Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,665,702	0	C	A	43.9%	33.9 / 24.6	43	A37S (GCG→TCG)	gadX	acid resistance regulon transcriptional activator; autoactivator
Reads supporting (aligned to +/- strand):  ref base C (17/6);  new base A (0/18);  total (17/26)
Fisher's exact test for biased strand distribution p-value = 6.89e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTTTATT  >  NC_000913/3665558‑3665848                                                                                                                                                  |                                                                                                                                                    gaACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAAc                                                                                                                                               >  1:546637/1‑151 (MQ=255)      aGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCA‑GGt                                                                                                                                         >  2:461542/1‑151 (MQ=255)         aaTGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCA‑GGTCAc                                                                                                                                      >  2:646651/1‑151 (MQ=255)         aaTGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCA‑GGTCAc                                                                                                                                      >  2:258324/1‑151 (MQ=255)                  aCTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTa                                                                                                                              >  1:277850/1‑150 (MQ=255)                  aCTTTTTTATGTGCATGAAGATTTAATCCCCCCTCCTTGACCAACGGGAGAAATAATGAAAGCGTGTCCCTTGACACAAATAAAAAATTTT‑CACCACACTTATCTACTCAAATTTGGCTCGCAACCGCAAAACCCA‑GGCCACCGCCATTaa                                                                                                                             <  2:689139/151‑1 (MQ=255)                         tATGTGCATGAAGATTTATTGCCTCCTCCTTGAGCATCGGGAAAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTCCTCAAATTTGGCTTGCATCCGAAAAAACCA‑GGTCACCGCCATTAAAATAGc                                                                                                                       <  2:601914/150‑1 (MQ=255)                           tgtgCATGAAGATTTAATCCCTCCTCCTTGAGCAGCGGGAAAAAAAATAAAAGCGTGTCCCTTGACACGAATACAAAATTTC‑CAACACACTTATCTACTCGAATTTGGCTTCCATCCAAAAAAACCG‑GGTCACCGCCATTAAAATAGCg                                                                                                                      <  1:140315/149‑1 (MQ=255)                               cATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTc                                                                                                                >  2:577107/1‑151 (MQ=255)                                agaaaGATTTAGTGCCTCCTCCTTGAGCATCGGAAGAAAAAATAAAAGTGTGTCCTTGGACAGAAAAAAAAAATTTT‑CAACTCCCTTATCCCATCAAATTTGGCTTGAACCCAAAAAACCCA‑GGTCCCCGCCATTAAAATAGCGa                                                                                                                     <  2:30315/142‑1 (MQ=255)                                   aaGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCTTTGACACGAATAAAAAATTTT‑CAACACACTTATCTCCTCGAATTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCa                                                                                                            <  1:487497/151‑1 (MQ=255)                                     gATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCAtt                                                                                                          >  1:227715/1‑151 (MQ=255)                                        ttAATGCCCCCTCCTGGAGCATCGGGAAAAATAATGAAGGCGTGCCCCTT‑ACAAAAAAAAAAAATTTTCCAACCCATTTATCTACCCAAATTTGGTTTCCACCCG‑AAAAACCAGGGTCACCGCCATTAAAATAGCGATATTCACCATTaa                                                                                                        <  2:386018/150‑1 (MQ=255)                                          aaTCCCTCCCCCTGGAGCATCGGGAAAAATAAAGAAAGGGTTTCCCTTGACACGAATAAAAAATTTA‑CAACACACTTATCTACTGGATTTTGGTTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCa                                                                                                     <  1:412592/151‑1 (MQ=255)                                              ctccctcctTGAGCACGGGGAAAAAAAATGAAAGCGTGCCCCTTGCCCCGAATACAAATTTTT‑CAACACTCTTATCTACCCGAATTTGCCTTGAATCCGCAAAACCCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATgg                                                                                                  <  1:589692/147‑1 (MQ=255)                                                  ctcctTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg                                                                                                >  2:297331/1‑148 (MQ=255)                                                  ctcctTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg                                                                                                >  1:573670/1‑148 (MQ=255)                                                       tGAGCATCGGGAAAAATAATGAAAGCGTGTCCCTTGACAAGAATAAAAAATTTT‑CAACACACTTATCTACTCAAATTTGGTTTGCATCCGAAAAAACCG‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAatat                                                                                         <  2:263659/150‑1 (MQ=255)                                                          acATCGGGAAAAATAATAAAAGCGTGTCCCTTGACACGAATAAAAAATTTT‑CAACACCCTTATCTCCTAAAATTTGGCTTCCTCCCGAAAAAACAG‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATAttt                                                                                     <  2:420511/150‑1 (MQ=255)                                                             gcggaaaaaaTAAGGAAAGCGTGCCCCTTCTCTATAAT‑CAAAATTTTAAAACACACTTTTCTCCCCGAGTTTGGCTTGCAGCATTAAAACCCA‑GGTCCCCGCCATTAAAATAGCGATATGCACCATTAACCATGGTGAGAATATATTTa                                                                                    <  1:18692/142‑1 (MQ=255)                                                                gaaaaaaaaaTGAAGGCTTGCCCCTTGACACAAAAAAAAATTTTA‑CAACACACTTTTCTACAAAAATTTGTATTGCACCCAAAAAACCCT‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATg                                                                                  <  2:601992/144‑1 (MQ=255)                                                                  aaaaaTAAAGAACGCGTGCCCTTTGACACAAATAAAAAATTTC‑CAACCCACTTATCTACTCAATTTGGGCTTGCA‑CCCAAAAAACCAGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCt                                                                               <  2:216561/147‑1 (MQ=255)                                                                    aaaTAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGc                                                                            >  1:177841/1‑150 (MQ=255)                                                                     aataatGAAGGCGTGTCCCTTGACACAAATAAAAAATTTT‑CAACCCTCTTATCTCCTCAAATTTGGCTTGCACCCGAAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCAt                                                                          <  1:188579/151‑1 (MQ=255)                                                                     aataatGAAAGCGTGTCCCTTGACACAAATACAAAATTTT‑CAACACACTTATCTACTCAAATTTGGCTTGCATCCCCAAAAACCA‑GGACACCGCCATTAAAATAGCGATATTCACCATTAAACAAGGTGAGAGTATATTTATGTCTTGCAt                                                                          >  2:649992/1‑151 (MQ=255)                                                                            aaaGCGTGTCCTTTGACACAAATAAAAAATTTT‑AAACACTCTTATCTACTCAAATTTGGCTTGCACCCAAAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCaa                                                                    <  2:114042/150‑1 (MQ=255)                                                                             aaGCGTGCCCTTTGACACAAAAAAAAAATTTT‑CAACACACTTATCTACTCAATTTTGGCTTGCACCCAAAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAAtt                                                                  <  1:449919/151‑1 (MQ=255)                                                                                     cccTTAACACAAAAAAAAAATTTC‑AACCACACTTATCTACTAAAATTTGGTGTCCACCCGAAAAACCCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGa                                                               <  2:181793/146‑1 (MQ=255)                                                                                      ccTTGACACGAATAAAAAATTTT‑CAACACACTTATCTACTCAATTTTGGCTTGCACCCGAAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTc                                                         <  1:425295/151‑1 (MQ=255)                                                                                             acGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGt                                                   >  1:19428/1‑150 (MQ=255)                                                                                               aaaTAAAAAATTTC‑AAACCCACTTATTTACTCGATTTTGGTTTGCATCCAAAAAAACCA‑GGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGt                                                <  1:442148/150‑1 (MQ=255)                                                                                                aaTAAAAAATTTT‑CAACACACTTATCTACTCAAATTTGGCTTGCACCCGCAAAACCCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTg                                               <  2:304194/151‑1 (MQ=255)                                                                                                   aCAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCA‑GGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGAtt                                            >  2:231024/1‑151 (MQ=255)                                                                                                   aCAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCACCCGCAAAACCCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGa                                              <  1:12567/149‑1 (MQ=255)                                                                                                     aaaaTTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGc                                          >  1:444666/1‑151 (MQ=255)                                                                                                       aaTTTA‑CAACACACTTATCTACTCAATTTTGGCTTGCACCCGAAAAACCCA‑GGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCAt                                        <  1:322544/151‑1 (MQ=255)                                                                                                           ttacAACACACTTATCTACTCAATTTTGGTTTGCACCCGAAAAACCCG‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAg                                      <  2:442186/147‑1 (MQ=255)                                                                                                            t‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTg                                   >  2:165511/1‑151 (MQ=255)                                                                                                                            aCTCTAATTGGGCTTCCACCCGAAAAAACCA‑GTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTAc                       <  2:153816/148‑1 (MQ=255)                                                                                                                               cGAATTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAAc                 >  1:695758/1‑151 (MQ=255)                                                                                                                                      ggCTTGCACCCGAAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTAc          <  1:611590/151‑1 (MQ=255)                                                                                                                                           acATCCAAAAAAACCG‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGttt     <  1:89011/150‑1 (MQ=255)                                                                                                                                              tCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTttatt  >  1:701214/1‑151 (MQ=255)                                                                                                                                                  |                                                                                                                                                    GAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTT‑CAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCA‑GGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTTTATT  >  NC_000913/3665558‑3665848

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑