Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,665,702	0	C	A	42.5%	62.5 / 20.4	47	A37S (GCG→TCG)	gadX	acid resistance regulon transcriptional activator; autoactivator
Reads supporting (aligned to +/- strand):  ref base C (25/2);  new base A (0/20);  total (25/22)
Fisher's exact test for biased strand distribution p-value = 2.37e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTG‑ACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTT  >  NC_000913/3665553‑3665844                                                                                                                                                       |                                                                                                                                               gTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTG‑ACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCa                                                                                                                                               <  2:446531/151‑1 (MQ=255)   gatgaACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTG‑ACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaa                                                                                                                                             <  2:318976/151‑1 (MQ=255)             tAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTG‑ACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTc                                                                                                                                    >  2:504327/1‑150 (MQ=255)                       aCTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTG‑ACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTa                                                                                                                          >  1:605295/1‑150 (MQ=255)                         ttttttATGTGAATGAAGTTTTAATGCCCCCTCCTTGAGAATCGGGAAAAAAAAGGAAGGCGGGTCCCTTG‑CCACGAATACAAAATTTTCAACACACTTATCTACACGAATTTGGCTTGCACCCGAAAAAACCAGGGCACCGCCATTaaa                                                                                                                        <  2:141530/150‑1 (MQ=255)                          tttttATGTGCATGAAGATTTAATGCCTCCCCCTGAAGCATCGGGAGAAATAATAAAAGCGTGTCCCTTG‑ACACAAAAAAAAAATTTCCAACACCCTTATCTACTCGAATTTGGCTTGCATCCGAAAAACCCAGGTCACCGCCATTaa                                                                                                                         <  2:63100/148‑1 (MQ=255)                           ttttATGAGCATGAAGATTTAATGCCTCCTCGTTGCGCATCGGGAGAAATATTGAAAGCGTGTCACTTG‑ACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAACAt                                                                                                                      >  2:407056/1‑150 (MQ=255)                            tttaaacgCATGAAGCGTTACTGCAACCTCTTTGCACATCGGGAGAAATAATGAAAGCTTGTCCCTTG‑ACACTAATACAAAACTATCAAGACACTTATCCACTTGAATTTGGCTTACATACACAATATCCAGGACACCGCGATTAAAAtcg                                                                                                                    >  2:135265/8‑149 (MQ=255)                                  tgCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTG‑ACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGatat                                                                                                              >  1:537272/1‑151 (MQ=255)                                        aaaaTTAAATCCCCCCTCCTTGAGTATCGGGAGAAAAAGAGAGAGCGGTCCCCGTG‑ATACAAATAAAAATTTTACAACACTTTTATTAACTCGAATTTGGCTTGAACCCCAAAAAACGAGGTCACCGCCATTAAAATAGCGATATTCAc                                                                                                          <  1:312580/146‑1 (MQ=255)                                            tttAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTG‑ACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTa                                                                                                     >  2:491737/1‑150 (MQ=255)                                             ttAATCCCTCCTCCTTGAGCATCGGAAAAAATAATAAAAGCGTGCCCCTTG‑ACACAAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTa                                                                                                     <  2:71487/149‑1 (MQ=255)                                              tAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTG‑ACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAAcc                                                                                                  >  2:404819/1‑151 (MQ=255)                                              tAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTG‑ACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAAcc                                                                                                  >  2:342380/1‑151 (MQ=255)                                                         cctTGAGCATGGGGAAAAATAATGAAGGCGTGCCCCTTA‑ACACAAATACAAAATTTTAAACACTCTTATCTACTCGAATTTGGCTTCCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGaa                                                                                        <  2:119791/150‑1 (MQ=255)                                                                cATCGGGAGAAATAATGAAAGCGTGTCCCTTG‑ACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTAACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATAttt                                                                                 >  2:645954/1‑150 (MQ=255)                                                                 atgggaaaaaaaaaTAAAAGCGTGTCCTTTG‑ACACAAAAAAAAATTTTCCAACCCACTTATCTCCTCAATTTTGGCTTGCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAatata                                                                                    <  1:248100/138‑1 (MQ=255)                                                                 agggggAAAAATAAAAAAAGCGTGTCCTTTG‑ACACGAATAAAAAATTTTCAACACACTTATCTCCAAGATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTAt                                                                               <  2:606765/148‑1 (MQ=255)                                                                 aTCGGGAAAAATAATGAAAGCGTGTCCCTTA‑ACACAAATAAAAAATTTTAAACCCACTTATCTACTCAAATTTGGTTGGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATAttt                                                                                 <  1:626852/149‑1 (MQ=255)                                                                  tCGGGAGAAATAATGAAAGCGTGTCCCTTG‑ACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATg                                                                              >  2:141647/1‑151 (MQ=255)                                                                   cGGGAGAAATAATGAAAGCGTGTCCCTTG‑ACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGt                                                                             >  1:435949/1‑151 (MQ=255)                                                                          aataatGAAAGCGTGTCCCTTG‑ACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCAt                                                                      >  1:660685/1‑151 (MQ=255)                                                                           ataataAAAGCTTGCCCCTTA‑ACAAAAATAAAAAATTTTCAACACTCTTATCTACTCAATTTTGTTTTCCACCCAAAAAAACCAGTAAACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATa                                                                     <  2:155099/151‑1 (MQ=255)                                                                             aatAAAAGCGTGTCCCTTG‑ACACGAAAAAAAATTTTTCAACCCCTTTATCTACTCAATTTTGTCTTGCATCCGAAAAACCCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACg                                                                   <  1:229212/151‑1 (MQ=255)                                                                                      gtgtCCCTTG‑ACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGAc                                                          >  1:395758/1‑151 (MQ=255)                                                                                           ccttggaccaaaaTAAAAAATTTAAAACACACTTATCTCCTAAATTTTGTTTTACACCCAAAAAACCCAGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAAt                                                       <  2:42667/139‑1 (MQ=255)                                                                                           ccTTGAACACAAAAACAAAATTTACAACCAATTTATCTCCGAAATTTTGGTTTGAACCCGAAAAAACAAGGTAACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACa                                                         <  2:416346/148‑1 (MQ=255)                                                                                           ccTTG‑ACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTc                                                     >  2:80566/1‑151 (MQ=255)                                                                                                 acacAAATAAAAAATTTCCAACACACTTATCTCCTCAAATTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCAt                                                 <  1:192821/150‑1 (MQ=255)                                                                                                  cacGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGt                                               >  2:583264/1‑151 (MQ=255)                                                                                                    cGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGt                                               >  2:209523/1‑149 (MQ=255)                                                                                                      aaTACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTg                                           >  2:355036/1‑151 (MQ=255)                                                                                                      aaTAAAAAATTTTCAACACATTTATCTACTCAATTTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTg                                           <  1:705635/151‑1 (MQ=255)                                                                                                             aaTTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCAt                                    >  2:706607/1‑151 (MQ=255)                                                                                                               ttttCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCAt                                    >  2:504071/1‑149 (MQ=255)                                                                                                                tttCAACACACTTATCTACTCGATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAg                                  <  1:86229/150‑1 (MQ=255)                                                                                                                tttAAACACACTTATCTACTCGATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAg                                  <  1:540716/150‑1 (MQ=255)                                                                                                                    aaCACACTTATCTACTCAATTTTGGCTTGCATCCGAAAAAACCAGGACACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGtt                                <  2:641961/148‑1 (MQ=255)                                                                                                                           ttATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAatat                      >  1:5868/1‑151 (MQ=255)                                                                                                                           ttATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAatat                      >  2:547247/1‑151 (MQ=255)                                                                                                                              tCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTAc                   >  2:540443/1‑151 (MQ=255)                                                                                                                                 aCTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACAt                 >  2:489754/1‑150 (MQ=255)                                                                                                                                    cGATTTTGGCTTGCATCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATaa               <  1:405854/149‑1 (MQ=255)                                                                                                                                    cGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAAc             >  1:546294/1‑151 (MQ=255)                                                                                                                                     gAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAAc             >  1:351881/1‑150 (MQ=255)                                                                                                                                        tttGGCTTCCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATaaa              <  2:45530/146‑1 (MQ=255)                                                                                                                                                 cATCCGAAAAACCCAGATCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGtt  <  2:330849/149‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                               GTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCCTCCTTGAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTG‑ACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTT  >  NC_000913/3665553‑3665844

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑