Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	49.0%	39.2 / 34.1	49	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (20/5);  new base A (0/24);  total (20/29)
Fisher's exact test for biased strand distribution p-value = 2.25e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATG  >  NC_000913/357743‑358037                                                                                                                                                      |                                                                                                                                                     aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCC‑GCCGcaacaa                                                                                                                                                    >  2:1121458/1‑150 (MQ=255)   aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCC‑GCCGCAACAAAAc                                                                                                                                                 <  1:625718/151‑1 (MQ=255)    aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCC‑GCCGCAACAAAAcc                                                                                                                                                <  2:312809/151‑1 (MQ=255)        tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCC‑GCCGCAACAAAAccgccg                                                                                                                                            >  2:303950/1‑151 (MQ=255)        tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCC‑GCCGCAACAAAAccgccg                                                                                                                                            >  1:451595/1‑151 (MQ=255)         aGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCC‑GCCGCAACAAAACCGCCGt                                                                                                                                           >  2:933041/1‑151 (MQ=255)         aGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCC‑GCCGCAACAAAACCGCCGt                                                                                                                                           >  2:1064709/1‑151 (MQ=255)                    cAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCC‑GCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                                 >  2:507270/1‑150 (MQ=255)                         ccAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                           >  1:1015747/1‑151 (MQ=255)                             ccGCAGCCCTGTGTCAGCGGCTCCCGTGTTTCTTTCCCCCAAACAC‑CCGCGCTTTTACCCAACGCCATGTGAAAAAATCCTTTGGGGGCGGTTGTCGCCCACTTTTTTTCCC‑GCCGCAAAAAACCCGCCGTTCTCTCCAGTAGTgg                                                                                                                            <  2:847560/146‑1 (MQ=255)                              cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                        >  2:313991/1‑149 (MQ=255)                                    ccTGTGTCAGCGGCTCCCGTGTTTCTTTCCCGCCAACAC‑CCGCGCTTTTACCCACCGCCATGTGAAAAAATGCCTCCGGGGCGGTTGTCTCCCAGTTATTTTCCC‑GCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgag‑a                                                                                                               <  2:977363/151‑1 (MQ=255)                                     cTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCagag                                                                                                                 >  2:738935/1‑149 (MQ=255)                                       gtgtCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑aaa                                                                                                             >  2:1092073/1‑150 (MQ=255)                                        tgtCGGCGGCTCCCGTATTTCATCCCCCCCACCCC‑CCGCGCTTTTTCCCACCCCCTTGTGCAAAACCGCCTGCGGGGCGTTTGTCTCCCAGTTATTTTCCC‑GCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAagag                                                                                                                 <  1:279673/146‑1 (MQ=255)                                            aGCGGCTACCGCGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGTGCAAgag‑acaaaacct                                                                                                       >  1:621916/1‑143 (MQ=255)                                                    cggTGATTC‑TTTCCCCCAAAAACCCGCGCTTTTACCCACCGCCTTGTGAAAAAATCCCTTCGGGGCGGCTTCCTGCCAGTTTTTTTCCC‑GCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCg                                                                                               <  2:1053551/149‑1 (MQ=255)                                                          ttCATTCCCGCCAACAC‑CCGCGCATTTACCCACCGCCATGTGAAAAAATCCCTTCGCGGCGGCTGTCTGCCAGTTTTTTTCCC‑GCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAt                                                                                           <  2:907598/149‑1 (MQ=255)                                                            cATTCCCGCCACCAC‑CCGCGCTTTTACCCACCGACTTGGGAAAAAATCCCTCCGGGGCGGCTGTCTGCCAGTTATTTCGCC‑GCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtgtt                                                                                        <  2:1015753/150‑1 (MQ=255)                                                              ttccccccaccaC‑CCGCGTATTGACCCACCCCCATGTCCAAAAATCCCTTGGCGGCGGCTTTCGGCAAGTTTTTTTTCC‑GCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGt                                                                                              <  1:1076680/136‑1 (MQ=255)                                                                 cccccAACAC‑CCGGGCTTTTACCCACCCCCATGTCAAAAAATCCCTTCGCGGCGGCTGTCTGCCGGTTATTTTCCC‑CCCACAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                                   <  2:850929/147‑1 (MQ=255)                                                                   gCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGGAAAAAAACTTTAAACCC‑CCATGTtgtgttgg                                                                                 >  1:577730/1‑147 (MQ=25)                                                                      aacac‑cCGCGCTTTTACCCACCCCCATGAGAAAAAATCCCTCGGGGGGGGCTGTCTGCCAGTTTTTTTCCC‑GCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCa                                                                                <  2:74411/148‑1 (MQ=255)                                                                       acac‑cCGCGCTTTTACCCACCCCCTTGTAAAAAATTCCCTTCGCGGCGCTTGTCTGCCAGTTTTTTTCCC‑GCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                                             <  2:1250969/150‑1 (MQ=255)                                                                           cccGCGTTTTTACCCACCGCTATGTCCAAAAAGCCCGGCGCGGCGGCTGTCTGCCGTTTTTTTTCCC‑GCCGCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                                                         <  1:661057/150‑1 (MQ=255)                                                                               cgcATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑AAAAAAATTTTAACCCCCCCTGTtgtgt                                                                                    >  1:119942/1‑136 (MQ=25)                                                                               cattttaacccAACGCCAGGTGAAAAAATCCCTGCGGGGGGGCTTTCGCCCAGTTTTTTTCCC‑CCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTgg                                                                     <  1:1165924/142‑1 (MQ=255)                                                                                    ttATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAG‑AAAAAAATTTTAAACCCCCCTTTTTTGTGGGGATCGCTGCTggggaa                                                                 >  2:889962/1‑146 (MQ=25)                                                                                      aTCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCACGAG‑AAAAAACTTTTGGCCCCGCCTGTTGTGTGGGGGTAGCTCCTGGTGACaa                                                               >  2:17465/1‑150 (MQ=25)                                                                                          aaCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGGGGG‑AAAAAACCTTTATACCCCCCTGTTGTGTGGGAATCGCCGCCggggaaaa                                                               >  1:1182390/1‑140 (MQ=21)                                                                                          aaCCCCATGTGCAAAAATGCCTCCGCGGCGGTTGTCTCCCAGTTTTTTTCCC‑GCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTgg                                                          <  2:58058/151‑1 (MQ=255)                                                                                            cGCCTTGTAAAAAAATCCCTCCGGGGCGGCTGTCTCCCAGTTTTTTTCCC‑GCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGa                                                         <  2:383547/150‑1 (MQ=255)                                                                                                  gtgAAAAAATCCCTCCGCGGGGCCTGTCTGCCGCTTATTTTCCC‑GCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGaa                                                  <  1:378251/151‑1 (MQ=255)                                                                                                   tgaaaaaaTCCCTCCGGGGCGGCTGTCTCCCAGCTTTTTTCCC‑GCCCAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAg                                                      <  2:705707/143‑1 (MQ=255)                                                                                                     aaaaaaTGCCTGCGGGGCGGTTGTCTGCCAGTTTTTTTCCC‑GCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTg                                               <  2:252473/150‑1 (MQ=255)                                                                                                      aaaaaTCCCTTCGCGGCGGTTGTCGGCCAGTTTTTTTCCC‑GCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTg                                               <  1:856320/150‑1 (MQ=255)                                                                                                       aaaaTGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAG‑GAAAAAAATTAAAACCCCCCTGTTGTTTTGGGATCGCTGCTGGGGACAAAGTTGGAAGGGGAggggg                                             >  1:868897/1‑147 (MQ=255)                                                                                                        aaaTCCCTCCGGGGCGGCTGTCTGCCGTTTTTTTTCCC‑CCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcgg                                            <  2:1224552/151‑1 (MQ=255)                                                                                                           tcccTTGGGGGCGGCTGCCTGCCAGTTTTTTTTCC‑CCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGAGAAGTgcggcg                                          <  2:543177/148‑1 (MQ=255)                                                                                                               ttCGCGGCGGCTGTCTGCCAGCTATTTTTCC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGG‑AAAAAAGTTTAAACCCCCCATGTTTTTTGGGGAAACCTGCTGGTAACAATTTgggaagggaaagggggggga                                        >  2:397764/1‑138 (MQ=255)                                                                                                               tccgcgGCGGCTGTCTCCCAGTTTTTTTCCC‑GCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggcg                                          <  1:357861/144‑1 (MQ=255)                                                                                                                       ggcTGTCTGCCAGCTATTTTTCC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAG‑GAAAAACTTTTAACCCCCCCTTTTTTGGGGGGATCGCTGGGGGGGACAAAGTGGGGAGGGAGGGGGGGGGAGTCAGcccc                                >  1:1183080/1‑148 (MQ=255)                                                                                                                                ccAGCTTTTTTCCC‑GCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc                           <  2:1037329/144‑1 (MQ=255)                                                                                                                                 ctttttttttcCC‑GCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgcg                       <  1:1210297/141‑1 (MQ=255)                                                                                                                                   gCTATTTTTCC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGTGGAAGGG‑AAAAAAATTTTAAACCGCCCTGTTGTGGGGGGAATGCGGCTGGGGAAAAAGTGGGAAGGGGAGGGGGGGGGAGCAGGTCCCGAAACGCGCCaaat                 >  1:1132010/1‑149 (MQ=255)                                                                                                                                      tttttcaccaccgcATAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTg                <  1:449533/140‑1 (MQ=255)                                                                                                                                      aTTTTTCC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAG‑GAAAAACTTTTAAACCCTCCTGTTTTTTGGGGATTGCTGCTGGGGAAAAAGTGGGAAGGGGAGGGGGGGGGAACAACCCCCGAAACGCGCCAAtt                 >  2:77512/1‑148 (MQ=255)                                                                                                                                       tttttCCGGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGa               <  2:1039031/150‑1 (MQ=255)                                                                                                                                       ttttcCC‑GCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTg                <  2:257123/148‑1 (MQ=255)                                                                                                                                            cc‑gccaAAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc           <  1:1145000/148‑1 (MQ=255)                                                                                                                                                    aacaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATg  <  1:1070430/150‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                     ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATG  >  NC_000913/357743‑358037

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑