGACCTTCTACAAGTGGCGTGCCAAGTTCGGCGGCATGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCga                                                                                                                                             <  2:27188/149‑1 (MQ=255)
 gcgAGCATGGCATCAGTTCGGCGACCTTCTACAAGTGGCGTGCCAAGTTCGGCGGCATGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCgag                                                                                                                                            <  6:357267/149‑1 (MQ=255)
  cgAGCATGGCATCAGTTCGGCGACCTTCTACAAGTGGCGTGCCAAGTTCGGCGGCATGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGcc                                                                                                                                               >  6:62038/1‑145 (MQ=255)
        tGGCATCAGTTCGGCGACCTTCTACAAGTGACGTGCCAAGTTCGGCGGCATGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATcc                                                                                                                                     <  1:19115/149‑1 (MQ=255)
            aTCAGTTCGGCGACCTTCTACAAGTGGCGTGCCAAGTTCGGCGGCATGGATGCATCATTGATGACAAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCCCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCag                                                                                                                                   >  5:239312/1‑147 (MQ=255)
                gTTCGGCGACCTTCTACAAGTGGCGTGCCAAGTTCGGCGGCATGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGc                                                                                                                              >  5:956/1‑148 (MQ=255)
                    ggCGACCTTCTACAAGTGGCGTGCCAAGTTCGGCTGCATGGATGCATCATTGATTACCAGGCTGCATGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACTCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATg                                                                                                                          <  6:300311/148‑1 (MQ=255)
                              tACAAGTGGCGTGCCAAGTTCGGCGGCATGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGatcatc                                                                                                                                      <  6:275963/126‑1 (MQ=255)
                              tACAAGTGGCGTGCCAAGTTCGGCGGCATGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGatcatc                                                                                                                                      >  5:275963/1‑126 (MQ=255)
                               aCAAGTGGCGTGCCAAGTTCGGCGGCATGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGtt                                                                                                               >  1:309212/1‑147 (MQ=255)
                               aCAAGTGGCGTGCCAAGTTCGGCGGCAGGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTgg                                                                                                              >  1:198615/1‑149 (MQ=255)
                                cAAGTGGCGTGCCAAGTTCGGCGGCATGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGt                                                                                                                <  7:108504/146‑1 (MQ=255)
                                cAAGTGGCGTGCCAAGTTCGGCGGCATGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTgg                                                                                                              <  6:956/148‑1 (MQ=255)
                                 aaGTGGCGTGCCAAGTTCGGCGGCATGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGt                                                                                                             >  6:340882/1‑148 (MQ=255)
                                   gTGGCGTGCCAAGTTCGGCGGCATGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTaaa                                                                                                          <  2:198615/149‑1 (MQ=255)
                                           ccAAGTTCGGCGGCATGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCAtct                                                                                                   <  5:62038/148‑1 (MQ=255)
                                                                 atcatTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGTTGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCga                                                                                        >  1:281358/1‑137 (MQ=255)
                                                                 atcatTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCga                                                                                        <  2:281358/137‑1 (MQ=255)
                                                                 atcatTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCgcag                                                                              >  7:118780/1‑147 (MQ=255)
                                                                       gatgaCCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTg                                                                                                               <  5:30662/108‑1 (MQ=255)
                                                                       gatgaCCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTg                                                                                                               >  6:30662/1‑108 (MQ=255)
                                                                         tgaCCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGgttc                                                                    <  6:345554/149‑1 (MQ=255)
                                                                              aGGCTGCGTGAACTGGAAGAGGAGAAGCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGgttcgtt                                                                 >  1:5226/1‑147 (MQ=255)
                                                                                             gAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTAt                                                 >  5:200520/1‑148 (MQ=255)
                                                                                                   gagaACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCa                                                               <  6:123217/128‑1 (MQ=255)
                                                                                                   gagaACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCa                                                               >  5:123217/1‑128 (MQ=255)
                                                                                                   gagaACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAAt                                            >  2:360325/1‑147 (MQ=255)
                                                                                                     gaACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGc                                        <  2:309212/149‑1 (MQ=255)
                                                                                                          gTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGcc                                   >  6:217386/1‑149 (MQ=255)
                                                                                                                 cAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGtt                            <  6:239312/149‑1 (MQ=255)
                                                                                                                  aagaagATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGttt                           <  1:360325/149‑1 (MQ=255)
                                                                                                                   agaagaTGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTg                          >  4:293100/1‑149 (MQ=255)
                                                                                                                    gaagaTGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTgg                         >  3:104496/1‑149 (MQ=255)
                                                                                                                    gaagaTGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTgg                         >  8:305676/1‑149 (MQ=255)
                                                                                                                    gaagaTGTACGCCGAGGAGCGCCTCAAGACCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTgg                         >  8:337172/1‑149 (MQ=255)
                                                                                                                    gaagaTGTACGCCGAGGAGCGCCTCAAGACCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTgg                         >  2:137519/1‑149 (MQ=255)
                                                                                                                      agaTGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGt                        <  5:217386/148‑1 (MQ=255)
                                                                                                                      agaTGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGt                        <  8:118780/148‑1 (MQ=255)
                                                                                                                         tGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTAt                      >  5:59641/1‑147 (MQ=255)
                                                                                                                         tGTACGCCGAGGAGCGCCTCAAGACCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCa                    <  7:337172/149‑1 (MQ=255)
                                                                                                                         tGTACGCCGAGGAGCGCCTCAAGACCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCa                    <  1:137519/149‑1 (MQ=255)
                                                                                                                          gTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAg                   >  6:10075/1‑149 (MQ=255)
                                                                                                                          gTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAg                   >  2:274129/1‑149 (MQ=255)
                                                                                                                                         ccTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGcc    >  5:98782/1‑149 (MQ=255)
                                                                                                                                          cTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAg                                                              >  2:364126/1‑90 (MQ=255)
                                                                                                                                          cTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAg                                                              <  1:364126/90‑1 (MQ=255)
                                                                                                                                          cTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGccc   >  6:150749/1‑149 (MQ=255)
                                                                                                                                           tCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGAc             >  2:138882/1‑138 (MQ=255)
                                                                                                                                           tCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGAc             <  1:138882/138‑1 (MQ=255)
                                                                                                                                           tCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGcccc  >  6:326184/1‑149 (MQ=255)
                                                                                                                                                |                                                                                                                                               
CGCGAGCATGGCATCAGTTCGGCGACCTTCTACAAGTGGCGTGCCAAGTTCGGCGGCATGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGCGAGATGGCGCAGCAGGCGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCC  >  NC_002947/3376243‑3376530

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑