Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	43.2%	28.6 / 25.5	44	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (16/9);  new base A (0/19);  total (16/28)
Fisher's exact test for biased strand distribution p-value = 5.14e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCA  >  NC_000913/357742‑358034                                                                                                                                                     |                                                                                                                                                   gATACGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac                                                                                                                                                    <  2:1419365/149‑1 (MQ=255)    aaccGTAGCGCATCAGGCATTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac                                                                                                                                                    <  1:1153321/143‑1 (MQ=255)    aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaaa                                                                                                                                                <  1:161167/150‑1 (MQ=255)    aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAc                                                                                                                                               >  2:46009/1‑151 (MQ=255)     aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCCAAAATGCCTTTGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                                              <  2:612915/151‑1 (MQ=255)     aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                                              >  2:971742/1‑151 (MQ=255)      gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccg                                                                                                                                             <  1:115949/151‑1 (MQ=255)          aGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGt                                                                                                                                         >  1:1016925/1‑151 (MQ=255)              cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctc                                                                                                                                     >  2:196561/1‑151 (MQ=255)                      aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                               >  2:848390/1‑149 (MQ=255)                        ttCTAGCCGTAGACCTGTGTCAGCGGATAACGGGATTATTTTCCGCCAGCAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTAGCGGAGGCTGTCTGCCCGCTTTTTTTCCGCCGTAACAACACAGCCGTTCTCTCGagtag                                                                                                                             >  1:749080/1‑149 (MQ=18)                          ccAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                         >  1:1349187/1‑151 (MQ=255)                               cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCCACAAAACCCCCGTTCTCTCCAGTAGTGGCggggg                                                                                                                    >  1:246514/1‑150 (MQ=255)                                    aCCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                     >  2:358554/1‑145 (MQ=255)                                       tgtgTCGGCGCCTCCCGTGTTTCTTTCCCCCAAACACCCGCCCTTTTACCCACCCCATTGTAAAAAAATGCCTCCGCGGGGGCTGTCTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAagag                                                                                                               <  2:96110/148‑1 (MQ=255)                                         tgtCAGCGGCTCCCTTGATTCTTTCCCCCAAACACCCGCGCTTTTCTCCAACCCTATGTGCAAAAATGCCTCCGGGGCGGCTGTCTGCCAGCTTTTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgaga                                                                                                              <  2:1298868/147‑1 (MQ=255)                                          gtCGGCGGCCACCGTGATTCTTTCCCCCCAACACCCCCGCTTTTATCCACCGCCAGGTAAAAAAATGCTTGCGCGGCGGTTGTCTCCAAGTTATTTTCCCGCGGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt                                                                                                           <  1:1054702/149‑1 (MQ=255)                                          gtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGaaaaa                                                                                                          >  2:1394542/1‑148 (MQ=255)                                                gtctccggTGATTCATTCCCGCCACCACCCGCGCATTTACCCACCGCCGTGTGAAAAAATCCCTCGGGGGCGGCTTCCTGCAAGTTATTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTaa                                                                                                  <  2:856802/144‑1 (MQ=255)                                                  cTACCGTGATGCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTCCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCACCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAg                                                                                                 <  2:418728/150‑1 (MQ=255)                                                     ccGTGATTCTTTCCCCCCAACACCCGCGCTTTTACCCACCCCCATGTCAAAAAATCCCTTGGGGGCGGTTTTCGGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGccc                                                                                              <  2:1418340/150‑1 (MQ=255)                                                      cGTGATTCATTTCCTCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGTGGCAGGGGAATAGA‑TTTataa                                                                                                >  2:407544/1‑144 (MQ=25)                                                       gTGATTCTTTCCCCCCACCACCCGCGCATTTACCCACCCCCATGTGAAAAAGTCCCTCCGCGGCGGCTGTCTCCCAGTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTc                                                                                           <  2:331831/151‑1 (MQ=255)                                                           ttCTTTCCCCCCAACACCCGCTTTTTTACCCACCCCCATGTGAAAAAAGCCCTGCGCGGCGGCTGTCGGCCAGTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCa                                                                                          <  2:330485/148‑1 (MQ=255)                                                           ttCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGGGaaaaaaacgtta                                                                                                   >  1:433823/1‑131 (MQ=25)                                                                       accacccGCGCATTAACCCACCGCCTTGTGAAAAAGTGCCTCCGCGGCGGCTGTCTGCAAATTTTTTCCCCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATc                                                                           <  2:752664/146‑1 (MQ=255)                                                                         caacCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGGGAGAAAAAGA‑GTTTTACCCACCCTGTTGTGTgggggtatg                                                                         >  1:994165/1‑144 (MQ=25)                                                                            ccGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGCGAGAAAAATA‑TTTATAACCCTCATGGTGTGTgggggagg                                                                          >  1:787421/1‑141 (MQ=25)                                                                               cgcTTTTACCCACCGCCATGTAAAAAAATCCCTCCGCGGCGGCTGTCTGCCAGCTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                                     <  2:1036301/149‑1 (MQ=255)                                                                                        ccaccgcctttggaaaaaaTTCCTTGGCGGGGGTTGTCGGCAAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAtgt                                                         <  2:1182550/137‑1 (MQ=255)                                                                                        ccAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAA‑TTTAAAACCCCCATGTTTTGTGGGGATAGCTGCT‑gggtaca                                                             >  2:66712/1‑142 (MQ=25)                                                                                        caaaccccttgaaaaaaaaTCCCCCCGGGGCGCTTGTCCGCCATTTTTTTCCCCCCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAtgt                                                         <  1:903391/137‑1 (MQ=255)                                                                                          acccccATGTAAAAAAATGCTTCCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAt                                                           <  2:128377/143‑1 (MQ=255)                                                                                          accccatggtaaaaaagTCCCTCCGCGGCGCCTTTCCGCCGTTTTTTTTCCCCCCCCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAAc                                                              <  1:1013458/132‑1 (MQ=255)                                                                                            ccccATGTAAAAAAATGCTGCCGGGGCGGCTGTCTGCCATTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAtgtg                                                        <  2:1287712/146‑1 (MQ=255)                                                                                                                  gcggcgGCTGTCTGCCAGTTTTTTTCCCCCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGc                                <  2:228930/150‑1 (MQ=255)                                                                                                                    gggggcTGTCTGCAATTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTgcggcg                                       <  1:358541/138‑1 (MQ=255)                                                                                                                    ggcgcttGTCTGCCATTTTTTTTCCCGCCCAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCt                               <  1:228120/143‑1 (MQ=255)                                                                                                                            tctcccggtttttttcCCCCCACAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcg                      <  1:300157/139‑1 (MQ=255)                                                                                                                              ggcaactttttttcCCGCCAAAACAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGa                          <  1:558210/135‑1 (MQ=255)                                                                                                                               gccacttATTTCCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcg                      <  2:788450/141‑1 (MQ=255)                                                                                                                               cctggctttttccccgccaCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcg                      <  1:173806/134‑1 (MQ=255)                                                                                                                                       tttttCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGGAAAAAACTTTTAAGACC‑TCTTGGTGTGGGGGAATCACCGCTGGGGAAAAAAGGGGAAGGGGAAG‑GGGGGGAATCAGCTCCAGAAACACGCCaaat              >  2:1019616/1‑145 (MQ=255)                                                                                                                                       tttccccgccaCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTaa                <  1:34111/140‑1 (MQ=255)                                                                                                                                               ccgcAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCa  <  1:1272687/151‑1 (MQ=255)                                                                                                                                               ccgaAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTc   <  2:830850/150‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                   GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCA  >  NC_000913/357742‑358034

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: ‑