Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,613,099	0	C	A	40.0%	95.8 / 31.3	50	V400V (GTC→GTA)	hyfR	hydrogenase‑4 transcriptional activator
Reads supporting (aligned to +/- strand):  ref base C (26/4);  new base A (0/20);  total (26/24)
Fisher's exact test for biased strand distribution p-value = 2.25e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCAGGCAATGGAAGACCTGCTCCAGCAGGTAGATATTGTGGCGAAGAGCGACAGTACGGTGTTGATTTGTGGTGAAACCGG‑AACTGG‑C‑AAA‑GAG‑GTGATCGCCAGAGCGATCCATCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCGTTTTGAAATTGCCGATGGCGGCACGTTGTTTCTCGATGAAATTGGCGAT  >  NC_000913/2612952‑2613249                                                                                                                                                            |                                                                                                                                                       ccAGGCAATGGAAGACCTGCTCCAGCAGGTAGATATTGTGGCGAAGAGCGACAGTACGGTGTTGATTTGTGGTGAAACCGG‑AACTGG‑C‑AAA‑GAG‑GTGATCGCCAGAGCGATCCATCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCaa                                                                                                                                                      >  1:677882/1‑150 (MQ=255)             aGACCTGCTCCAGCAGGTAGATATTGTGGCGAAGAGCGACAGTACGGTGTTGATTTGTGGTGAAACCGG‑AACTGG‑C‑AAA‑GAG‑GTGATCGCCAGAGCGATCCATCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCt                                                                                                                                         <  2:121193/151‑1 (MQ=255)                    cTCCAGCAGGTAGATATTGTGGCGAAGAGCGACAGTACGGTGTTGATTTGTGGTGAAACCGG‑AACTGG‑C‑AAA‑GAG‑GTGATCGCCAGAGCGATCCATCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATcc                                                                                                                                  >  2:662410/1‑151 (MQ=255)                     tCCAGCAGGTAGATATTGTGGCGAAGAGCGACAGTACGGTGTTGATTTGTGGTGAAACCGG‑AACTGG‑C‑AAA‑GAG‑GTGATCGCCAGAGCGATCCATCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATccc                                                                                                                                 >  1:1259075/1‑151 (MQ=255)                      ccAGCAGGTAGATATTGTGGCGAAGAGCGACAGTACGGTGTTGATTTGTGGTGAAACCGG‑AACTGG‑C‑AAA‑GAG‑GTGATCGCCAGAGCGATCCATCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATcccc                                                                                                                                <  2:621080/151‑1 (MQ=255)                      ccAGCAGGTAGATATTGTGGCGAAGAGCGACAGTACGGTGTTGATTTGTGGTGAAACCGG‑AACTGG‑C‑AAA‑GAG‑GTGATCGCCAGAGCGATCCATCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATcccc                                                                                                                                <  2:1039049/151‑1 (MQ=255)                        agcagGTAGATATTGTGGCGAAGAGCGACAGTACGGTGTTGATTTGTGGTGAAACCGG‑AACTGG‑C‑AAA‑GAG‑GTGATCGCCAGAGCGATCCATCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGc                                                                                                                              >  2:771983/1‑151 (MQ=255)                                   atTGTGGCGAAGAGCGACAGTACGGTGTTGATTTGTGGTGAAACCGG‑AACTGG‑C‑AAA‑GAG‑GTGATCGCCAGAGCGATCCATCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTgg                                                                                                                   >  2:114884/1‑151 (MQ=255)                                                    cAGTAGGGTTTTGATTTG‑GGGAAAACCGG‑AACCGG‑A‑AAAGGAG‑GTGACCGCGAGAGCATTCCACCAATTA‑AC‑CCCG‑CGCCGCAACAAGCCGCTGGAAAAAACCATCTGCGCTCCCACCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCg                                                                                                    <  2:1216819/149‑1 (MQ=255)                                                    cAGTACGGTGTTGATTTGTGGTGAAACCGG‑AACTGG‑C‑AAA‑GAG‑GTGATCGCCAGAGCGATCCATCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGt                                                                                                  >  1:1143667/1‑151 (MQ=255)                                                        gtggTGTTTTTTTGGGGAAAAACGGG‑AAGGGG‑A‑AAA‑GTG‑GTGACCGCCAAAGCGCTCCACCATCTT‑‑G‑CCCGCCGACGACATAGGCCGGGAGTAAAAACCAGCGGCGCGGCCGTCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCg                                                                                                    <  1:170979/143‑1 (MQ=255)                                                        aCGGTTTTGTTTTGTGG‑AAAACCGG‑AACCGGAA‑AAA‑GAG‑TGGACCCCCAGGGC‑AACCATAAACCT‑AGCCCCG‑CGCCGCGAAAAGCCGCTGGCAAAAAACAACGGCGCTCCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCa                                                                                                <  2:606654/149‑1 (MQ=255)                                                         gggtttttttttGGGGTGAACCGGG‑ACCGGA‑A‑AAA‑GGG‑TTGCCCGCAAGAGCCATCAATCACCTT‑CC‑CCCG‑CGCGGAAACAACCCGCTGGACAAAATCAACTGCGCCGCCACCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGa                                                                                             <  2:292166/142‑1 (MQ=255)                                                          gttgtttttttGTGGT‑AAACCGGAAACTGA‑A‑AAA‑GGG‑GTGCCCCAAGGAGCGCCCCATCACTTT‑CG‑CCCG‑CGCCGCAAAAAGCCGCGGGTAAAAATCAACGGCGCTACCTCCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCAt                                                                                               <  1:1199229/140‑1 (MQ=255)                                                          gggtttGATTTGGGGTAAAACCGG‑AAACGG‑A‑AAA‑GGGTGTGACCCCAGGGGCGTCCCACCACTTT‑CC‑CCCG‑GGCCGCAACAGCCCGTTGGAAAAAACAACCGGCGCCCCCACCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATg                                                                                              <  2:648688/146‑1 (MQ=255)                                                          ggTGTTG‑TTTGGGGGAAAACCCG‑AACGGG‑CAAAA‑GGG‑GTGACCCCAGGAGCAACCCACCACCTT‑GC‑CCCG‑CGCCGCAAAAAGCCGCTGGTAAAAATCAACTGCGCTCCCACCCCCGCCAGTCTTCTGGAAAGTGAGTTAt                                                                                                       <  2:466565/140‑1 (MQ=255)                                                             gtTGATTTGTGGTGAAACCGG‑AACTGG‑C‑AAA‑GAG‑GTGATCGCCAGAGCGATCCATCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACaa                                                                                          >  1:467709/1‑150 (MQ=255)                                                                tgttttggggaaaaCCGG‑AACCGGAA‑AAA‑GGG‑GTGACCGCCGGAGCGATCCATAAACTT‑AC‑CCCG‑CGCCGCGAAAGGCCGCTGGTAAAAATCAACTGCGCTGCCACCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAg                                                                                        <  2:721783/139‑1 (MQ=255)                                                                gATTTGTGGTGAAACCGG‑AACTGG‑C‑AAA‑GAG‑GTGATCGCCAGAGCGATCCATCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAggg                                                                                      >  2:1074838/1‑151 (MQ=255)                                                                  tttGTGGTAAAACGGG‑AACGGG‑A‑AAA‑GAG‑GTGACCGCCAGGGCGATCCATAACCTT‑AG‑CCCG‑CGCCGCGACAAGCCGCTGGTAAAAATCAACGGCGCTGCCACCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAgg                                                                                       <  2:192158/148‑1 (MQ=255)                                                                   ttgggggaaaaCCCG‑AAATGG‑AAAAA‑GAG‑TTGCTGCCCAGAGCGTCCCAACATTTG‑AC‑CCGG‑CGCCGCGAAAAGCCGTTGGAAAAAATCATCTGGGCTGCCCCCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAgggg                                                                                     <  2:335364/142‑1 (MQ=255)                                                                        gggAAACCGGAAACGGA‑A‑AAA‑GGG‑GTGACCGCAAGAGCGATCCATAAACTT‑AC‑CCCG‑CGACGCAACAACCCGCTGGAAAAAAACAACTGCGCTGCCACCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGttt                                                                                <  2:1077183/148‑1 (MQ=255)                                                                          gAAACCGG‑AACTGG‑C‑AAA‑GAG‑GTGATCGCCAGAGCGATCCATCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTg                                                                            >  1:259684/1‑151 (MQ=255)                                                                            aaccgg‑aaccgg‑A‑AAAGGAG‑GGGACCGCAGAAGCGCCCCACAACCTT‑AC‑CCCG‑GGCCGCAACAAGCCGCTGGTAAAAATCACCTGCGCTGCCACCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGc                                                                                    <  2:274847/142‑1 (MQ=255)                                                                                   aaCTGG‑C‑AAA‑GAG‑GTGATCGCCAGAGCGATCCATCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGAtt                                                                    >  2:286962/1‑151 (MQ=255)                                                                                           aaaa‑GGG‑GTGACCGCAAGAGCGACCCA‑AAACTTGGG‑CCCG‑CGCCGCAAAAAGCCGCTGGAAAAAATCAACTGCGCTGCCACCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATAc                                                               <  2:259788/149‑1 (MQ=255)                                                                                            aaagggg‑gTGACCGCCAGAGCGCCCCATCATCTT‑GC‑CCCG‑CGACGCAACAACCCGCTGTAAAAAACCACCGGCGCTGCCCCCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATAcc                                                              <  2:1244371/145‑1 (MQ=255)                                                                                              a‑gag‑GTGATCGCCAGAGCGATCCATCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCAt                                                           >  2:1056228/1‑151 (MQ=255)                                                                                                tag‑GTGATCGCCAGAGCGATCCATCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATc                                                          >  1:22944/2‑151 (MQ=255)                                                                                                        tCGCCAGAGCGATCCATCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCg                                                   >  1:155937/1‑151 (MQ=255)                                                                                                           ccAGAGCGATCCATCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCGttt                                                >  2:434011/1‑151 (MQ=255)                                                                                                            cAGAGCGATCCATCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCGtttt                                               >  2:560182/1‑151 (MQ=255)                                                                                                               agCGATCCATCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCGTTTTGa                                             >  2:1305276/1‑150 (MQ=255)                                                                                                                 cGATCCATCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCGTTTTGAAAt                                          >  1:602106/1‑151 (MQ=255)                                                                                                                  gATCCATCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCGTTTTGAAAtt                                         >  1:1309348/1‑151 (MQ=255)                                                                                                                        tCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCGTTTTGAAATTGCCGAt                                   >  2:1071053/1‑151 (MQ=255)                                                                                                                          accTT‑CG‑CCCG‑CGACGCAAGAAGCCGGTGGTAAAAATCAACGGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCGTTTTGAAATTGCCGAt                                   <  1:163298/147‑1 (MQ=255)                                                                                                                          aaCTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCGTTTTGAAATTGCCGATgg                                 >  1:201560/1‑151 (MQ=255)                                                                                                                           cacttgcccccG‑CGCCGCGAAAGGCCGCGGTAAAAAATCACCTGCGCTGCCTCCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCGTTTTGAAATTGCCGa                                    <  1:1321313/141‑1 (MQ=255)                                                                                                                           cacttacccccG‑CGACGCAAAAGGCCGTGGTTAAAAATCAACTGCGCCCCCACCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCGTTTTGAAAtt                                         <  1:780877/136‑1 (MQ=255)                                                                                                                               ttgccccG‑CGACGAGAAAACCGTTTGGTAAAAATCAACGGCGCTCCCACCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCGTTTTGAAATTGCCGATg                                  <  2:157246/143‑1 (MQ=255)                                                                                                                                aG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCGTTTTGAAATTGCCGATggcggc                             >  2:984627/1‑150 (MQ=255)                                                                                                                                aG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCGTTTTGAAATTGCCGATggcggc                             >  1:71283/1‑150 (MQ=255)                                                                                                                                   ccgg‑cgacgcgacAAGCCGCTGGTAAAAATCACCTGCGCTCCCACCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCGTTTTGAAATTGCCGATggcgg                              <  2:493097/144‑1 (MQ=255)                                                                                                                                   cccG‑CGCCGGAAAAAGCCGTGGATAAAAACCAACTGCGCTCCCACCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCGTTTTGAAATTGCCGATggcggc                             <  2:562721/148‑1 (MQ=255)                                                                                                                                   cccG‑CGCCGCAAAAAGCCGCGGGTAAAAATCACCGGCGCTGCCACCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCGTTTTGAAATTGCCGATGGCGGCACg                          <  2:361730/151‑1 (MQ=255)                                                                                                                                          acgcgacAAGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCGTTTTGAAATTGCCGATGGCGGCACGTTGttt                    >  2:300485/1‑151 (MQ=255)                                                                                                                                            gcgacAAGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCGTTTTGAAATTGCCGATGGCGGCACGTTGTTtct                  >  1:1139308/1‑151 (MQ=255)                                                                                                                                                 aaGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCGTTTTGAAATTGCCGATGGCGGCACGTTGTTTCTCGATg             >  2:857007/1‑151 (MQ=255)                                                                                                                                                  aGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCGTTTTGAAATTGCCGATGGCGGCACGTTGTTTCTCGATg             >  1:988588/1‑150 (MQ=255)                                                                                                                                                            cAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCGTTTTGAAATTGCCGATGGCGGCACGTTGTTTCTCGATGAAATTGGCGAt  >  1:857287/1‑151 (MQ=255)                                                                                                                                                            |                                                                                                                                                       CCAGGCAATGGAAGACCTGCTCCAGCAGGTAGATATTGTGGCGAAGAGCGACAGTACGGTGTTGATTTGTGGTGAAACCGG‑AACTGG‑C‑AAA‑GAG‑GTGATCGCCAGAGCGATCCATCAACTT‑AG‑CCCG‑CGACGCGACAAGCCGCTGGTCAAAATCAACTGCGCTGCCATCCCCGCCAGTCTTCTGGAAAGTGAGTTATTCGGTCATGACAAAGGGGCGTTTACTGGTGCGATTAATACCCATCGTGGTCGTTTTGAAATTGCCGATGGCGGCACGTTGTTTCTCGATGAAATTGGCGAT  >  NC_000913/2612952‑2613249

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑