Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 345,428 T→C 16.3% intergenic (+145/‑295) prpB → / → prpC 2‑methylisocitrate lyase/2‑methylcitrate synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP009273345,4280TC16.3% 61.4 / 2.2 39intergenic (+145/‑295)prpB/prpC2‑methylisocitrate lyase/2‑methylcitrate synthase
Reads supporting (aligned to +/- strand):  ref base T (11/20);  new base C (5/2);  total (17/22)
Fisher's exact test for biased strand distribution p-value = 1.08e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCG  >  CP009273/345280‑345560
                                                                                                                                                    |                                                                                                                                    
aTAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGCCGGATAAGACGGATGGCGTCGCATCCGCCAACCGATGCCTGATGCGCCGCTGACGt                                                                                                                                      >  2:415348/1‑149 (MQ=255)
   aaaagCGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGAc                                                                                                                                   <  2:47428/149‑1 (MQ=255)
   aaaaaCGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACACCCGATGCCTGATGCGCCGCTGACGTGAc                                                                                                                                   >  1:421971/1‑149 (MQ=255)
         gCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGCCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTCACGTGACTTATCa                                                                                                                             <  1:335150/149‑1 (MQ=255)
           ccGTTGATTGTATTCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCGGCTGACGTGACTTATCAgg                                                                                                                           <  1:339996/149‑1 (MQ=255)
           ccGTTGATTGTATTCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAgg                                                                                                                           <  1:340062/149‑1 (MQ=255)
                gATTGTATTCGACAGCCGATGCCTGATGCGTCGATGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGATGTGCACTATCAGGCCTAc                                                                                                                      >  1:299326/1‑149 (MQ=17)
                 aTTGTATTCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCAACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGGCAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACg                                                                                                                     >  1:442289/1‑149 (MQ=255)
                   tGTATTCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCCCCGCTGGAGGGACTTATCAGGCCTACggg                                                                                                                   >  1:139917/1‑149 (MQ=255)
                    gTATTCGACACCGCATGCCTGATGGGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACgggg                                                                                                                  <  2:48473/149‑1 (MQ=255)
                               ccGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTgaactgaact                                                                                                       >  2:238789/1‑149 (MQ=25)
                               ccGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTgaactgaact                                                                                                       >  2:39252/1‑149 (MQ=25)
                               ccGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTgaactgaact                                                                                                       >  2:39278/1‑149 (MQ=25)
                                   tGCCGGGTGGGTCGGTGGCGCGACGTATCAGGCCTACGAGGTGCACTGAAGTGTAGGTCGGATAAGACGGATGGCGCTGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAg                                                                                                   <  2:14480/149‑1 (MQ=14)
                                       tGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCg                                                                                               <  1:32730/149‑1 (MQ=255)
                                              tCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGCATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGGGCGCTGAACTGTAGGTCGGATAAGa                                                                                        >  2:260080/1‑149 (MQ=255)
                                                          cTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCg                                                                            <  1:211292/149‑1 (MQ=40)
                                                            tATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCa                                                                          <  1:25156/149‑1 (MQ=40)
                                                              tCAGGCCTACGAGGTGCACTGGCCTGTAGGTCGGATAAGCCGGATGGCGTCGCATCCGACATCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATc                                                                        <  2:158644/149‑1 (MQ=255)
                                                                           gTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGc                                                           >  2:279789/1‑149 (MQ=38)
                                                                           gTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCCCCGCTGACGCGACTTATCAAGCCCACGGGGGGCACTGAACTGTAGGGCGGATAAAACGCATAGCGTCGCACCCGACAACCGAtac                                                           >  2:107344/1‑147 (MQ=11)
                                                                            tGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCATAACGGGTGCAATGAACTGTGGGACGGATAAGACGCAGAGCGACGcaaccgacaaccgacacc                                                          >  1:370023/1‑145 (MQ=11)
                                                                              cACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCa                                                                                                                             >  1:287591/1‑80 (MQ=255)
                                                                              cACTGAACTGTAGGTCGGATAAGACGGATCGCGTCGCATCCGACAACCGATGCGTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCTCAGAACTGTAGGTCGGATAAGTCGCATAGCGGCGCATCCGACAACCGATGCCtc                                                        >  2:257109/1‑148 (MQ=11)
                                                                               aCTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAAcc                                                                >  1:164879/1‑140 (MQ=39)
                                                                               aCTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGa                                                       >  2:115050/1‑149 (MQ=38)
                                                                               aCTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAAcc                                                                <  2:164879/140‑1 (MQ=14)
                                                                                cTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGAt                                                      <  2:50691/149‑1 (MQ=37)
                                                                                    aCTGGAGGGCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATgcgc                                                  <  1:175091/149‑1 (MQ=255)
                                                                                       gTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGcgccgc                                               <  1:374740/149‑1 (MQ=37)
                                                                                             cGGATAAACCGGATGGCGTTGCATTCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGAcgc                                         <  2:391929/149‑1 (MQ=255)
                                                                                                aTAAGCCGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGAc                                      <  2:404237/149‑1 (MQ=17)
                                                                                                    gACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTAc                                                                                                                      >  2:168834/1‑65 (MQ=255)
                                                                                                              gTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCCACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAAACGATCCTAGACGCGCCGCTGACGCGACTTATCAGGCCTACg                        <  1:112947/149‑1 (MQ=11)
                                                                                                                cGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGACCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCGGACGCGACTTATCAGGCCTACggg                      >  1:174745/1‑149 (MQ=17)
                                                                                                                          agccGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGCACTGaa            <  2:467781/147‑1 (MQ=25)
                                                                                                                          aaCCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGCACTGaa            <  1:365614/149‑1 (MQ=34)
                                                                                                                                tGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCAGCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGCACTGAACTGTAg      <  1:75953/149‑1 (MQ=25)
                                                                                                                                   cTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTc   <  1:396427/149‑1 (MQ=35)
                                                                                                                                    tGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCg  <  1:35015/149‑1 (MQ=35)
                                                                                                                                                    |                                                                                                                                    
ATAAAAAACGCCCGTTGATTGTATTCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCG  >  CP009273/345280‑345560

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑