Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,336,901	0	T	A	41.9%	33.2 / 18.5	31	Y44F (TAT→TTT)	adiC	arginine:agmatine antiporter
Reads supporting (aligned to +/- strand):  ref base T (15/3);  new base A (0/13);  total (15/16)
Fisher's exact test for biased strand distribution p-value = 3.22e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.30e-01

GACGTTGGTTTGATAACCGAGAAACGGGCCAAAGCAGCGGCGGGCGTAAGCGTAAGAACCACCAGGACTTGGGTCGAGGAACGACATTTTGG‑CGTATACCATCGAGAGCCCCAGTGCACCGATAATCGTCACCAACCATCCATAAATGG‑CAA‑TCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGAAAAACACCTGACCCCATAATATTCCCCGACACCATCAGGGTGACGGGGATTAAGCCCACTTTGTGAGCATCAGCATCCGAAGACATAATTAAACTCCTGCGAAGGC  >  NC_000913/4336759‑4337051                                                                                                                                                |                                                                                                                                                         gACGTTGGTTTGATAACCGAGAAACGGGCCAAAGCAGCGGCGGGCGTAAGCGTAAGAACCACCAGGACTTGGGTCGAGGAACGACATTTTGG‑CGTATACCATCGAGAGCCCCAGTGCACCGATAATCGTCACCAACCATCCATAAATGG‑c                                                                                                                                                  >  1:791424/1‑150 (MQ=255)   cGTTGGTTTGATAACCGAGAAACGGGCCAAAGCAGCGGCGGGCGTAAGCGTAAGAACCACCAGGACTTGGGTCGAGGAACGACATTTTGG‑CGTATACCATCGAGAGCCCCAGTGCACCGATAATCGTCACCAACCATCCATAAATGG‑CAA‑t                                                                                                                                              <  2:779469/151‑1 (MQ=255)      tGGTTTGATAACCGAGAAACGGGCCAAAGCAGCGGCGGGCGTAAGCGTAAGAACCACCAGGACTTGGGTCGAGGAACGACATTTTGG‑CGTATACCATCGAGAGCCCCAGTGCACCGATAATCGTCACCAACCATCCATAAATGG‑CAA‑Tccc                                                                                                                                           >  1:462276/1‑151 (MQ=255)        gTTTGATAACCGAGAAACGGGCCAAAGCAGCGGCGGGCGTAAGCGTAAGAACCACCAGGACTTGGGTCGAGGAACGACATTTTGG‑CGTATACCATCGAGAGCCCCAGTGCACCGATAATCGTCACCAACCATCCATAAATGG‑CAA‑TCCCGc                                                                                                                                         <  2:794352/151‑1 (MQ=255)          ttGATAACCGAGAAACGGGCCAAAGCAGCGGCGGGCGTAAGCGTAAGAACCACCAGGACTTGGGTCGAGGAACGACATTTTGG‑CGTATACCATCGAGAGCCCCAGTGCACCGATAATCGTCACCAACCATCCATAAATGG‑CAA‑TCCCGcc                                                                                                                                        >  2:337903/1‑150 (MQ=255)           tGATAACCGAGAAACGGGCCAAAGCAGCGGCGGGCGTAAGCGTAAGAACCACCAGGACTTGGGTCGAGGAACGACATTTTGG‑CGTATACCATCGAGAGCCCCAGTGCACCGATAATCGTCACCAACCATCCATAAATGG‑CAA‑TCCCGcc                                                                                                                                        >  2:124470/1‑149 (MQ=255)                aCCGAGAAACGGGCCAAAGCAGCGGCGGGCGTAAGCGTAAGAACCACCAGGACTTGGGTCGAGGAACGACATTTTGG‑CGTATACCATCGAGAGCCCCAGTGCACCGATAATCGTCACCAACCATCCATAAATGG‑CAA‑TCCCGCCAGTa                                                                                                                                    >  1:359793/1‑148 (MQ=255)                      aaaCGGGCAAAAGCAGCGGGGGGGGAAAGCGAAAAAACCCCCAGGACTGGGGCCGAGGAACGACATTTGGG‑GTTATCCCACCGAGACCCCCAGTGCCCCGATAACCGCCCCCAACCACCAAAAAAGGG‑CAA‑TCCCGCCAGTAGAGGCCa                                                                                                                             <  1:15002/149‑1 (MQ=255)                              cAAAGCAGCGGCGGGCGTAAGCGTAAGAACCACCAGGACTTGGGTCGAGGAACGACATTTTGG‑CGTATACCATCGAGAGCCCCAGTGCACCGATAATCGTCACCAACCATCCATAAATGG‑CAA‑TCCCGCCAGTAGAGGCCAGGTTTGCAgg                                                                                                                   >  1:803901/1‑151 (MQ=255)                               aaaGCAGCGGGGGGGGAAAGCGAAAAACCCACCAGGCTTGGGGTCGAGGAACGACTTTTTGG‑CGTATCCCACCGAGACCCCCAGTGCCCAGATAATCGTCCCCAACCATCCAAAAATGG‑CAA‑CCCCGCCAGTAGAGGCCAGGTTTGCa                                                                                                                     <  1:529807/148‑1 (MQ=255)                                 agcagcGGCGGGCGTAAGCGTAAGAACCACCAGGACTTGGGTCGAGGAACGACATTTTGG‑CGTATACCATCGAGAGCCCCAGTGCACCGATAATCGTCACCAACCATCCATAAATGG‑CAA‑TCCCGCCAGTAGAGGCCAGGTTTGCAGGTa                                                                                                                 >  2:644587/1‑150 (MQ=255)                                      cggcggGCGTAAGCGTAAGAACCACCAGGACTTGGGTCGAGGAACGACATTTTGG‑CGTATACCATCGAGAGCCCCAGTGCACCGATAATCGTCACCAACCATCCATAAATGG‑CAA‑TCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGa                                                                                                            >  2:111298/1‑150 (MQ=255)                                        gcgggcgTAAGCGAAAGACCCACCAGGCTTTGGGTGGAGGAACGACATTTTGG‑CGTATCCCATCGAGACCCCCAGTGCACCAATAATCTTCCCCAACCATCCAAAAATGG‑CAA‑TCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGaaaa                                                                                                         <  2:466740/151‑1 (MQ=255)                                                      aagAACCACCAGGCCTGGGGTGGAGGAACGACTTTTTGG‑CGTATACCAGCGAGACCCCCAGTGCACCGATAACCGTCACCAACCACCCAAAAATGC‑CAA‑CCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGAAAAACACCTGAccc                                                                                              <  1:62992/148‑1 (MQ=255)                                                           cccccgggcttggggTCGAGGAACGACATTTTGG‑CTTATCCCATCGAGAGCCCCAGTGCACCAAAAATCGTCCCAAACCATCAAAAAATGG‑CAA‑TCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGAAAAACACCTGACCCCATAatat                                                                                      <  2:279201/139‑1 (MQ=255)                                                                       gggTGGAGGAACGACTTTTTGG‑CTTATACCATCGAGACCCCCAGTGCCCCGATAATCGTCACCACCCACCCAAAAATGA‑CAA‑TCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGAAAAACACCTGACCCCATAATATTCCCCGACACCa                                                                          <  2:253197/151‑1 (MQ=255)                                                                       gggTCGAGGACCGACATTTTGG‑CGTACACCATCGGGACCCCCGGTGCCCCGATAATCGCCACCACCCA‑CCAAAAAAGG‑CAACCCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGAAAAACACCTGACCCCATAATATTCCCCGACAcc                                                                           <  1:228388/150‑1 (MQ=255)                                                                       gggTCGAGGAACGACATTTTGG‑CGTATACCATCGAGAGCCCCAGTGCACCGATAATCGTCACCAACCATCCATAAATGG‑CAA‑TCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGAAAAACACCTGACCCCATAATATTCCCCGACAcc                                                                           >  1:379377/1‑150 (MQ=255)                                                                           cGAGGAACGACATTTTGG‑CGTATACCATCGAGAGCCCCAGTGCACCGATAATCGTCACCAACCATCCATAAATGG‑CAA‑TCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGAAAAACACCTGACCCCATAATATTCCCCGACACCATc                                                                        >  2:636570/1‑149 (MQ=255)                                                                                       ttttGG‑CGTATACCATCGAGAGCCCCAGTGCACCGATAATCGTCACCAACCATCCATAAATGG‑CAA‑TCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGAAAAACACCTGACCCCATAATATTCCCCGACACCATCAGGGTGACGGGGAt                                                          >  2:729981/1‑151 (MQ=255)                                                                                        tttGGCCGTATCCCACCGAGACCCCCAGTGCCCCGAAAACCG‑CCCCAACCCACCAAAAAAGGCCAA‑TCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGAAAAACACCTGACCCCATAATATTCCCCGACACCATCAGGGTGACg                                                               <  1:71766/146‑1 (MQ=255)                                                                                           gg‑CGTATCCCATCGAGAGCCCCAGTGCCCCGATAATCGTCCCCAACCATCCATAAATGG‑CAA‑TCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGAAAAACACCTGACCCCATAATATTCCCCGACACCATCAGGGTGACGGGGATTAAg                                                      <  2:791474/151‑1 (MQ=255)                                                                                                        cGAGAGCCCCAGTGCACCGATAATCGTCACCAACCATCCATAAATGG‑CAA‑TCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGAAAAACACCTGACCCCATAATATTCCCCGACACCATCAGGGTGACGGGGATTAAGCCCACTTtgtg                                           >  2:87579/1‑150 (MQ=255)                                                                                                                        ccGATAATCGTCACCAACCACCCAAAAAGGG‑CAA‑CCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGAAAAACACCTGACCCCATAATATTCCCCGACACCATCAGGGTGACGGGGATTAAGCCCACTTTGTGAGCATCAGCATCCGaa                           <  2:338361/150‑1 (MQ=255)                                                                                                                        ccGAAAATCGCCCCCAACCATCAAAAAAGGG‑CAA‑TCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGAAAAACACCTGACCCCATAATATTCCCCGACACCATCAGGGTGACGGGGATTAAGCCCACTTTGTGAGCATCAGCATCCGaa                           <  1:415009/150‑1 (MQ=255)                                                                                                                         cgaaaaccgcccccacccacCCAAAAAGGC‑AAA‑CCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGAAAAACACCTGACCCCATAATATTCCCCGACACCATCAGGGTGACGGGGATTAAGCCCACTTTGTGAGCATCAGCATCCGa                            <  1:645128/136‑1 (MQ=255)                                                                                                                             aaTCGTCACCAACCATCCATAAATGG‑CAA‑TCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGAAAAACACCTGACCCCATAATATTCCCCGACACCATCAGGGTGACGGGGATTAAGCCCACTTTGTGAGCATCAGCATCCGAAGACAt                      >  1:732950/1‑150 (MQ=255)                                                                                                                                   caccacCCACCAAAAAAGGG‑CAA‑TCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGAAAAACACCTGACCCCATAATATTCCCCGACACCATCAGGGTGACGGGGATTAAGCCCACTTTGTGAGCATCAGCATCCGAAGACATaa                    <  2:645670/146‑1 (MQ=255)                                                                                                                                     ccacccaTCCAAAAAGGG‑CAA‑CCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGAAAAACACCTGACCCCATAATATTCCCCGACACCATCAGGGTGACGGGGATTAAGCCCACTTTGTGAGCATCAGCATCCGAAGACAt                      <  1:284325/142‑1 (MQ=255)                                                                                                                                     ccaaccaTCCATAAATGG‑CAA‑TCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGAAAAACACCTGACCCCATAATATTCCCCGACACCATCAGGGTGACGGGGATTAAGCCCACTTTGTGAGCATCAGCATCCGAAGACATAATTAAACt             >  1:729450/1‑151 (MQ=255)                                                                                                                                       aaccaTCCATAAATGG‑CAA‑TCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGAAAAACACCTGACCCCATAATATTCCCCGACACCATCAGGGTGACGGGGATTAAGCCCACTTTGTGAGCATCAGCATCCGAAGACATAATTAAACTcc           >  1:321849/1‑151 (MQ=255)                                                                                                                                           atccaaAAATGG‑CAA‑TCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGAAAAACACCTGACCCCATAATATTCCCCGACACCATCAGGGTGACGGGGATTAAGCCCACTTTGTGAGCATCAGCATCCGAAGACATAATTAAACTCCTGc        <  1:94329/150‑1 (MQ=255)                                                                                                                                                tAAATGG‑CAA‑TCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGAAAAACACCTGACCCCATAATATTCCCCGACACCATCAGGGTGACGGGGATTAAGCCCACTTTGTGAGCATCAGCATCCGAAGACATAATTAAACTCCTGCGAAGGc  >  1:136601/1‑151 (MQ=255)                                                                                                                                                |                                                                                                                                                         GACGTTGGTTTGATAACCGAGAAACGGGCCAAAGCAGCGGCGGGCGTAAGCGTAAGAACCACCAGGACTTGGGTCGAGGAACGACATTTTGG‑CGTATACCATCGAGAGCCCCAGTGCACCGATAATCGTCACCAACCATCCATAAATGG‑CAA‑TCCCGCCAGTAGAGGCCAGGTTTGCAGGTAACAGAAAAACACCTGACCCCATAATATTCCCCGACACCATCAGGGTGACGGGGATTAAGCCCACTTTGTGAGCATCAGCATCCGAAGACATAATTAAACTCCTGCGAAGGC  >  NC_000913/4336759‑4337051

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑