Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,665,702	0	C	A	33.3%	54.9 / 12.3	36	A37S (GCG→TCG)	gadX	acid resistance regulon transcriptional activator; autoactivator
Reads supporting (aligned to +/- strand):  ref base C (22/2);  new base A (0/12);  total (22/14)
Fisher's exact test for biased strand distribution p-value = 7.27e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTTTATTA  >  NC_000913/3665556‑3665849                                                                                                                                                   |                                                                                                                                                    atgaACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaa                                                                                                                                                 <  1:204728/151‑1 (MQ=255)     aCGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAAcc                                                                                                                                              >  1:42191/1‑150 (MQ=255)         gTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTc                                                                                                                                         >  2:346660/1‑151 (MQ=255)                          ttATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGc                                                                                                                        >  2:160737/1‑151 (MQ=255)                           tATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCg                                                                                                                       >  2:304559/1‑151 (MQ=255)                                       gATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCAtt                                                                                                           >  1:251664/1‑151 (MQ=255)                                                   cctcctTAATCATCGGGAAAAATAATGAAGGGTTGCCCCTTGACACGAATAAAAAATTTTCAACCCCCTTATCTCCTCAATTTGGGTTTCCACCCGCAAACCCCGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg                                                                                                 <  1:98071/149‑1 (MQ=255)                                                      cctTGAGCATGGGGAAAAATAATAAAGGCGTTTCCCTGGACACAAAAAAAAAATTTTCAACACATTTATCTCCGCAATTTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat                                                                                            <  2:216712/151‑1 (MQ=255)                                                             cATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATAttt                                                                                      >  1:330640/1‑150 (MQ=255)                                                                             aaacgcttgccccTTACCACAAATAAAAACTTTTAAACACTCTTATCTGCACAAATTTGTTTTGCATCCAAAAAACCCAGCACTCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCaa                                                                     <  2:217745/141‑1 (MQ=255)                                                                              aaggCGTGTCCTTTGACACAAATACAAAATTTTCAACACCTTTATCTACTCGATTTTGGCTGGCATCCGAAAAACCCAGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCa                                                                      <  2:192126/146‑1 (MQ=255)                                                                                aGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAAtt                                                                   >  2:180592/1‑150 (MQ=255)                                                                                     ccccgttGACAGGAAAAAAAAATTATCAACACTCTTATCTTTGCTAATTGGTCTTGCACGCGAAAAAACGAGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGa                                                                <  1:394458/143‑1 (MQ=255)                                                                                       ccctggccattaaTATAAAATTTCCAACGCTCTCTTTTATTCAAATTTGTTTTGCATCCCAAAAAAGCAGTACGCCGCCATTAAAATAGCGATATTCACCATGAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTa                                                                  <  1:158176/133‑1 (MQ=255)                                                                                       ccctgaacacAAATAAAAAATTTACACCACCCTTATCTCCCCAATTTTGGTTTGCATCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAAtt                                                           <  2:163443/145‑1 (MQ=255)                                                                                         cTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGACATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTcc                                                         >  1:321435/1‑151 (MQ=255)                                                                                              cacGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGt                                                    >  1:135230/1‑151 (MQ=255)                                                                                               acGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGt                                                    >  2:121315/1‑150 (MQ=255)                                                                                                 gAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGt                                                 >  2:327536/1‑151 (MQ=255)                                                                                                  aaaaaaaaaTTTTAAACACACTTATCTACTGAATTTTGGTTTGAACCCAAAAAACCCGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATg                                                     <  1:278953/141‑1 (MQ=255)                                                                                                       aaatTTTTAAACACCTTTATCTCCTCAATTTTGGTTTGCATCCGAAAAACCCGGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGAtt                                             <  2:264858/149‑1 (MQ=255)                                                                                                       aaaaTTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGc                                           >  2:272164/1‑151 (MQ=255)                                                                                                        aaaTTTCCAACCCTCTTATCTACCCACATTTGCCTCGCACCCCAAAAACCCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTGGCATACGCAATTAGACAATTCCCATGTAGTGATTGCa                                          <  1:304441/151‑1 (MQ=255)                                                                                                         aaTTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCAt                                         >  1:180870/1‑151 (MQ=255)                                                                                                          aTTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCAt                                         >  1:345693/1‑150 (MQ=255)                                                                                                           ttttCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCAt                                         >  2:69851/1‑149 (MQ=255)                                                                                                              tCAACACACTTATCTACTCTAATTTAGCTTGCATCCGCAAAAACCAAACCACCGCCTTTAAAATAGTGACATTCATCATTAACCATGGTGAGACTATATTTATGTCTTGCATAAGCAATTAGACAATTCCCATGTAGTAATTGCATATTTg                                    >  1:4257/1‑151 (MQ=255)                                                                                                                aaCACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGa                                   >  1:242044/1‑150 (MQ=255)                                                                                                                       ttATCTACTCAAATTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAat                             <  2:166622/149‑1 (MQ=255)                                                                                                                        tATCTTCTCTATTTTGGCTGTCATCCGAAAAAACCGGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAatat                           <  2:177201/150‑1 (MQ=255)                                                                                                                        tATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATAtt                          >  2:5141/1‑151 (MQ=255)                                                                                                                                  aaTTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACat                >  1:326908/1‑151 (MQ=255)                                                                                                                                      tGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATAtt             >  1:301204/1‑150 (MQ=255)                                                                                                                                             cATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGttt      >  2:139804/1‑150 (MQ=255)                                                                                                                                                ccGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTtta     <  2:256289/148‑1 (MQ=255)                                                                                                                                                 cGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTttatta  >  1:225382/1‑150 (MQ=255)                                                                                                                                                   |                                                                                                                                                    ATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTTTATTA  >  NC_000913/3665556‑3665849

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑