Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,665,702	0	C	A	42.2%	71.9 / 23.4	45	A37S (GCG→TCG)	gadX	acid resistance regulon transcriptional activator; autoactivator
Reads supporting (aligned to +/- strand):  ref base C (23/3);  new base A (0/19);  total (23/22)
Fisher's exact test for biased strand distribution p-value = 6.32e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACT  >  NC_000913/3665555‑3665841                                                                                                                                                     |                                                                                                                                            gatgaACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTGGCTTGCAACCGCaaa                                                                                                                                          <  1:656295/151‑1 (MQ=255)     aaCGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAAc                                                                                                                                       >  1:512732/1‑150 (MQ=255)         aGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGt                                                                                                                                  >  2:349951/1‑151 (MQ=255)                aagaaACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAACATTTTCAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGcc                                                                                                                           >  2:666390/1‑151 (MQ=255)                       ttttttATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTaaa                                                                                                                     >  2:131458/1‑150 (MQ=255)                               gtgCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGat                                                                                                             >  1:739053/1‑150 (MQ=255)                                  cATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTc                                                                                                         >  2:320718/1‑151 (MQ=255)                                      aaGATTAAATGCCCCCTCCTTGAGCCGGGGAAAAAATAATAAAAGAGTCTCCCTTGCCAAAAAAAAAAAATTAACAA‑CACTCTTACCCACACGAATTTGGTTTGCACCCCAAAAAACCGGGACACCGCCATTAAAATAGCGATATTCACCa                                                                                                     <  1:123183/151‑1 (MQ=255)                                                 cctcctcctTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGt                                                                                          >  1:614662/1‑151 (MQ=255)                                                 ccccctcctGGAGCACCGGGAAAAAAAATAAAAGCGTGTCCCTTGACACAAATAAAAAATTTTAAA‑CACACTTATCTACTCGATTTTGGCTTGCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGt                                                                                          <  2:698257/148‑1 (MQ=255)                                                    cctcctTGAGCATCGGGAAAAAAAATGAAAGCGTGTCCCTTGACACAAAAAAAAAATTTTCAA‑CACACTTATCTCCTCAATTTTGGCTTGCACCCAAAAAAACCGGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTga                                                                                        <  2:43383/150‑1 (MQ=255)                                                    cctcctTGAGCATCGGGAAAAAAAATAAAGGCGTGTCCCTTGACACAAATA‑AAAATTTTCAACCCCCCTTATCTACCCAATTTTGTTTTCCACCCGAAAAACCAAGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTga                                                                                        <  2:695950/150‑1 (MQ=255)                                                       cctTGAGCATGGGGAAAAAAAATGAAAGCGTGCCCCTTGACACGAATAAAAAATTTTCAC‑CACACTTATCTACTCAATTTTGGTTTGCATCCGAAAAACCCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTga                                                                                        <  1:665099/147‑1 (MQ=255)                                                       cctGGAGAATCGGAAAAAATAATAAAAGCGTGTCCTTGCACACAAAAACAAAATTTTCAA‑CCCACTTATCTACTCAATTTGGGCTTCCACCCACAAAAACCGGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTga                                                                                        <  1:49656/147‑1 (MQ=255)                                                          tGAGCATCGGGAAAAATAATGAAAGCGTGTCCCTTGACACAAATACAAAATTTTCAA‑CACCCTTATCTACTCAATTTTGTTTTGCACCAGAAAAAACCAGGACACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAatat                                                                                  <  2:180109/150‑1 (MQ=255)                                                           gAGCATGGGGAAAAATAATGAAAGCGTGTCCTTTGACACAAATAAAAAATTTTCAA‑CACACTTATCTACAAAATTTTGGCTTGCACCCAAAAAAACCGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAatata                                                                                 <  2:641588/150‑1 (MQ=255)                                                            aGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATAtt                                                                               >  1:414438/1‑151 (MQ=255)                                                               acggggAAAAAAAAAGAAAGCTTTCCCATATACACAAATACAAAATTTTAAA‑CACAATTATCTACTCAAATTTGTCTTCATTCCCAAAAAACCGGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTAt                                                                            <  1:29412/148‑1 (MQ=255)                                                                 cGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGt                                                                          >  1:521924/1‑151 (MQ=255)                                                                  gggAAAAATAATGAAGGGGTGTCCCTTGACACAAATAAAAAATTTTCAA‑CACATTTATCTACTCAATTTGGGTTTGCACCCGAAAAACCAAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATg                                                                           <  1:794667/149‑1 (MQ=255)                                                                   ggAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCt                                                                        >  1:310362/1‑151 (MQ=255)                                                                    gagaAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCtt                                                                       >  2:731672/1‑151 (MQ=255)                                                                       aaaTAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGc                                                                     >  1:818395/1‑150 (MQ=255)                                                                       aaaTAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGc                                                                     >  2:747716/1‑150 (MQ=255)                                                                         ataatGAAAGCGTGTCCCTGGACACAAAAAAAAAATTTACAA‑CACACTTATCTACTCAATTTTGGTTTCCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATa                                                                  <  2:817192/151‑1 (MQ=255)                                                                           aatAAAAGCTTGTCCCTTAACAAAAATACAAAATTTAAAA‑CACCTTTATCTACTCAATTTTGCCTTGAACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACg                                                                <  2:386807/151‑1 (MQ=255)                                                                            atGAAAGCGTGCCCCTTGACACAAATAAAAAATTTACAA‑CACATTTATCTACTAGATTTTGGTTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGc                                                               <  2:407845/151‑1 (MQ=255)                                                                             tGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGc                                                               >  1:524718/1‑150 (MQ=255)                                                                              gAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCa                                                              >  2:627943/1‑150 (MQ=255)                                                                                        cccTTGACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAAtt                                                   >  2:583235/1‑151 (MQ=255)                                                                                             gACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCAt                                              >  1:815703/1‑151 (MQ=255)                                                                                               cacaAATAAAAAATTTCCAA‑CACCTTTTTCTCCTCGAATTTGGTTTGCCCCCGAAAAACCCAGTACACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATg                                             <  1:177674/150‑1 (MQ=255)                                                                                                      aCAAAATTTTCAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGAtt                                     >  1:185114/1‑151 (MQ=255)                                                                                                                     acacTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACtt                        >  2:609731/1‑150 (MQ=255)                                                                                                                      cacTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTa                       >  1:102207/1‑150 (MQ=255)                                                                                                                         ttttctcCTCAAATTTGGCTTGCATCCAAAAAAACCGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGAc                          <  2:335381/141‑1 (MQ=255)                                                                                                                         ttATCTACTCGAATTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAat                     <  1:226428/149‑1 (MQ=255)                                                                                                                           aTCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATAtt                  >  2:704902/1‑150 (MQ=255)                                                                                                                             cTACTCGATTTTGGTTTGCACCCAAAAAAACCAGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAatat                   <  1:382988/147‑1 (MQ=255)                                                                                                                                   gAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAAc          >  2:674148/1‑150 (MQ=255)                                                                                                                                     aTTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACat        >  2:794075/1‑150 (MQ=255)                                                                                                                                      tttGGCTTGCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACa         <  2:783020/148‑1 (MQ=255)                                                                                                                                      tttGGCTCGCAACCCCAAAAACCAGGACACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTa                 <  2:236439/140‑1 (MQ=255)                                                                                                                                         ggCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTa    <  2:155026/150‑1 (MQ=255)                                                                                                                                            ttGCATCCGAAAAAACCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACt  <  1:385701/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                            GATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACT  >  NC_000913/3665555‑3665841

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: ‑