Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,540,323 G→T 9.7% S221S (TCC→TCA)  PP_4872 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,540,3230GT 9.7% 129.3 / 2.3 45S221S (TCC→TCA) PP_4872hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (21/19);  new base T (2/3);  total (23/22)
Fisher's exact test for biased strand distribution p-value = 6.65e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGTTGATGATCTTGTCAACGCGCCCCGGGCGGTCGATACGGGTGGAGTCGATCTCGTACCAGCCCTGCGGGGTATCGCGGCGCACGAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCTTGTCCTGCCAGTAGTCGTAGTGGGCGATGCGGCGCAGCGAAGCCTCGAT  >  NC_002947/5540190‑5540466
                                                                                                                                     |                                                                                                                                               
ggTTGATGATCTTGTCAACGCGCCCCGGGCGGTCGATACGGGTGGAGTCGATCTCGTACCAGCCCTGCGGGGTATCGCGGCGCACGAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGc                                                                                                                                   >  8:29741/1‑148 (MQ=255)
        atCTTGTCAACGCGCCCCGGGCGGTCGATACGGGTGGAGTCGATCTCGTACCAGCCCTGCGGGGTATCGCGGCGCACGAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCAATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGac                                                                                                                          >  2:254819/1‑149 (MQ=255)
            tGTCAACGCGCCCCGGGCGGTCGATACGGGTGGAGTCGATCTCGTACCAGCCCTGCGGGGTATCGCGGCGCACGAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCGCTCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGcccacc                                                                                                                      >  1:303641/1‑149 (MQ=255)
             gTCAACGCGCCCCGGGCGGTCGATACGGGTGGAGTCGATCTCGTACCAGCCCTGCGGGGTATCGCGGCGCACGAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCg                                                                                                                     >  1:172047/1‑149 (MQ=255)
                        ccGGGCGGTCGATACGGGTGGAGTCGATCTCGTACCAGCCCTGCGGGGTATCGCGGCGAACGAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCg                                                                                                          >  4:279615/1‑149 (MQ=255)
                        ccGGGCGGTCGATACGGGTGGAGTCGATCTCGTACAAGCCATGCCGGGTATCGCGGCGCACGAAGGCGGTGCCGCGCACGTCGGTCAAGGTCTCGATCTTCTCCCCGTAGGACACGCGCTGGGCCACCTAGACCACCGCACGCtcgtcg                                                                                                          >  4:226525/1‑149 (MQ=255)
                                          tGGAGTCGATCTCGTACCAGCCCTGCGGGGTATCGCGGCGCACGAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATg                                                                                        <  1:40643/149‑1 (MQ=255)
                                                 gATCTCGTACCAGCCCTGCGGGGTATCGCGGCGCACGAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGgcgc                                                                                 >  3:270112/1‑149 (MQ=255)
                                                   tctcGTACCAGCCCTGCGGGGTATCGCGGCGCACGAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTg                                                                               >  7:68024/1‑149 (MQ=255)
                                                       gTACCAGCCCTGCGGGGTATCGCGGCGCACGAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTg                                                                               <  4:270112/145‑1 (MQ=255)
                                                         aCCAGCCCTGCGGGGTATCGCGGCGCACGAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATc                                                                          >  2:286141/1‑148 (MQ=255)
                                                            aGCCCTGCGGGGTATCGCGGCGCACGAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTTGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGAt                                                                       >  7:170363/1‑148 (MQ=255)
                                                             gCCCTGCGGGGTATCGCGGCGCACGAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCAATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCa                                                                     <  1:254819/149‑1 (MQ=255)
                                                                cTGCGGGGTATCGCGGCGCACGAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGCCCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGa                                                                  >  5:169925/1‑149 (MQ=255)
                                                                cTGCGGGGTATCGCGGCGCACGAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGa                                                                  >  7:152531/1‑149 (MQ=255)
                                                                cTGCGGGGTATCGCGGCGCACGAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGa                                                                  >  4:136428/1‑149 (MQ=255)
                                                                   cGGGGTATCGCGGCGCACGAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATc                                                                <  7:29741/148‑1 (MQ=255)
                                                                   cGGGGTATCGCGGCGCACGAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCg                                                               <  3:136428/149‑1 (MQ=255)
                                                                    ggggTATCGCGGCGCACGAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGgcg                                                                                  >  6:962/1‑129 (MQ=255)
                                                                       gTATCGCGGCGCACGAAGGCGGTGCCGCGCTCGTCGGTGATGGTCTCGATCTTCTCCCCGTTGTACAGGCGCTGGGCCACCTCGACCACCGCAGTCTCGGCGTTGCCGAACAGCAGGATGTCGGCTCTGGCATCGATCAGGATCGAGTg                                                           <  2:2551/149‑1 (MQ=255)
                                                                        tATCGCGGCGCACGTAGGCGGTGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTTGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGa                                                          >  4:163812/1‑149 (MQ=255)
                                                                                cgcACGAAGGCGGTGGCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTTGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCtt                                                  <  6:254442/149‑1 (MQ=255)
                                                                                 gcACGAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCTTg                                                 <  8:68024/149‑1 (MQ=255)
                                                                                  cACGAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGCGCCCCCTCGACCACCGCACGCTCGGCGTTGCCGAACACCAGCAGGTCGGCCCTGGCATCGATCAGGATCGAGTGCCGAAcaatgt                                                >  5:236246/1‑144 (MQ=255)
                                                                                   aCGAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCTTGTc                                               >  6:162703/1‑149 (MQ=255)
                                                                                     gAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCTTGTCCt                                             >  1:201392/1‑149 (MQ=255)
                                                                                            gTGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTTGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCTTGTCCTGCCaata                                      <  3:163812/149‑1 (MQ=255)
                                                                                             tGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCTTGTCCTGCCagtag                                     <  3:279615/149‑1 (MQ=255)
                                                                                               ccGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCTATCAGGATCGAGTGACGAACCTTGTCCTGCCAGTAGTc                                   <  6:169925/149‑1 (MQ=255)
                                                                                                 gcgcACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCTTGTCCTGCCagtag                                     <  1:185494/145‑1 (MQ=255)
                                                                                                 gcgcACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCTTGTCCTGCCagtag                                     >  2:185494/1‑145 (MQ=255)
                                                                                                  cgcACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCTTGTCCTGCCAGTAGTCGTa                                <  2:172047/149‑1 (MQ=255)
                                                                                                     aCGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCTTGTCCTGCCAGTAGTCGTAGTg                             >  4:59851/1‑149 (MQ=255)
                                                                                                      cGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCTTGTCCTGCCAGTAGTCGTAGTgg                            <  3:59851/149‑1 (MQ=255)
                                                                                                       gTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCTTGTCCTGCCAGTAGTCg                                  <  1:204117/142‑1 (MQ=255)
                                                                                                       gTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCTTGTCCTGCCAGTAGTCg                                  >  2:204117/1‑142 (MQ=255)
                                                                                                          ggTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCTTGTCCTGCCAGTAGTCGTAGTGGGCGa                        <  8:152531/149‑1 (MQ=255)
                                                                                                                ggTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCTTGTCCTGCCAGTAGTCGTAGTGGGCGATgcggc                  >  8:14967/1‑149 (MQ=255)
                                                                                                                 gTCTCGATCTTCTCCCCGTTTGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCTTGTCCTGCCAGTAGTCGTAGTGGGCGATgcggcg                 <  8:170363/149‑1 (MQ=255)
                                                                                                                            ctcCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCTTGTCCTGCCAGTAGTCGTAGTGGGCGATGCGGCGCAGCGaa          <  5:162703/145‑1 (MQ=255)
                                                                                                                            ctcCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCTTGTCCTGCCAGTAGTCGTAGTGGGCGATGCGGCGCAGCGa           <  1:171088/144‑1 (MQ=255)
                                                                                                                            ctcCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCTTGTCCTGCCAGTAGTCGTAGTGGGCGATGCGGCGCAGCGAAGc        <  3:118269/147‑1 (MQ=255)
                                                                                                                             tcCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCTTGTCCTGCCAGTAGTCGTAGTGGGCGATGCGGCGCAGCGAAGCCt      >  8:174377/1‑148 (MQ=255)
                                                                                                                               cccGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCTTGTCCTGCCAGTAGTCGTAGTGGGCGATGCGGCGCAGCGAAGCCt      <  7:174377/146‑1 (MQ=255)
                                                                                                                                ccGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCTTGTCCTGCCAGTAGTCGTAGTGGGCGATGCGGCGCAGCGAAGCCTCGAt  <  6:280380/149‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                               
GGTTGATGATCTTGTCAACGCGCCCCGGGCGGTCGATACGGGTGGAGTCGATCTCGTACCAGCCCTGCGGGGTATCGCGGCGCACGAAGGCGGTGCCGCGCACGTCGGTGATGGTCTCGATCTTCTCCCCGTTGGACAGGCGCTGGGCCACCTCGACCACCGCACGCTCGGCGTTGCCGAACAGCAGGATGTCGGCGCTGGCATCGATCAGGATCGAGTGACGAACCTTGTCCTGCCAGTAGTCGTAGTGGGCGATGCGGCGCAGCGAAGCCTCGAT  >  NC_002947/5540190‑5540466

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: ‑