Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,578,290	0	A	C	51.2%	47.1 / 63.2	44	V146G (GTG→GGG)	gntR	d‑gluconate inducible gluconate regulon transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base A (13/8);  new base C (0/22);  total (13/31)
Fisher's exact test for biased strand distribution p-value = 5.56e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.11e-07

ATGATAGTACGTTCGTCGAGACGTGCGCCGAGATAGGCAATGTGGCGATGCCCGCGAGCAATAATGGCAGTGGTCATCTGGCGTGCTGCTTCAAAGTTATCAAAACCGACGGCGATATCAAGGCATGGCGACTTG‑CTGTCCATCAGTTCCACCACGGG‑AATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTCCGGTTTATAACCGTAGTGCGCCAGCA  >  NC_000913/3578140‑3578437                                                                                                                                                        |                                                                                                                                                     atgatAGTACGTTCGTCGAGACGTGCGCCGAGATAGGCAATGTGGCGATGCCCGCGAGCAATAATGGCAGTGGTCATCTGGCGTGCTGCTTCAAAGTTATCAAAACCGACGGCGATATCAAGGCATGGCGACTTG‑CTGTCCATCAGTTcca                                                                                                                                                      >  1:259180/1‑151 (MQ=255)  tgatAGTACGTTCGTCGAGACGTGCGCCGAGATAGGCAATGTGGCGATGCCCGCGAGCAATAATGGCAGTGGTCATCTGGCGTGCTGCTTCAAAGTTATCAAAACCGACGGCGATATCAAGGCATGGCGACTTG‑CTGTCCATCAGTTccac                                                                                                                                                     <  2:393104/151‑1 (MQ=255)    atAGTACGTTCGTCGAGACGTGCGCCGAGATAGGCAATGTGGCGATGCCCGCGAGCAATAATGGCAGTGGTCATCTGGCGTGCTGCTTCAAAGTTATCAAAACCGACGGCGATATCAAGGCATGGCGACTTG‑CTGTCCATCAGTTccacca                                                                                                                                                   <  2:235236/151‑1 (MQ=255)     tAGTACGTTCGTCGAGACGTGCGCCGAGATAGGCAATGCGGCGATGCCCGCGAGCAATAATGGCAGTGGTCATCTGGCGTGCTGCTTCAAAGTTATCAAAACCGACGGCGATATCAAGGCATGGCGACTTG‑CTGTCCATCAGTTccacca                                                                                                                                                   >  1:221582/1‑150 (MQ=255)          cGTTCGTCGAGACGTGCGCCGAGATAGGCAATGTGGCGATGCCCGCGAGCAATAATGGCAGTGGTCATCTGGCGTGCTGCTTCAAAGTTATCAAAACCGACGGCGATATCAAGGCATGGCGACTTG‑CTGTCCATCAGTTCCACCACGGG‑aa                                                                                                                                            >  1:521293/1‑151 (MQ=255)              cgtcgAGACGTGCGCCGAGATAGGCAATGTGGCGATGCCCGCGAGCAATAATGGCAGTGGTCATCTGGCGTGCTGCTTCAAAGTTATCAAAACCGACGGCGATATCAAGGCATGGCGACTTG‑CTGTCCATCAGTTCCACCACGGG‑AATAcc                                                                                                                                        <  1:121315/151‑1 (MQ=255)                tcgAGACGTGCGCCGAGATAGGCAATGTGGCGATGCCCGCGAGCAATAATGGCAGTGGTCATCTGGCGTGCTGCTTCAAAGTTATCGAAACCGACGGCGATATCAAGGCATGGCGACTTG‑CTGTCCATCAGTTCCACCACGGG‑AATAccc                                                                                                                                       <  2:239445/150‑1 (MQ=255)                 cgAGACGTGCGCCGAGATAGGCAATGTGGCGATGCCCGCGAGCAATAATGGCAGTGGTCATCTGGCGTGCTGCTTCAAAGTTATCAAAACCGACGGCGATATCAAGGCATGGCGACTTG‑CTGTCCATCAGTTCCACCACGGG‑AATACCCGc                                                                                                                                     <  1:524679/151‑1 (MQ=255)                                      aatgggggCGATGCCCGCGAAAAATAAGGGCGGTGGTCTTCGGGCGTGCTGCTTAAAAGTTAACAACCCCGCCGGCAATATAAAGGCATGGCGACTTC‑CTGTCCATCAGTCCCCCCAGGGG‑AATCCCCGCCACTTCAATCATCTTTAAgg                                                                                                                 <  1:183739/144‑1 (MQ=255)                                      aaagggggcgcgccccGCGAAAAATAGGGGCGGTGCTCTTCGGGCGTGCTTCTTCAAAGTTAAAAAACCCGCCGGCGATACAAAGGCAGGGCGCTTTC‑CTGTCCATCATTCCCCCCACGGA‑AATCCCCGCCACTTCAATCATCTTTAAgg                                                                                                                 <  1:529921/137‑1 (MQ=255)                                      aaaTGTGGCGATCCCCGCGAGAAATAATGGCAGTGTTCATCGGGCGTGCTGCTTAAAATTTAAAAAAACCGACGGCGATATAAAGGCATGGCGTCTTG‑CTGTCCATCATTCCCCCCACGGA‑AATCCCCGCCACTTCAATCATCTTTAAgg                                                                                                                 <  2:657935/149‑1 (MQ=255)                                             gCGAGGCCCGCGAGCAAAAATGGCAGTGGTCATCTGGCGTGCTGTTTCAAATTAAACAAACCCGACGGCGATATCAGGGCAGGGCGTTTTG‑CTGCCCATCAGTTCCGCCGCGGG‑AATCCCCGCCACTTCAATCATCTTTAAGGTGCgcgg                                                                                                          <  1:579620/150‑1 (MQ=255)                                                       cgAGAAAAAAGGGCAGGGGTCATCGGGCGTGCTGCTTAAAAGTTACAAAACCCGACGGCGATATCAAGGCAGGGCGACTTG‑CTGCCCATCAGTCCCACCACGGA‑AATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTa                                                                                                <  2:92050/150‑1 (MQ=255)                                                        gAGCAATAATGGCAGTGGTCATCTGGCGTGCTGCTTCAAAGTTATCAAAACCGACGGCGATATCAAGGCATGGCGACTTG‑CTGTCCATCAGTTCCACCACGGG‑AATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACg                                                                                              >  2:358031/1‑151 (MQ=255)                                                           cccttatgtttttGGTCCTCTGGCGTGCTGCTTCCCCGTTCTCAAAACCGACGGCGATATCAAGGCATGGCGACTTG‑CTGTCCATCAGTTTAACCAAGGG‑AATACCAGCAACTTCAATCATCTTTAAGGTGGGCGGCGTGTGGGTACGtt                                                                                            >  2:385701/13‑150 (MQ=255)                                                           cAATAATGGCAGTGGTCATCTGGCGTGCTGCTTCAAAGTTATCAAAACCGACGGCGATATCAAGGCATGGCGACTTG‑CTGTCCATCAGTTCCACCACGGG‑AATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGtt                                                                                            >  1:184513/1‑150 (MQ=255)                                                           cAATAATGGCAGTGGTCATCTGGCGTGCTGCTTCAAAGTTATCAAAACCGACGGCGATATCAAGGCATGGCGACTTG‑CTGTCCATCAGTTCCACCACGGG‑AATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGtt                                                                                            >  2:494539/1‑150 (MQ=255)                                                           aaaaaagggCGGTGGTCATCGGGGGTGCTGCTTAAAAGTTAAAAAACCCGCCGGCAATATAAAGGCATGGCGATTTG‑CTGCCCATCAGTCCCCCCAGGGG‑AATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGtt                                                                                            <  1:675041/143‑1 (MQ=255)                                                             ataatGGCAGTGGTCATCTGGCGTGCTGCTTAAAATTTATCAAACCCGACGGCGATATCAGGGCATGGCGTCTTG‑CTGCCCATCATTTCCCCCAGGGG‑AATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCgg                                                                                         <  2:584587/151‑1 (MQ=255)                                                                atGGCGGTGGTCACCGGGCGGGCTGTTTCAATTTTATCAAACCCGACGGCGATACCAAGGCAGGGCGACTTG‑CGCCCCATCATTTCCCCCACGGG‑AATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGa                                                                                      <  2:184262/151‑1 (MQ=255)                                                                      gTGATCATCTGGCGTGCTGCTAAAAAGTTAAAAAACCCGCCGGAAATATCAAGGCATGGCTTTTTG‑TTCCCCACCATTCCCACCAGGGG‑AATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATc                                                                                 <  1:330020/150‑1 (MQ=255)                                                                       ggttcttcgggCGTGCTGCTTAAAATTTACCAAACCCGACGGCAATATCAAGGCATGGCGTTTTG‑CTGTCCATCATTCCCCCCACGGG‑AATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATc                                                                                 <  2:682066/140‑1 (MQ=255)                                                                          tCATCTGGCGTGCTGCTAAAAAGTTATAAAACCCGACGGCGATATCAAGGCATGGCGACTTG‑CTGTCCATCAGTCCCCCCACGGA‑AATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGc                                                                             <  2:149895/150‑1 (MQ=255)                                                                          tCATCGGGCTTGCTCTTGAAAAGTAATAAAAACGGACGGCGATATCAAGACCTGGC‑TCTTGTCTGTCCATATTTCCCACCAGGGA‑AATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGcc                                                                            <  1:462295/151‑1 (MQ=255)                                                                          tCATCGGGCGTGCTGCTAAAAATTTAAAAAACCCGGGGGCGATATAAAGGCAGGGCGTTTTG‑CTGTCCATCATTCCCCCCGCGGA‑AATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGc                                                                             <  2:374749/150‑1 (MQ=255)                                                                             tCTGGCGTGCTGCTTCAAAGTTATCAAAACCGACGGCGATATCAAGGCATGGCGACTTG‑CTGTCCATCAGTTCCACCACGGG‑AATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGt                                                                          >  1:158824/1‑150 (MQ=255)                                                                                 gCGTGCTGCTTCAAAGTTATCAAAACCGACGGCGATATCAAGGCATGGCGACTTG‑CTGTCCATCAGTTCCACCACGGG‑AATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGata                                                                     >  1:374536/1‑151 (MQ=255)                                                                                        tctTAAAATTTAAAAAACCCGACGGCGATATAAGGGCATGGCGACTTG‑CTTTCCATCAGTCCCCCCGCGGG‑AATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAgg                                                              <  1:502196/150‑1 (MQ=255)                                                                                          ttaaaattaataaaacCCGCCGGAGATATAAAGGCATGGCGCTTTG‑TTCTCCATCATTCCCCCCGGGGA‑AATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGgag                                                            <  1:460086/139‑1 (MQ=255)                                                                                          ttaaaaTTTAACAAACCCGAGGGCGATATAAAGGCATGGCGATTTG‑CTGTCCTTCAGTCCCCCCAGGGA‑AATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGgag                                                            <  2:192867/148‑1 (MQ=255)                                                                                          ttaaaaTTTAACAAACCCGACGGCGATATAAAGGCAGGGCGACTTG‑CTGTCCATCAGTCCCACCAGGGA‑AATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGgag                                                            <  2:302614/148‑1 (MQ=255)                                                                                          ttCAAAGTAAACAAACCCGGCGGAGATATCAAGGCTTGGCGCTTTC‑CTGTCCATCAGTCCCCCCAGGGA‑AGTACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGgag                                                            <  1:108564/151‑1 (MQ=255)                                                                                          tgcAAAGTTACCAAACCGGACGGCGTAACCAAGGAATGGACTCTTC‑CGGCCTAACAGCCCCCCCACGGG‑AATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGgag                                                            <  2:421982/149‑1 (MQ=255)                                                                                                    aaaaacCCGACGGCAATATCAGGCCAGGGCGTTTTG‑CTGTCCATCAGTCCCCCCAGGGG‑AATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGAtt                                                  <  1:476846/149‑1 (MQ=255)                                                                                                         cccgccgGCGATATCAAGGCAGGGCTATTTG‑CTGTCC‑TCCGTTCCCCCCGGGGAAACCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAgg                                             <  1:311660/150‑1 (MQ=255)                                                                                                         cccgccgGCGATATCAAGGCAGGGCGACTTG‑CTGTCCATCATTCCCCCCACGGA‑AATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAgg                                             <  2:158822/150‑1 (MQ=255)                                                                                                                    tatCAAGGCATGGCGACTTG‑CTGTCCATCAGTTCCACCACGGG‑AATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCt                                   >  1:469019/1‑150 (MQ=255)                                                                                                                    tatCAAGGCATGGCGACTTG‑CTGTCCATCAGTTCCACCACGGG‑AATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCt                                   >  1:70736/1‑150 (MQ=255)                                                                                                                    taccAAGGCATGGCGACTTC‑CTTTCCACCAGTCCCCCCAGGGA‑AATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTc                                  <  2:292814/148‑1 (MQ=255)                                                                                                                          ggCATGGCGACTTG‑CTGTCCATCAGTTCCACCACGGG‑AATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCAttt                             >  1:580438/1‑150 (MQ=255)                                                                                                                                     ttG‑CTGTCCATCAGTTCCACCACGGG‑AATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTCCGGTTTATaa                  >  1:66049/1‑150 (MQ=255)                                                                                                                                     ttG‑CTGTCCATCAGTCCCCCCACGGA‑AAGACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTCCGGTTTATAAc                 <  2:603611/151‑1 (MQ=255)                                                                                                                                     ttG‑CTGTCCATCACTCCCACCACGGA‑AATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTCCGGTTTATAAc                 <  2:140730/151‑1 (MQ=255)                                                                                                                                         cTGCCCATCAGTCCCCCCACGGA‑AATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTCCGGTTTATAACCg               <  2:669822/150‑1 (MQ=255)                                                                                                                                           gTCCATCAGTTCCACCACGGG‑AATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTCCGGTTTATAACCGTAg            >  1:682491/1‑151 (MQ=255)                                                                                                                                           gTCCATCAGTTCCACCACGGG‑AATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTCCGGTTTATAACCGTAg            >  2:190516/1‑151 (MQ=255)                                                                                                                                            tCCATCATTCCCCCCGCGGG‑AATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTCCGGTTTATAACCGTAg            <  2:254991/150‑1 (MQ=255)                                                                                                                                                     tCCCCCACGGA‑AATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTCCGGTTTATAACCGTAGTGCGCCAGCa  <  2:252725/151‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                                     ATGATAGTACGTTCGTCGAGACGTGCGCCGAGATAGGCAATGTGGCGATGCCCGCGAGCAATAATGGCAGTGGTCATCTGGCGTGCTGCTTCAAAGTTATCAAAACCGACGGCGATATCAAGGCATGGCGACTTG‑CTGTCCATCAGTTCCACCACGGG‑AATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTCCGGTTTATAACCGTAGTGCGCCAGCA  >  NC_000913/3578140‑3578437

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑