Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	417,533	0	T	G	57.7%	‑5.8 / 16.4	26	V131G (GTG→GGG)	phoB	response regulator in two‑component regulatory system with PhoR
Reads supporting (aligned to +/- strand):  ref base T (7/4);  new base G (15/0);  total (22/4)
Fisher's exact test for biased strand distribution p-value = 2.21e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.76e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGAAGAGGTGATTGAGATGCAGGGATTAAGTCTCGACCCGACATCTCACCGAGTGATGGCGGGCGAAGA‑GCCGCTGGA‑GATGGGGCCGACA‑GAATTTAAACTGCTGCACTTTTTTATGACGCATCCTGAGCGCGTGTACAGCCGCGAGCAGCTGTTAAACCACGTCTGGGGAACTAACGTGTATGTGGAAGACCGCACGGTCGATGTCCACATTCGTCGCCT  >  NC_000913/417308‑417746                                                                                                                                                                                                                                  |                                                                                                                                                                                                                         tACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGGGGAAGAGGGGAt                                                                                                                                                                                                                       >  1:1048781/1‑229 (MQ=255)      ggcggcTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGAAGAGGTGATTgaga                                                                                                                                                                                                                  >  1:1717337/1‑229 (MQ=255)       gcggcTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGGGGGAGGGGGGATTgaggt                                                                                                                                                                                                                 >  1:1078490/1‑227 (MQ=255)        cggcTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGAAGAGGGGATTGAGATg                                                                                                                                                                                                                >  1:1612454/1‑229 (MQ=255)        cggcTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGGGGAAGGGGGGGTTgggaat                                                                                                                                                                                                                >  1:1941830/1‑227 (MQ=255)                                  acCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGAAGAGGGGGTTGAGATGCAGGGATTAAGTCTCGACCCGACAtc                                                                                                                                                                                      >  1:1905433/1‑229 (MQ=255)                                              aGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGAAGGGGTGATTGAGATGCAGGGATTAAGTCTCGACCCGACCACTCACCGAGTGAt                                                                                                                                                                          >  1:229128/1‑229 (MQ=255)                                              aGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGGGGAAGAGGGGATTGAGATGCAGGGGTTAAGTCTCGACCCGACATCTCACCGCGGGAt                                                                                                                                                                          >  1:1545379/1‑229 (MQ=255)                                              aGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGGGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGGGGAAGGGGGGATTTAGATGCAGGGATTTAGGCTCGACCCGAAATCTCGCCGAGGGAt                                                                                                                                                                          >  1:602805/1‑229 (MQ=255)                                                                          gATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGGAGAGGTGATTGAGATGCAGGGGTTAATTCTCGACCCGACATCTCACCGAGTGATGGCGGGGGGAGA‑GACGCTgggagcgggt                                                                                                                                             >  2:446874/1‑221 (MQ=255)                                                                           aTGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGAAGAGGGGATTGGGATGCa                                                                                                                                                                                                              >  1:875438/1‑164 (MQ=255)                                                                           aTGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGAAGAGGGGATTGAGATGCAGGGATTAAGTCTCGACCCGACATCTCACCGAGGGATGGCGGGGGGAAA‑GACGCCGGAGGATgggc                                                                                                                                            >  1:1593466/1‑228 (MQ=255)                                                                                  ccGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGGGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGGGGGAGAGGGGATTGAGATGCAGGGATTAAGTCTCGa                                                                                                                                                                                               >  1:349148/1‑172 (MQ=255)                                                                                                                              ggCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGGAGAGGGGATTGAGATGCAGGGATTAAGTCTCGACCCGACATCTCACCGAGGGATGGCGGGCGGAGA‑GCCGcc                                                                                                                                                       >  1:699474/1‑166 (MQ=255)                                                                                                                              ggCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGCGGAAGAGGTGATTGAGAGGCAGGGGTTAAGTCTCGACCCGACAt                                                                                                                                                                                       >  1:740166/1‑136 (MQ=255)                                                                                                                                                    aGCCGTTTTCGCCGACGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGGAGAGGTGATTGAGATGCAGGGATTAAGTCTCGACCCCACATCCCACCGCGTGATGGCGGGCGGAGAGGCGGCTGG‑‑GATGGGGGCGGCACAAATTTAACCTCCGGACCTTTTTTTTG‑CTCAACCCTAGCGCGGGTACAACCCCGcgcacgcgg                                                                     >  2:1695436/1‑220 (MQ=255)                                                                                                                                                    aGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGAAGAGGTGATTGAGATGCAGGGATTAAGTCTCGACCCGACATCTCACCGAGGGATGGCGGGGGGAGA‑GCCGGCGGA‑GATGGGGGCCGCA‑GAAATTAAAACGCTGCCATTTTTTATGAAGCACCCttggg                                                                                             >  1:1072675/1‑197 (MQ=255)                                                                                                                                                    aGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGAAGAGGGGATTGAGATGCAGGGATTAAGTCTCGACCCGACATCTCACCGAGTGATGGCGGGCGGGGA‑GACGCAGGG‑GATGGGGGCGCCA‑GAATTTAAACTGCTGCGCCTTTTTTTTTCGCATCCTGAGCGCGCGTGCATACCCGcgcagcggcttat                                                                 >  2:239661/1‑222 (MQ=255)                                                                                                                                                    aGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGGGGGAGAGGGGATTGAGATGCAGGGATTAAGGCTCCACCCGACATCTCACCGCGGGGTGGGGGGCGGGGA‑GGCGGTGGG‑GAAGGGGcgggcc                                                                                                                                      >  2:52179/1‑156 (MQ=255)                                                                                                                                                      ccGTTTTCGCCGAAGGGGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGAAGGGGTGATTGAGATGCAGGGATTAAGTCTCGACCCGACATCTCACCGAGTGATGGCGGGCGAAGA‑GCCGCTGGA‑GATGGGGCCGACA‑GAATTTAAACTGCTGCACTTTTTTATGACGCATCCTGAGCGCGTGTACAGCCGCGAGCAGCTGTTAAAcc                                                               <  1:809673/229‑1 (MQ=255)                                                                                                                                                                       gCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGAAGAGGTGATTGATATGCAGGGATTAAGTCTCGACCCGACATCTCTCCGAGTGATGGCGGGCGAAGA‑GCCGCTGGA‑GATGGGGCCGACA‑GAATTTAAACTGCTGCACTTTTTTATGACGCATCCTGAGCGCGTGTACAGCCGCGAGCAGCTGTTAAACCACGTCTGGGGAACTAAc                                              <  1:1086377/229‑1 (MQ=255)                                                                                                                                                                                   aagcAAAGCGATAAGGGGCCTATTTTCGCCAAGGGCGGTGGAAGAGGTAATTTAGATGCAGGGGTGAATCGTCGCCCCGACATCTCACCGAGTGAGGGCGGGCGAAGA‑ACCGCTGTA‑GATGGGGCCGACA‑GAATTTAAACTGCTGCACTTTTTTATGACGCATCCTGAGCGCGTGTACAGCCGCGAGCAGCTGTTAAACCACGTCTGGGAAACTAACGTATATGTGGa                                   <  2:840702/225‑1 (MQ=255)                                                                                                                                                                                                                  aTGGCGGTGGAAGAGGTGATTGAGATGCAGGGATTAAGTCCCGACCCGACATCTCACCGGGTGATGGCGGGGGGAGA‑GCCGCTGGG‑GATGGGGCGGCCC‑GAAATTTAACTGCTGGACCTTTTTTTTAAGCATCCCGAGCGCGGGGACAGCCCCCGGAGGCTGGTGAACAACGGCTCGGGGACTATCGGGCAGGTGGAGGACCGCCCGCGGGATGTGcacctctctcgc    >  2:793813/1‑219 (MQ=255)                                                                                                                                                                                                                   tGGCGGTGGAAGGGGTGATTGAGAAGCAGGGATTAAGTCTCGACACGACATCTCACCGAGTGATGGCGGGCGTAGA‑GCCGCTGGA‑GATGGGGCCGACA‑GAATTTAAACTGCTGCACTTTTTTATGACGCATCCTGAGCGCGTGTACAGCCGCGAGCAGCTGTTAAACCACGTCTGGGGAACTAACGTGTATGTGGAAGACCGCACGGTCGATGTCCACATTCGTCGCCt  <  1:569521/229‑1 (MQ=255)                                                                                                                                                                                                                   tGGCGGTGGAAGAGGGGATTTAGATGCAGGGATTAAGTCTCGACCCCACATCTCACCGAGTGATGGCGGGGGGAGA‑GCCGCTGGG‑GATGGGGGCGGCA‑GAAATTTAAATGCTGCCCTTTTTTTTGACGCAACCTGAGCGCGGGGAAAGcccccggc                                                                           >  2:1151445/1‑150 (MQ=255)                                                                                                                                                                                                                        gTGGAAGAGGGGATTGAGATGCAGGGATTAAGTCTCGACCCGACATCTCACCGAGTGATGGCGGGCGAAGA‑GCCGCTGGA‑GATGGGGCCGACA‑GAATTTAAACTGCTGCACTTTTTTATGACGCATCCTg                                                                                                >  1:241788/1‑130 (MQ=255)                                                                                                                                                                                                                                  |                                                                                                                                                                                                                         TACCTGGCGGCTCCGGTATCCAGTTCATCAAACACCTCAAGCGCGAGTCGATGACCCGGGATATTCCAGTGGTGATGTTGACCGCCAGAGGGGAAGAAGAAGATCGCGTGCGCGGCCTTGAAACCGGCGCGGATGACTATATCACCAAGCCGTTTTCGCCGAAGGAGCTGGTGGCGCGAATCAAAGCGGTAATGCGCCGTATTTCGCCAATGGCGGTGGAAGAGGTGATTGAGATGCAGGGATTAAGTCTCGACCCGACATCTCACCGAGTGATGGCGGGCGAAGA‑GCCGCTGGA‑GATGGGGCCGACA‑GAATTTAAACTGCTGCACTTTTTTATGACGCATCCTGAGCGCGTGTACAGCCGCGAGCAGCTGTTAAACCACGTCTGGGGAACTAACGTGTATGTGGAAGACCGCACGGTCGATGTCCACATTCGTCGCCT  >  NC_000913/417308‑417746

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑