Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	45.5%	54.3 / 13.0	44	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (22/2);  new base C (0/20);  total (22/22)
Fisher's exact test for biased strand distribution p-value = 2.62e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGT‑CATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTG  >  NC_000913/357733‑358023                                                                                                                                                     |                                                                                                                                                 cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTc                                                                                                                                                 <  2:224275/149‑1 (MQ=255)    aGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCTCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTccgcc                                                                                                                                             >  2:1092402/1‑150 (MQ=255)       ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaa                                                                                                                                         <  1:251860/151‑1 (MQ=255)          gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaaca                                                                                                                                       >  2:554344/1‑150 (MQ=255)             aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAc                                                                                                                                   >  2:996983/1‑151 (MQ=255)                             acattcccAGCCGCAGACTTGTTTCAGGGGCCCCCGTGATTCATTCCCGCAAAAAACCGCCCTTTTACCCAACCCCA‑GGTCAAAAAATCCCTCCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAACAAAACCGCCGTtctct                                                                                                                        <  2:1083644/140‑1 (MQ=255)                              cAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                   >  2:138569/1‑150 (MQ=255)                               aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGC‑AAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagtagt                                                                                                                >  2:663064/1‑151 (MQ=255)                                   ccAGCCTCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                               >  2:109120/1‑149 (MQ=255)                                   ccAGCCGCGGCCTTGTGTCAGGGGCTCCCTTGTTTCATTTCCCCCAACACCCGCGCTTTTACCCACCGCCA‑TGTAAAAAAATCCTTTCGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                             <  1:134995/151‑1 (MQ=255)                                     aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                           >  2:839109/1‑151 (MQ=255)                                     aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                           >  1:901648/1‑151 (MQ=255)                                     aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                           >  2:256701/1‑151 (MQ=255)                                       ccGCAGCCTTGTGCCAGGGCCTCCCGTGATTCTTTCCCCCCAACACCCGCGCATTTACCCAACCCCA‑TGTGAAAAAATGCCTTCGCGGCGGCTGTCTCCCACTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                         <  1:9772/151‑1 (MQ=255)                                        cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                         >  1:793438/1‑150 (MQ=255)                                         gCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggt                                                                                                        >  1:386719/1‑149 (MQ=255)                                         gCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                           >  2:488940/1‑147 (MQ=255)                                            gcccTTTGTCGGCGGCTACCGTGTTTCATCCCCGCCAACACCCGCGCATTTACCCAACGCCA‑TGTGAAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                                                                                     <  1:929375/148‑1 (MQ=255)                                               cTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCACGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggggcg                                                                                                     >  1:62353/1‑143 (MQ=255)                                                         gtccccggtgtTTCATTCCCGCCACCACCCGCG‑TTTTAACCCACCCCATTGGGAAAAAATGCCTTCGGGGGGGCTGTCGCCAAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgaga                                                                                                  <  2:759033/133‑1 (MQ=255)                                                           caaCCTTGCTTCATTCCCGCCAACACCCGCGCTTTTAACCAACGCCT‑TGGACAAAAATTCCCCCGCGCCGTCTGTCTGCCATCTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTaa                                                                                       <  2:70570/147‑1 (MQ=255)                                                           cTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGGAAAAAgatgtt                                                                                        >  2:407911/1‑143 (MQ=25)                                                              cgttaaTTCTTTCCCCCAAACACCCGCGTTTTAACCCACCCCCA‑TGTGAAAAAATGCCTCCGGGGCGCCTGTCTGCCTGTTATTTTCCCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCt                                                                                           <  2:675674/137‑1 (MQ=255)                                                              ccGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGGGAGAAATaacatttaaac                                                                                    >  2:75430/1‑139 (MQ=25)                                                              ccGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAAAGAAAAAACtttttatcc                                                                                   >  1:956624/1‑144 (MQ=25)                                                                 tGATTCATCCCCCCCAACACCCGCGCTTTTACCCAACGCCT‑TGTAAAAAAATGCTTCCGCGGGGGCTGTCTCCCAGCTATTTTCCCGCCAAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCg                                                                                  <  2:1070312/148‑1 (MQ=255)                                                                                accacccGCCCATTTACCAACCGCCT‑GGTAAAAAATGGCCTGCGCGGCGGCTGTCGGCCATTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGT‑CATGTTGTGTGGCAAt                                                                <  1:506855/145‑1 (MQ=255)                                                                                aacaacCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGCGAGAAAAAAAATTTAACCCCC‑CCTGTTGTGTgggg                                                                  >  2:609613/1‑146 (MQ=21)                                                                                 acaccCGCCCATTCACCCAACCCCT‑GGTAAAAAAATCCCTTCGCGGCGGTTGTCTGCCAGCTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGT‑CATGTTGTGTGGCa                                                                  <  1:612365/147‑1 (MQ=255)                                                                                         gcattcccccAACTCCA‑TGAACAAAAAGGCCTCCGCGGCGCCTTCCTCCCAGCTTTTTTCCCGCCGCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGT‑CATGTTGTGTGGCAATCGCTGCTgg                                                       <  2:124077/142‑1 (MQ=255)                                                                                            tttccccacccccA‑TGAGAAAAAATCCCTCCGGGGCGGCTTTCGCCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGT‑CATGTTGTGTGGCAATCGCTGCTGGTa                                                     <  2:486361/138‑1 (MQ=255)                                                                                            tttACCCAACGCCT‑TGTGAAAAAATGCTTCCGCGGCGGCTGTCTCCCAGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGT‑CATGTTGTGTGGCAATCGCTGCTGGTa                                                     <  1:627872/149‑1 (MQ=255)                                                                                                tCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAACTTTTAAACCCT‑CCTGTTGTGTGGGGATTGCTGCTGGtgaaaa                                                 >  1:423473/1‑144 (MQ=25)                                                                                                    accgccagtggaaaaaaTCCCTTCGGGGCGGCTGTCGCCCATTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGT‑CATGTTGTGTGGCAATCGCTGCTGGTAACaa                                                 <  2:133230/134‑1 (MQ=255)                                                                                                           tgtgCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAAATTTTAACCCCC‑CCTGTTTTGTGGGAAACGCCGCTGGGGAAAAAGTGGAAAggg                                      >  1:70883/1‑150 (MQ=255)                                                                                                            gtgAAAAATTCCCTTCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGT‑CATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAgg                                       <  1:937868/148‑1 (MQ=255)                                                                                                               cAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAAATTTTAACCCCC‑CCTGTTGTGTGGGGATCGCGTCTGGGAAAAAAGTGGGAAGGGGAggg                                 >  1:818723/1‑149 (MQ=255)                                                                                                                aaaagtccattCGCGGCGGCTGTCTCCGCGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGT‑CATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAg                                   <  2:48734/139‑1 (MQ=255)                                                                                                                 aaatTGCCTCCGGGGCGGCTGTCCCCCATTTTTTTTCCCCCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGT‑CATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcg                               <  1:442887/151‑1 (MQ=255)                                                                                                                     tGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGCGAGAAAAAAATTTTAAAACCC‑CCTCTTGTGGGGGAAACGCTGGTGGGGAAAATGTGGGAAGGGGAGGggggcg                            >  2:213372/1‑150 (MQ=255)                                                                                                                        cTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGGGCAAAAAATTTAAATCCTTCCACTTTGTG‑GGGGATTGCTGCTGGGAACATTATGGAAAaggggagag                                >  2:813350/1‑137 (MQ=255)                                                                                                                            gcggcgGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGT‑CATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAAt                         <  1:296838/146‑1 (MQ=255)                                                                                                                              ggcggcTTTCTCCCAGTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGT‑CATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCt                    <  1:225570/149‑1 (MQ=255)                                                                                                                                          ccggtttttttcCCGCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGT‑CATGTTGTGTGGCAATCGCTGCTGGTAACAATGTAGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCt       <  1:516877/143‑1 (MQ=255)                                                                                                                                          ccAGCTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGT‑CATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc            <  2:896195/145‑1 (MQ=255)                                                                                                                                               ttttttcCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGT‑CATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTg  <  1:841908/148‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                 CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGT‑CATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTG  >  NC_000913/357733‑358023

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑