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%	85.7 / 16.5	47	V105G (GTC→GGC)	pdeF	cyclic di‑GMP phosphodiesterase PdeF
Reads supporting (aligned to +/- strand):  ref base A (32/1);  new base C (0/14);  total (32/15)
Fisher's exact test for biased strand distribution p-value = 4.39e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

CAGTAATCCTACAAATGCAGCAAACTGGAAAAGTATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGG‑TATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATGCCGCCCAGCTGAAAAA  >  NC_000913/2628492‑2628764                                                                                                                                       |                                                                                                                                            cAGTAATCCTACAAATGCAGCAAACTGGAAAAGTATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGG‑TATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGt                                                                                                                                       >  1:904932/1‑140 (MQ=255)    tAATCCTACAAAGGCAGCAAACTGAAAAAGTATAAGAAACAGCGTTGCAGAAAACACAATCTGCCAGAATATACGCGGGAAAATAAAACGGG‑TATCCCCATGTGAAACGTTGTTCCGCGGGGGAGAAAAGCCCCTGTAAc                                                                                                                                    <  2:904932/140‑1 (MQ=255)    tAATCCTAAAAATGCAGCAAACTGAAAAAGTATCAGAAACAGCGTTGCAGGAAACACAATCTGCAAGAATATACGCTGGAAAATTAAACGGG‑TATCACCATGTAAAACGTTGTTACGCCGGGGAGAAAAGCCCCTGTAAc                                                                                                                                    <  1:1096691/140‑1 (MQ=255)          aaaaaaTGCAGCAAACTGAAAAAGTATCAGAAACAGCGTGGCAGGAAACACAATCTGCCAAAATATCCGCT‑GGAAAATAAACGGGTTACCACCATGTGAAACGTTGTTACGCGGGGGAGAAAAGCCCCTGTAACCGcccc                                                                                                                              <  2:1103781/137‑1 (MQ=255)            aaaaTGCAGCAAACGGAAAAAGTATAAGAAACAGCGTTGCAGGAAACAAAATCTGCCAGAATATACGCGGGAAAATTAAACGGG‑TATCCCCATGTAAAACGTTGTTACGCGGGGGAGAAAAGCCCCTGTAACCGCCCCaa                                                                                                                            <  2:374940/139‑1 (MQ=255)              aaTGCAACAAACGGAAAAAGTATCAAAAACAGCGTTGCAGAAAACACAATCTGCAAAAATATCCGCGGGAAAATAAAACGGG‑TATCCCCATGTAAAACGTTGTTACGCGGGGGAGTAAAGCCCCTGTAACCGCCCCAACa                                                                                                                          <  2:1007357/140‑1 (MQ=255)              aaTGCAAAAAACTGAAAAATTATAAAAAACAGCGTTGCAGAAAACACAATCTGCAAGAATATACGCGGGAAAATAAAACGGG‑TATCCCCATGTAAAACGTTTTTACGCGGGGGAGAAAAGCCCCTGTAACCGCCCCAACa                                                                                                                          <  2:986777/140‑1 (MQ=255)                 gcagcaAACTGGAAAAGTATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGG‑TATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACagag                                                                                                                       >  2:337226/1‑140 (MQ=255)                 gcaacaAACGGAAAAAGTATAAAAAACAGCGTTGCAGAAAACACAATCTGCCAAAATATCCGCGGGAAAATTAAACGGG‑TATCACCATGTAAAACGTTGTTCCGCGGGGGAGTAAAGCCCCTGTAACCGCCCCAACagag                                                                                                                       <  2:693536/140‑1 (MQ=255)                   agcaAACTGGAAAAGTATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGG‑TATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGaa                                                                                                                     >  1:986777/1‑140 (MQ=255)                         cTGGAAAAGTATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGG‑TATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGaatgataa                                                                                                               >  1:20694/1‑140 (MQ=255)                          tGGAAAAGTATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGG‑TATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGaatgataat                                                                                                              >  2:937483/1‑140 (MQ=255)                          gggAAAAGTATCAAAAACAGCGTTGCAGAAAACACAATCTGCCAGAATATACGCGGGAAAATTAAACGGG‑TATCACCATGTGAAACGTTGTTACGCGGGGGAGAAAAGCCCCTGTAACCGCCCCAACAGAGaatgataat                                                                                                              <  2:831356/139‑1 (MQ=255)                          ggaaaaaGTATCAAAAACAGCTTTGCAGAAAACACAATCTGCCAAAATATACGCTGGAAAATAAAACGGG‑TATCACCATGTGAACCGTTGTTACGCGGGGGAGAAAAGCCCCTGTAACCGCCCCAACAGAGaatgataat                                                                                                              <  2:138818/137‑1 (MQ=255)                           ggAAAAGTATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGG‑TATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGaatgatctgt                                                                                                             >  1:1226503/1‑136 (MQ=255)                               aaGTATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGG‑TATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAAtgataatgataa                                                                                                         >  1:222718/1‑140 (MQ=255)                                    aaaaaaaCAGCGTGGCAGGAAACACAATCTGCAAAAATATACGCGGGAAAATAAAACGGG‑TATCACCATGTAAACCGTTGTTACGCGGGGGAGAAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATaaaa                                                                                                    <  2:952755/136‑1 (MQ=255)                                        aaaCAGGGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGAAAATAAACCGGT‑TATCACCATGTAAAACGTTGTTACGCGGGGGAGAAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAg                                                                                                <  2:419006/140‑1 (MQ=255)                                        aaaCAGCGTTGCAGGAAACAAAATCTGCCAGAATATACGCGGGAAAATAAAACGGG‑TATCCCCATGTGAAACGTTGTTACGCCGGGGAGAAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAg                                                                                                <  2:735214/140‑1 (MQ=255)                                        aaaCAGCGTTGCAGAAAACACAATCTGCCAGAATATACGGGGGAAAATAAAACGGG‑TACCCCCATGTGAAGGGTTGTTACGCCGGGGAGAAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAg                                                                                                <  2:623585/140‑1 (MQ=255)                                              cGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGG‑TATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTa                                                                                          >  1:805252/1‑140 (MQ=255)                                                ttGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGG‑TATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAAt                                                                                        >  1:419006/1‑140 (MQ=255)                                                          cacaATCTGCCAGAATATACGCTGGAAAATTAAACGGT‑TATCACCATGTAAAACGTTGTTACGCCGGGGAGTAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGttt                                                                              <  2:735996/140‑1 (MQ=255)                                                             aaTCTGCCAGAATATACGCTGGGAAATTAAACGGG‑TATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGt                                                                           >  1:691845/1‑140 (MQ=255)                                                               tCTGCCAGAATATACGCTGGGAAATTAAACGGG‑TATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTaa                                                                         >  1:735996/1‑140 (MQ=255)                                                                    cAGAATATACGCTGGGAAATTAAACGGG‑TATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAAcc                                                                    >  2:56358/1‑140 (MQ=255)                                                                       aaTATACGCGGGAAAATTAAACGGG‑TATCCCCATGTGAAACTTTGTTACGCGGGGGAGAAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAg                                                                 <  2:805252/140‑1 (MQ=255)                                                                         tataCGCTGGGAAATTAAACGGG‑TATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGct                                                               >  2:843657/1‑140 (MQ=255)                                                                         tataCGCTGGGAAATTAAACGGG‑TATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGct                                                               >  2:237284/1‑140 (MQ=255)                                                                                tGGGAAATTAAACGGG‑TATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCata                                                        >  1:573202/1‑140 (MQ=255)                                                                                  ggAAATTAAACGGG‑TATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATAtt                                                      >  2:1360526/1‑140 (MQ=255)                                                                                  ggAAATTAAACGGG‑TATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATAtt                                                      >  1:1108783/1‑140 (MQ=255)                                                                                  ggAAATTAAACGGG‑TATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATAtt                                                      >  2:1232636/1‑140 (MQ=255)                                                                                                  aTCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATcc                                       >  1:638196/1‑140 (MQ=255)                                                                                                         tgtgAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGc                                >  1:376155/1‑140 (MQ=255)                                                                                                         tgtgAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGc                                >  1:894828/1‑140 (MQ=255)                                                                                                          gtgAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCg                               >  2:247532/1‑140 (MQ=255)                                                                                                             aaagtttgttACCCGGGGAAAAAAAGCCCTTAAAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATc                            <  2:551890/135‑1 (MQ=255)                                                                                                             aaaCGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATc                            >  2:317270/1‑140 (MQ=255)                                                                                                                 gttgttACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTg                        >  1:551890/1‑140 (MQ=255)                                                                                                                 gttgttACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTg                        >  1:698298/1‑140 (MQ=255)                                                                                                                   tgttACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGc                      >  1:1036012/1‑140 (MQ=255)                                                                                                                     ttACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCaa                    >  2:850148/1‑140 (MQ=255)                                                                                                                            ggggAGAAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATgccgcc             <  1:210111/140‑1 (MQ=255)                                                                                                                            ggggAAAAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATgccgcc             <  2:1048535/140‑1 (MQ=255)                                                                                                                             gggAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATGCCGccc            >  2:470589/1‑140 (MQ=255)                                                                                                                             gggAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATGCCGccc            >  2:322070/1‑140 (MQ=255)                                                                                                                             gggAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATGCCGccc            >  1:1278412/1‑140 (MQ=255)                                                                                                                             gggAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATGCCGccc            >  1:1048535/1‑140 (MQ=255)                                                                                                                             gggAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATGCCGccc            >  1:870628/1‑140 (MQ=255)                                                                                                                                    aaGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATGCCGCCCAGCTGaa     <  2:1108783/140‑1 (MQ=255)                                                                                                                                       aCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATGCCGCCCAGCTGaaaaa  <  1:56358/140‑1 (MQ=255)                                                                                                                                       aCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATGCCGCCCAGCTGaaaaa  >  1:579664/1‑140 (MQ=255)                                                                                                                                       |                                                                                                                                            CAGTAATCCTACAAATGCAGCAAACTGGAAAAGTATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGG‑TATCACCATGTGAAACGTTGTTACGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATGCCGCCCAGCTGAAAAA  >  NC_000913/2628492‑2628764

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑