Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_tpiA4,295,9760CT28.9% 46.9 / 21.4 45intergenic (+266/+376)gltP/yjcOglutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
Reads supporting (aligned to +/- strand):  ref base C (20/12);  new base T (5/8);  total (25/20)
Fisher's exact test for biased strand distribution p-value = 1.91e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.50e-01
Rejected as consensus: Frequency below/above cutoff threshold.

GTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGC  >  NC_000913_3_pae_tpiA/4295828‑4296122
                                                                                                                                                    |                                                                                                                                                  
ggcGGATAAGGCGTTTATGCCGCATACTACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAAc                                                                                                                                                    <  2:251215/147‑1 (MQ=12)
gTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAAc                                                                                                                                                    >  1:451752/1‑149 (MQ=32)
     aTAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTg                                                                                                                                               >  2:70979/1‑149 (MQ=17)
        aGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGCCAGCGCAATAGCCTGCTTTAGCGTGATTTTGTAGATCGGATACGGCGTTTACGCCGCATCCGACATCAACGCctgctg                                                                                                                                            >  2:400037/1‑149 (MQ=11)
           cGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGa                                                                                                                                         <  2:480063/149‑1 (MQ=32)
            gTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCATACGCCAGACCGCGCAATAGCATGATTTAGAGTAATATTCAAAGTGGGATAAGGCGTTTACGCCTCATCCGACATCAATGCCTGATACGAc                                                                                                                                        >  2:477482/1‑149 (MQ=11)
               tgtcccGCATCCGACATGAACGCCTGAGGCGACGCTTATCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATGTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCt                                                                                                                                     <  2:294442/145‑1 (MQ=11)
                  gCCGCATCCGACATCAACGCCTGATGCGACACTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGc                                                                                                                                  >  2:327693/1‑149 (MQ=18)
                   ccGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACGGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACCTCAATGCCTGATGCGAGCCTTGcc                                                                                                                                 >  2:440601/1‑149 (MQ=11)
                       aTCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGt                                                                                                                             <  2:311209/149‑1 (MQ=21)
                        tCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCCGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATACGACGCTTGCCGCGTc                                                                                                                            >  1:370690/1‑149 (MQ=255)
                         ccGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCTAGCCAGCGCCATAGCCTGATTTAGCGTGATCTTGTAGGTCGGAAAAGTCGTTTACGCCGCATCCCACCGCAACCCCTGAACCGACGCTTACcgagcct                                                                                                                           >  2:388380/1‑144 (MQ=11)
                          cGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGCTAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCtt                                                                                                                          <  1:477482/149‑1 (MQ=25)
                              aTCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCa                                                                                                                      >  1:429478/1‑149 (MQ=38)
                                  aCGCCTGATGCGCAGCCTAACGCGCTCAATCAGGCCTACGTCAAACAGCGCAATCGTCCGATCTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGcc                                                                                                                  <  1:36556/149‑1 (MQ=11)
                                  aCGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAAGcc                                                                                                                  >  2:330153/1‑149 (MQ=37)
                                                     aCGCTTCTTATCAGGCCTACGAAAGACAGCGCAATCGCCTGATTTAGCGTGATTTTGTAGGGCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATa                                                                                               <  2:290436/149‑1 (MQ=11)
                                                     aCGCGTCTTATCAGGCTTCAGCCAGAGAGCGCAATAGTCTGATTTCGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATa                                                                                               <  2:186169/149‑1 (MQ=11)
                                                     aCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATa                                                                                               <  1:168533/149‑1 (MQ=39)
                                                         gTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCt                                                                                           >  1:424227/1‑149 (MQ=38)
                                                                     cTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGc                                                                                                                                                  <  1:166783/82‑1 (MQ=25)
                                                                           caaaCAGCGCAATGGTCTGATTGAGCGTGATTTAGTATGTCGGACAAGGCGTTTACGCCGCGCCCGGCATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGt                                                                         <  2:317381/146‑1 (MQ=11)
                                                                           cAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCTTGATTTAGCGTCAtttgtc                                                                         >  1:167345/1‑146 (MQ=255)
                                                                                 gcgcAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGACGCtt                                                                                                                                    <  2:281755/84‑1 (MQ=18)
                                                                                            tGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGtt                                                        <  1:327693/149‑1 (MQ=37)
                                                                                              aTTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTatc                                                                                                              <  2:383916/93‑3 (MQ=255)
                                                                                              aTTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACg                                                                                                              >  1:383916/1‑93 (MQ=255)
                                                                                                  agtctGATTTTGTAGGTCGGATAAGGCGTTTCCGCCCCCTCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAACAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGTCGTTTATGcc                                                  <  1:46018/145‑1 (MQ=11)
                                                                                                    cGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGAc                                                                                                                                        <  1:379250/61‑1 (MQ=255)
                                                                                                    cGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGAc                                                                                                                                        >  2:379250/1‑61 (MQ=255)
                                                                                                    cGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCACTAGCCTGATTTAGCGTGATTTTCTGGGTCGGATACGTCCTTTATGCCGc                                                >  2:280783/1‑149 (MQ=11)
                                                                                                     gTGATGTTGTCAGTCGAATAGGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTCACGTGCTTTTGTCGGTCGGATAAGGCGCTAATGCCGCa                                               >  2:439465/1‑149 (MQ=11)
                                                                                                            tGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACa                                        <  2:451752/149‑1 (MQ=38)
                                                                                                                 ggtggATAGGGCGTTTACCCCGCACCCGGCATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAAc                                   <  2:268767/146‑1 (MQ=11)
                                                                                                                     gATCAGGCGTTTACGCCCGATCGGCCGTCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCt                               <  1:277384/149‑1 (MQ=11)
                                                                                                                             gTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTCTAGGTCAGATAAGGCGGTTATGCCCCATCCGACATCAACGCCTGATGCTAc                       >  2:344320/1‑149 (MQ=11)
                                                                                                                                  cgccgcATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTc                                                                                                                            >  1:132835/1‑43 (MQ=255)
                                                                                                                                    ccgcATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAAc                >  2:430874/1‑149 (MQ=35)
                                                                                                                                     cgcATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCCCATCCGTCCTCAACACCTGATGTGACGCtttcct               >  1:233171/1‑145 (MQ=11)
                                                                                                                                        aTCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGa                                          >  2:123725/1‑119 (MQ=38)
                                                                                                                                            gACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACa                                        <  2:93625/117‑1 (MQ=38)
                                                                                                                                            gACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACa                                        >  1:93625/1‑117 (MQ=38)
                                                                                                                                             aCATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATGCCAGACAGCGCAATAGCCTGATTTCGCGTGCTTTTGTAGGTCGGATAAGGCGTTTATGCAGCATAGGACATCAACGCCTGATTCGACACTTACCACGCCTTAt       >  2:154315/1‑149 (MQ=11)
                                                                                                                                               aTCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGCCGCTTAGGGGGTCTTATCa     >  1:143819/1‑149 (MQ=255)
                                                                                                                                                  aaCGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTg                                                                                >  2:239185/1‑71 (MQ=34)
                                                                                                                                                  aaCGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTg                                                                                <  1:239185/71‑1 (MQ=34)
                                                                                                                                                  aaCGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGc  >  2:488762/1‑149 (MQ=32)
                                                                                                                                                    cGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTa                                                      <  1:325756/95‑1 (MQ=31)
                                                                                                                                                    |                                                                                                                                                  
GTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGC  >  NC_000913_3_pae_tpiA/4295828‑4296122

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: ‑