Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_vch_tpiA4,296,0900CT32.4% 23.2 / 18.6 34intergenic (+266/+376)gltP/yjcOglutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
Reads supporting (aligned to +/- strand):  ref base C (12/11);  new base T (6/5);  total (18/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.72e-01
Rejected as consensus: Frequency below/above cutoff threshold.

GGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGC  >  NC_000913_3_vch_tpiA/4295945‑4296236
                                                                                                                                                 |                                                                                                                                                  
ggATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTAAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATACGACATCAATGcc                                                                                                                                                 >  1:62985/1‑149 (MQ=12)
 gATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACTGCGCATTAGCCTGATTTAGCGTGATTTTGTAGGTCGGATTAGCCGTTTACGCCGCATCTGTCATCAATGCCt                                                                                                                                                >  1:136737/1‑149 (MQ=11)
 gATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCt                                                                                                                                                <  1:210644/149‑1 (MQ=17)
  aTAAGGCGTTTATGCCGCATCCGACATCAACGCCTAATGCGACGCTTAACGAGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGCTTTAGCCTGGTTTTGTAGGTCAGATAAGGCTTTTCCGACGACTCCGCGATCAATGCCTg                                                                                                                                               >  2:175201/1‑149 (MQ=11)
     aGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATg                                                                                                                                            <  1:346338/149‑1 (MQ=32)
     aGGCGTTTATCCCGCATCCGACATCGACGCCTGATGCGATGCTTAAGTCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCGTGCTTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATg                                                                                                                                            <  1:432955/149‑1 (MQ=11)
         gTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGAc                                                                                                                                        >  2:210644/1‑149 (MQ=32)
                            tCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCTCGTCTTATCAg                                                                                                                     >  1:47649/1‑149 (MQ=25)
                              aaCGCCTGATTCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGc                                                                                                                   <  1:180001/149‑1 (MQ=255)
                              aaCGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCACTGCCTGATGCCACGCTTGCGGCATCTTATCAGGc                                                                                                                   >  1:217362/1‑149 (MQ=11)
                              aaCGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGc                                                                                                                                                  <  1:139880/118‑1 (MQ=18)
                              aaCGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGc                                                                                                                                                  >  2:139880/1‑118 (MQ=17)
                                                          tATCAAGCCTACGCCAGACACCACAATATCCTGATTTAGCCTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGTATACGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGAtt                                                                                       <  2:248008/149‑1 (MQ=11)
                                                           aTCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAg                                                                                                                     >  1:30780/1‑118 (MQ=18)
                                                           aTCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAg                                                                                                                     <  2:30780/118‑1 (MQ=255)
                                                                  cTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTTTAGGTCGGATAAGTCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACCTCACACAGCGCTATCGCTTGCtttctcgtcc                                                                               >  2:314366/1‑142 (MQ=11)
                                                                  cTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAACAGCCTGACTAAGCGtac                                                                               >  1:79254/1‑147 (MQ=255)
                                                                   tACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTa                                                                                                                <  2:412176/115‑1 (MQ=37)
                                                                   tACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTa                                                                                                                >  1:412176/1‑115 (MQ=40)
                                                                        cAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACCTCGCCGCCGTATCCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTTATTTAGCGTGATTTTGt                                                                         >  1:60374/1‑149 (MQ=11)
                                                                            cAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTGCGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGt                                                                     <  1:295320/149‑1 (MQ=255)
                                                                                 cAATAGCCAGATTTAGCGTCATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGAGGGTTGCCGCGTCTTAACGGGCCTACGCCAGACAGCGCAGTAGCCAGAATTAGCGAGATTTTGTAGGTCGGAt                                                                >  2:372217/1‑149 (MQ=11)
                                                                                    tAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAg                                                                       <  2:230465/139‑1 (MQ=14)
                                                                                      gCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCCGGACTCCGCTATACAGCGCTATAGCCTGCTTTCGCGTGCTTTTGTAGGTCGGATAAGGc                                                           >  1:388920/1‑149 (MQ=11)
                                                                                            tttAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCt                                                                                                                                                <  1:194766/58‑1 (MQ=255)
                                                                                            tttAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCt                                                                                                                                                <  1:194075/58‑1 (MQ=255)
                                                                                               aGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCCCATCCAACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGcc                                                  <  1:261745/149‑1 (MQ=255)
                                                                                                     aTTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATcc                                            >  1:397785/1‑149 (MQ=39)
                                                                                                             ggTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCaa                                    >  2:252152/1‑149 (MQ=39)
                                                                                                             ggTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTATGTAGGTCGGTTAAGGCGTTTTAGCCGCATGCGACATCaa                                    >  2:83709/1‑149 (MQ=14)
                                                                                                                  gATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCt                               <  2:397785/149‑1 (MQ=38)
                                                                                                                    tAAGCCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTAGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTCATTCAGCGTGTTTTTGTAGGTCGGATAAGGCCTTTATGCCGCATCCGACATCAACGCCTgt                             <  1:372217/149‑2 (MQ=11)
                                                                                                                                gccgcATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTaa                 <  1:252152/149‑1 (MQ=34)
                                                                                                                                               aaCGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGc  >  1:145776/1‑149 (MQ=32)
                                                                                                                                                 |                                                                                                                                                  
GGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGC  >  NC_000913_3_vch_tpiA/4295945‑4296236

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: ‑