Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,067,029 C→T 8.9% A170T (GCA→ACA)  PP_4464 ← LysR family transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,067,0290CT 8.9% 122.0 / 2.5 45A170T (GCA→ACA) PP_4464LysR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (22/19);  new base T (2/2);  total (24/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.48e-01

AATTAGGCGTCACTCCGGCCTCATGAAACCATTTATCGACCATTGGCCGGATAAGCCCCGATGCCTTAAGAGCAACTATAGGCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGCCCAAATCCGCTTGCCCCGAATTGACTCGATGGGTAATGAGCTCTCTATGCTCAACATCCAAATCGATTTTGATACC  >  NC_002947/5066885‑5067176
                                                                                                                                                |                                                                                                                                                   
aaTTAGGCGTCACTCCGGCCTCATGAAACCATTTATCGACCATTGGCCGGATAAGCCCCGATGCCTTAAGAGCAACTATAGGCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGTAaca                                                                                                                                                 >  2:70551/1‑149 (MQ=255)
     ggCGTCACTCCGGCCTCATGAAACCATTTATCGACCATTGGCCGGATAAGCCCCGATGCCTTAAGAGCAACTATAGGCAACCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAgat                                                                                                                                            <  4:271058/149‑1 (MQ=255)
      gCGTCACTCCGGCCTCATGAAACCATTTATCGACCATTGGCCGGATAAGCCCCGATGCCTTAAGAGCAACTATAGGCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAgat                                                                                                                                            >  1:189272/1‑148 (MQ=255)
             tCCGGCCTCATGAAACCATTTATCGACCATTGGCCGGATAAGCCCCGATGCCTTAAGAGCAACTATAGGCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGAc                                                                                                                                    >  2:14121/1‑149 (MQ=255)
                   cTCATGAAACCATTTATCGACCATTGGCCGGATAAGCCCCGATGCCTTAAGAGCAACTATAGGCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGTACTGATa                                                                                                                               >  3:252686/1‑148 (MQ=255)
                    tCATGAAACCATTTATCGACCATTGGCCGGATAAGCCCCGATGCCTTAAGAGCAACTATAGGCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTaaa                                                                                                                             >  8:168347/1‑149 (MQ=255)
                      aTGAAACCATTTATCGACCATTGGCCGGATAAGCCCCGATGCCTTAAGAGCAACTATAGGCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGATAAAt                                                                                                                            >  7:107244/1‑148 (MQ=255)
                        gAAACCATTTATCGACCATTGGCCGGATAAGCCCCGATGCCTTAAGAGCAACTATAGGCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAAc                                                                                                                         >  5:92475/1‑149 (MQ=255)
                           aCCATTTATCGACCATTGGCCGGATAAGCCCCGATGCCTTAAGAGCAACTATAGGCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGTAACACAGATGATTGGACTGCTAAATAACGTa                                                                                                                      <  1:70551/149‑1 (MQ=255)
                             cATTTATCGACCATTTGCGGGATTAGCCCCGCTGCCTTAACAGCAACTATAGGCACCACATATAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATATGAGCGTCAGGCGATGCAACACTGATTATTGGACTGCTAAATAACGTaga                                                                                                                    <  4:259578/149‑1 (MQ=255)
                              aTTTATCGACCATTGGCCGGATGAGCCCCGATGCCTTAAGAGCAACTATAGGCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTagag                                                                                                                   >  2:144240/1‑149 (MQ=255)
                                   tCGACCATTGGCCGGATAAGCCCCGATGCCTTAAGAGCAACTATAGGCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCttt                                                                                                               <  7:168347/148‑1 (MQ=255)
                                     gACCATTGGCCGGATAAGCCCCGATGCCTTAAGAGCAACTATAGGCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGa                                                                                                             <  4:294369/148‑1 (MQ=255)
                                        cATTGGCCGGATAAGCCCCGATGCCTTAAGAGCAACTATAGGCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCt                                                                                                          >  4:274946/1‑148 (MQ=255)
                                           tGGCCGGAGAAGCCCAGATGCCTTAAGAGCAACTATAGTCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTcc                                                                                                       <  8:107244/148‑1 (MQ=255)
                                             gCCGGATAAGCCCCGATGCCTTAAGAGCAACTATAGGCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACt                                                                                                                                   >  3:164040/1‑118 (MQ=255)
                                             gCCGGATAAGCCCCGATGCCTTAAGAGCAACTATAGGCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACt                                                                                                                                   <  4:164040/118‑1 (MQ=255)
                                                      gCCCCGATGCCTTAAGAGCAACTATAGGCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGc                                                                                              >  8:41666/1‑146 (MQ=255)
                                                          cGATGCCTTAAGAGCAACTATAGGCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTg                                                                                       <  2:189272/149‑1 (MQ=255)
                                                                cTTAAGAGCAACTATAGGCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAata                                                                                 >  8:193055/1‑149 (MQ=255)
                                                                    agagCAACTATAGGCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGc                                                                              <  7:193055/148‑1 (MQ=255)
                                                                          aCTATAGGCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGCCCAAATc                                                                       >  4:18010/1‑149 (MQ=255)
                                                                                ggCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGCCCAAATCCGCtt                                                                  <  6:92475/148‑1 (MQ=255)
                                                                                ggCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGCCCAAATCCGCtt                                                                  <  4:239492/148‑1 (MQ=255)
                                                                                 gCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGCCCAAATCCGCTTGc                                                                >  4:192790/1‑149 (MQ=255)
                                                                                        aTCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGc                                                                              >  6:49506/1‑128 (MQ=255)
                                                                                        aTCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGc                                                                              <  5:49506/128‑1 (MQ=255)
                                                                                             aCTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGCCCAAATCCGCTTGCCCCGAATTGAc                                                     <  1:144240/148‑1 (MQ=255)
                                                                                             aCTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGCCCAAATCCGCTTGCCCCGAATTGACt                                                    >  5:126047/1‑149 (MQ=255)
                                                                                              cTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGccc                                                                            >  8:301385/1‑124 (MQ=255)
                                                                                              cTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGccc                                                                            <  7:301385/124‑1 (MQ=255)
                                                                                              cTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGCCCAAATCCGCTTGCCCCGAATTGACTc                                                   >  5:322111/1‑149 (MQ=255)
                                                                                               tGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGCCCAAATCCGCTTGCCCCGAATTGACTc                                                   >  5:121847/1‑148 (MQ=255)
                                                                                                  cTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGCCCAAATCCGCTTGCCCCGAATTGACTCGATg                                               <  6:121847/149‑1 (MQ=255)
                                                                                                       aGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATCCAACACAGATGATAGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGCCCAAATCCGCTTGCCCCGAATTGACTCGATGGGTaa                                          >  1:162982/1‑149 (MQ=255)
                                                                                                        gTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGCCCAAATCCGCTTGCCCCGAATTGACTCGATGGGTAAt                                         <  3:274946/149‑1 (MQ=255)
                                                                                                         tAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGTAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGCCCAAATCCGCTTGCCCCGAATTGACTCGAt                                                <  5:132656/141‑1 (MQ=255)
                                                                                                         tAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGTAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGCCCAAATCCGCTTGCCCCGAATTGACTCGAt                                                >  6:132656/1‑141 (MQ=255)
                                                                                                               ccGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGCCCAAATCCGCTTGCCCCGAATTGACTCGATGGGTAATGAGctc                                   >  2:244816/1‑148 (MQ=255)
                                                                                                                         cGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGCCCAAATCCGCTTGCCCCGAATTGACTCGATGGGTAATGAGCTCTCTATGCTCa                         >  7:142143/1‑148 (MQ=255)
                                                                                                                          gAAATTTGAGCGTCATGCGATTCAACACAGATGATTGGACTGCTAAATAACGTAGATCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGCCCAAATCCGCTTGCCCCGAATTGACTCGATGGGTAATGAGCTTTCTATGCTCaa                        <  3:261591/148‑1 (MQ=255)
                                                                                                                                  aGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGCCCAAATCCGCTTGCCCCGAATTGACTCGATGGGTAATGAGCTCTCTATGCTCAACATCCaaa                <  7:41666/148‑1 (MQ=255)
                                                                                                                                  aGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGCCCAAATCCGCTTGCCCCGAATTGACTCGATGGGTAATGAGCTCTCTATGCTCAACATCCaaa                <  1:244816/148‑1 (MQ=255)
                                                                                                                                     gTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGCCCAAATCCGCTTGCCCCGAATTGACTCGATTGGTAATGAGCTCTCTATGCTCAACATCCAAATCGa            <  3:18010/149‑1 (MQ=255)
                                                                                                                                               gCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGCCCAAATCCGCTTGCCCCGAATTGACTCGATGGGTAATGAGCTCTCTATGCTCAACATCCAAATCTATTTTGATAcc  >  7:152888/1‑149 (MQ=255)
                                                                                                                                                |                                                                                                                                                   
AATTAGGCGTCACTCCGGCCTCATGAAACCATTTATCGACCATTGGCCGGATAAGCCCCGATGCCTTAAGAGCAACTATAGGCACCCCATCTAACTGACTTGCAGTAACGACCGCGCTCTGCGAAATTTGAGCGTCAGGCGATGCAACACAGATGATTGGACTGCTAAATAACGTAGAGCTTTGATCTTCCAGACCTGGCGAGATTGACAATATGCCCAAATCCGCTTGCCCCGAATTGACTCGATGGGTAATGAGCTCTCTATGCTCAACATCCAAATCGATTTTGATACC  >  NC_002947/5066885‑5067176

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: ‑