Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,628,625	0	A	C	29.8%	72.2 / 24.0	47	V105G (GTC→GGC)	pdeF	cyclic di‑GMP phosphodiesterase PdeF
Reads supporting (aligned to +/- strand):  ref base A (30/3);  new base C (0/14);  total (30/17)
Fisher's exact test for biased strand distribution p-value = 1.99e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

CTCGCCAGTAATCCTACAAATGCAGCAAACTGGAAAAGTATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATGCCGCCCAGCTG  >  NC_000913/2628487‑2628759                                                                                                                                           |                                                                                                                                       cTCGCCAGTAATCCTACAAATGCAGCAAACTGGAAAAGTATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGAc                                                                                                                                       >  1:180124/1‑140 (MQ=255)         tAATCCTACAAATGCAGCAAACTGGAAAAGTATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAAc                                                                                                                               >  1:751039/1‑140 (MQ=255)             ccaaCAAAGGCAGAAAACTGGAAAAGTATAAGAAACAGCGTTGCAGGAAACAAAATCTGCAAAAATATCCGCGGGAAAATAAAACGGGTATCACCATGTGAAACGTTGTTACGCGGGGGAGAAAAGCCCCTGTAACCGcc                                                                                                                           <  2:1325410/137‑1 (MQ=255)             ccTACAAATGCAGCAAACTGGAAAAGTATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGcc                                                                                                                           <  1:1612288/140‑1 (MQ=255)                aCAAATGCAGCAAACTGGAAAAGTATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCa                                                                                                                        >  2:873164/1‑140 (MQ=255)                aCAAATGCAGCAAACTGGAAAAGTATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCa                                                                                                                        >  1:960519/1‑140 (MQ=255)                   aaTGCAGCAAACTGGAAAAGTATCAGAAACAGCGTTGCAGGAAACACAATCTTCTAGAATATACGCGGGGAAATTAAGCGGTTATCACCATGAAAAATGTTGTTACGCCGGGGAATAAAGACCCTGTAACCGCCCCAACa                                                                                                                     <  2:1662872/140‑1 (MQ=255)                   aaTGCAGCAAACTGGAAAAGTATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACa                                                                                                                     >  1:310412/1‑140 (MQ=255)                       cagcaAACTGGAAAAGTATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAgaga                                                                                                                 >  1:1334648/1‑140 (MQ=255)                               ggaaaaaGTATCAAAAACAGCGTTGCAGAAAACAAAATCTGCCAAAATATCCGCTGGAAAATAAACCGGGTACCCCCATGTAAAACGTTTTTACGCGGGGGAGAAAAGCCCCTGTAACCGCCCCAACAGAGaatgataat                                                                                                         <  2:960519/137‑1 (MQ=255)                                gaaaaaGTATCAAAAACAGCGTTGCAGGAAACAAAATCTGCCAGAATATACGCTGGAAAATTAAACGGGTATCCCCATGTAAAACGTTGTTACGCGGGGGAGAAAAGCCCCTGTAACCGCCCCAACAGAGaatgataatg                                                                                                        <  2:681557/138‑1 (MQ=255)                                 gAAAAGTATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGaatgataatga                                                                                                       >  1:1492302/1‑140 (MQ=255)                                             aaccAGCGTTGCGGGAAACACAACCTCCCAAAATATACGGTGGAAAATAAAACGGATACCCCCATCGGAACCGTTGTTACGCGGGGGAATAAAGTCCCTTTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAg                                                                                           <  2:1252773/137‑1 (MQ=255)                                                cAGCGTGGCAGAAACCACAATCTGCAAAAATATACGCTGGAAAATAAAACGGTTATCCCCATGTAAAACGTTGTTACGCGGGGGAGAAAAGCCCCTGAAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCg                                                                                        <  2:1334648/140‑1 (MQ=255)                                                 aGCGTTGAAGAAAACACAATCTGCAAAAATATCCGCTGGAAAATAAACCGGGTACCCCAATGTAAAACTTTGTTCCCCGGGGGAGAAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGt                                                                                       <  2:1413929/140‑1 (MQ=255)                                                  gCGTGGCAGGAAACACAATCTCCCAGAATATACGGGGGGAAATTAAAGGGGTATCACCATGTGAAACGTTGTTCCGCGGGGGAGAAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGtt                                                                                      <  2:751039/140‑1 (MQ=255)                                                       gCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGa                                                                                 >  2:1901136/1‑140 (MQ=255)                                                             aaCACAATCTGCCAGAATATCCGCTGGGAAATTAAACGGGTATCCCCATGTGAAACGTTTTTACGCGGGGGAGAAAAGCCCTTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAgtgt                                                                           <  1:1498827/140‑4 (MQ=255)                                                               cacaATCTGCAAAAATATACGCGGGGAAATTAAACGGGTATCCCCATGTAAAACTTTGTTACGCGGGGGAATAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGttt                                                                         <  2:180124/140‑1 (MQ=255)                                                                acaATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTc                                                                        >  2:854184/1‑140 (MQ=255)                                                                      tGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTaaaa                                                                  >  1:961384/1‑140 (MQ=255)                                                                         agaaaTATACGCGGGAAAATTAAACGGGTATCACCATGTAAAACGTTGTTACGCGGGGGAGAAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAAcc                                                               <  2:437110/137‑1 (MQ=255)                                                                          aaaaTATACGCTGGAAAATAAAACGGGTATCACCATGTAAAACGTTGTTCCGCGGGGGAGAAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAAccc                                                              <  2:310412/138‑1 (MQ=255)                                                                              tatcCGCGGGAAAATTAAACGGGTATCCCCATGGAAAACGTTGTTACGCGGGGGAGAAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGct                                                          <  2:1133078/140‑1 (MQ=255)                                                                              tatcCGCGGGAAAATAAAACGGGTACCCCCATGTAAAACGTTGTTCCGCGGGGGAGAAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGct                                                          <  2:1893635/140‑1 (MQ=255)                                                                               ataCGTAGGAAAATTAAGGGGTTATCCCCATGCGAACCGTTGTTCCGCCGGGAAGTAAGACCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGctc                                                         <  2:961384/140‑1 (MQ=255)                                                                               ataCGCTGGAAAATTAAACGGGTATCACCATGTGAAACGTTGTTACGCGGGGGAGAAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGctc                                                         <  1:587287/140‑1 (MQ=255)                                                                                taCGCTGGGAAATTAAACGGGTATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGctct                                                        >  2:1948594/1‑140 (MQ=255)                                                                                  cGCTGGGAAATTAAACGGGTATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGc                                                      >  2:1006231/1‑140 (MQ=255)                                                                                      gggAAATTAAACGGGTATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCatct                                                  >  1:437110/1‑138 (MQ=255)                                                                                      gggAAATTAAACGGGTATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCatat                                                  >  2:1134696/1‑140 (MQ=255)                                                                                      gggAAATTAAACGGGTATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCatat                                                  >  1:1126868/1‑140 (MQ=255)                                                                                      gggAAATTAAACGGGTATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCatat                                                  >  1:1893635/1‑140 (MQ=255)                                                                                      gggAAATTAAACGGGTATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCatat                                                  >  2:1806909/1‑140 (MQ=255)                                                                                           ataaaaCGGTTATCACCATGTGAAACGTTGTTACGCGGGGGAAAAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCg                                             <  2:94628/137‑1 (MQ=255)                                                                                                 cGGGTATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACaaa                                       >  1:1465914/1‑140 (MQ=255)                                                                                                       tCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATccc                                 <  1:1134696/140‑1 (MQ=255)                                                                                                        cACCATGTAAAACGTTGTTCCGCGGGGGAAAAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCt                                <  2:247924/140‑1 (MQ=255)                                                                                                             tgtaAACCGTTTTTCCGCGGGGGAGAAAAGCCCCTGGACCCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGc                           <  2:1126868/140‑1 (MQ=255)                                                                                                              gtgAAACGTTGTTACGCCGTGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCg                          >  2:664070/1‑140 (MQ=255)                                                                                                              gtgAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTTCGGACAAAAATCCCTAAGGCg                          >  2:571873/1‑140 (MQ=255)                                                                                                              gtgAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCg                          >  2:636277/1‑140 (MQ=255)                                                                                                              gtgAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCg                          >  1:247924/1‑140 (MQ=255)                                                                                                              gtgAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCg                          >  1:2039475/1‑140 (MQ=255)                                                                                                              gtgAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCg                          <  1:1901136/140‑1 (MQ=255)                                                                                                               tgAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGa                         >  2:1915596/1‑140 (MQ=255)                                                                                                                  aaCGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATcc                      >  1:1539790/1‑140 (MQ=255)                                                                                                                   aCGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATccc                     >  2:1372211/1‑140 (MQ=255)                                                                                                                    cGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCt                    >  2:1632222/1‑140 (MQ=255)                                                                                                                         ttACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCaa               >  1:609435/1‑140 (MQ=255)                                                                                                                           ccgcgGGGGAGAAAGGACGGTGTCGCCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATg             <  2:1735076/139‑1 (MQ=255)                                                                                                                                 gggAGTAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATGCCGccc       <  1:873164/140‑1 (MQ=255)                                                                                                                                 gggAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATGCCGccc       >  1:704562/1‑140 (MQ=255)                                                                                                                                      aaaaGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATGCCGCCCAGCTg  <  1:1806909/139‑1 (MQ=255)                                                                                                                                        aaGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATGCCGCCCAGCTg  <  2:1745332/138‑1 (MQ=255)                                                                                                                                        aaGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATGCCGCCCAGCTg  >  1:1745332/1‑138 (MQ=255)                                                                                                                                           |                                                                                                                                       CTCGCCAGTAATCCTACAAATGCAGCAAACTGGAAAAGTATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATGCCGCCCAGCTG  >  NC_000913/2628487‑2628759

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑