Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,040,611 C→T 8.9% A242T (GCA→ACA)  PP_0900 ← PAP2 family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,040,6110CT 8.9% 124.1 / 2.3 45A242T (GCA→ACA) PP_0900PAP2 family protein
Reads supporting (aligned to +/- strand):  ref base C (19/22);  new base T (2/2);  total (21/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.48e-01

AGCGGTTTGCCCGACGCATGTTCATGGCAGGGGTACCGCGGGGACAGGTGTTTGCTGATGTGTTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGATCAACCAGCAGAACACTGCCGTCCACACATTGTGCGACAGGAAGTGCGCCCCCTGCATCATCCTGCCCACC  >  NC_002947/1040485‑1040756
                                                                                                                              |                                                                                                                                                 
aGCGGTTTGCCCGACGCATGTTCATGGCAGGGGTACCGCGGGGACAGGTGTTTGCTGATGTGTTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGc                                                                                                                             >  2:3016/1‑149 (MQ=255)
         cccGACGCATGTTCATGGCAGGGGTACCGCGGGGACAGGTGTTTGCTGATGTGTTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGcc                                                                                                                    >  8:2784/1‑149 (MQ=255)
                    ttCATGGCAGGGGTACCGCGGGGACAGGTGTTTGCTGATGTGTTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACg                                                                                                                                <  8:41524/126‑1 (MQ=255)
                      cATGGCAGGGGTACCGCGGGGACAGGTGTTTGCTGATGTGTTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGa                                                                                                        <  5:253804/148‑1 (MQ=255)
                              gggTACCGCGGGGACAGGTGTTTGCTGATGTGTTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAAc                                                                                                >  7:290021/1‑148 (MQ=255)
                                    cgcgGGGACAGGTGTTTGCTGATGTGTTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTaa                                                                                         >  4:8240/1‑149 (MQ=255)
                                     gcgGGGACAGGTGTTTGCTGATGTGTTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAAt                                                                                        <  1:3016/149‑1 (MQ=255)
                                     gcgGGGACAGGTGTTTGCTGATGTGTTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAAt                                                                                        <  8:290021/149‑1 (MQ=255)
                                          gACAGGTGTTTGCTGATGTGTTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGAc                                                                                   <  3:8240/149‑1 (MQ=255)
                                            cAGGTGTTTGCTGATTTGTTCGTCGAGCTTGCCTGAGTAGCATTTGAAGTGCGATGGGCCGCAAAGCGGCCCCTCTTTCTTGCGGCGCTGCGCTCGGCGACGTGCACCTCGGCCAGCCCCCGCCGATAGAGAAGCAGGTAATACGAccc                                                                                 <  6:196861/149‑1 (MQ=255)
                                            cAGGTGTTTGCTGATGTGTTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGAccc                                                                                 >  4:108273/1‑149 (MQ=255)
                                             aGGTGTTTGCTGATGTGTTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGAccc                                                                                 >  6:233111/1‑148 (MQ=255)
                                                 ggttGCTGATGTGTTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATAGCACCCCaaac                                                                            >  4:113656/3‑147 (MQ=255)
                                                     gCTGATGTTTTCGTCGAGCATGCCTTAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTTCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGTGAACCAGGTAATACGACCCCAATCCGa                                                                         <  7:221595/148‑1 (MQ=255)
                                                     gCTGATGTGTTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGa                                                                         <  7:2784/148‑1 (MQ=255)
                                                     gCTGATGTGTTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGAt                                                                        >  3:306405/1‑149 (MQ=255)
                                                       tGATGTGTTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCccgcc                                                                                                          >  3:214635/1‑113 (MQ=255)
                                                       tGATGTGTTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCccgcc                                                                                                          <  4:214635/113‑1 (MQ=255)
                                                       tGATGTGTTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGa                                                                         <  8:225417/146‑1 (MQ=255)
                                                       tGATGTGTTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGa                                                                         >  7:225417/1‑146 (MQ=255)
                                                       tGATGTGTTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGATc                                                                       >  1:5240/1‑148 (MQ=255)
                                                        gATGTGTTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGATCaa                                                                     >  4:123154/1‑149 (MQ=255)
                                                           gtgtTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGCCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCCGCCGCCGCCGATAGAGAACGAGGTAAAACGACCCCAATCCGATCagc                                                                    >  4:218906/1‑145 (MQ=255)
                                                            tgtTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGATCAACcag                                                                 <  4:306405/149‑1 (MQ=255)
                                                                     aGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGATCCAGGTAATACGACCCCAATCCGATCAACCAGCAGAACACt                                                        <  3:184113/149‑1 (MQ=255)
                                                                                 tAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATaga                                                                                                    <  6:34410/93‑1 (MQ=255)
                                                                                 tAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATaga                                                                                                    >  5:34410/1‑93 (MQ=255)
                                                                                      tttGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGa                                                                                    >  7:273457/1‑104 (MQ=255)
                                                                                      tttGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGa                                                                                    <  8:273457/104‑1 (MQ=255)
                                                                                        tGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGATCAACCAGCAGAACACTGCCGTCCACACATTGTGc                                      <  3:113656/148‑1 (MQ=255)
                                                                                            gTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGATCAACCAGCAGAACACTGCCGTCCACACATTGTGCGACAg                                 <  3:123154/149‑1 (MQ=255)
                                                                                             tGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGATCAACCAGCAGAACACTGCCGTCCACACATTGTGCGACAgg                                <  5:233111/149‑1 (MQ=255)
                                                                                               cGAAGGGCCGCAAAGCGGCCCCTCTTTCATGTGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGATCAACCAGCAGAACACTGcc                                                     >  8:101940/1‑126 (MQ=255)
                                                                                               cGAAGGGCCGCAAAGCGGCCCCTCTTTCATGTGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGATCAACCAGCAGAACACTGcc                                                     <  7:101940/126‑1 (MQ=255)
                                                                                               cGAAGGGCCGCAAAGCGGCCCCTCTTTCATGTGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGATCAACCAGCAGAACACTGcc                                                     >  6:292689/1‑126 (MQ=255)
                                                                                               cGAAGGGCCGCAAAGCGGCCCCTCTTTCATGTGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGATCAACCAGCAGAACACTGcc                                                     <  5:292689/126‑1 (MQ=255)
                                                                                               cGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGATCAACCAGCAGAACACTGCCGTCCACACATTGTGCGACAGGaa                              <  2:5240/149‑1 (MQ=255)
                                                                                                 aaGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGATCAACCAGCAGAACACTGCCGTCCACACATTGTGCGACAGGAAGt                            >  2:254330/1‑149 (MQ=255)
                                                                                                    ggCCGCAAAGCGGCCCCTCTTTCTTGCGGCGCTGGGCTAGGCGACGTTCACGTCGTCCAGCCCCCTCCGATAGAGAACCAGGTAATACGACCCCAATCCGATCAACCAGCAGAACACTGCCGTc                                                  <  6:282517/124‑1 (MQ=255)
                                                                                                       cGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGATCAACCAGCAGAACACTGCCGTCCACACATTGTGCGACAGGAAGTGCGccc                      >  2:50226/1‑149 (MQ=255)
                                                                                                        gCAAAGCGGCCCCTCTTTCATGCGGCGCTGGGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGATCAACCAGCAGAACACTGCCGTCCACACATTGTGCGACAGGAAGTGCGcccc                     >  1:28046/1‑149 (MQ=255)
                                                                                                               ggCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGATCAACCAGCAGAACACTGCCGTCCACACATTGTGCGACAGGAAGTGCGCCCCCTGcatc              <  2:28046/149‑1 (MQ=255)
                                                                                                                  cccTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGATCAACCAGCAGAACACTGCCGTCCACACATTGTGCGACAGGAAGTGCGCCCCCTGCatcatc           <  3:108273/149‑1 (MQ=255)
                                                                                                                     tctTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGATCAACCAGCAGAACACTGCCGTCCACACATTGTGCGACAGGAAGTGCGCCCCCTGCATCATCCTg        >  6:159003/1‑149 (MQ=255)
                                                                                                                           ctGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGATCAACCAGCAGAACACTGCCGTCCACACATTGTGCGACAGGAAGTGCGCCCCCTGCATCATCCTGCCCAcc  <  3:218906/148‑1 (MQ=255)
                                                                                                                             gcggcgCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGATCAACcag                                                                 <  7:333261/84‑1 (MQ=255)
                                                                                                                             gcggcgCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGATCAACcag                                                                 >  8:333261/1‑84 (MQ=255)
                                                                                                                              |                                                                                                                                                 
AGCGGTTTGCCCGACGCATGTTCATGGCAGGGGTACCGCGGGGACAGGTGTTTGCTGATGTGTTCGTCGAGCATGCCTGAGTAGCATTTGAAGTGCGAAGGGCCGCAAAGCGGCCCCTCTTTCATGCGGCGCTGCGCTCGGCGACGGGCACCTCGGCCAGCCCCCGCCGATAGAGAACCAGGTAATACGACCCCAATCCGATCAACCAGCAGAACACTGCCGTCCACACATTGTGCGACAGGAAGTGCGCCCCCTGCATCATCCTGCCCACC  >  NC_002947/1040485‑1040756

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: ‑