Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,235,039	0	A	G	22.0%	94.2 / 24.7	50	E34E (GAA→GAG)	fadR	fatty acid metabolism regulon transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base A (15/24);  new base G (3/8);  total (18/32)
Fisher's exact test for biased strand distribution p-value = 7.24e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.56e-01

TCATTAAGGCGCAAAGCCCGGCGGGTTTCGCGGAAGAGTACATTATTGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTACAGCGTCTGGCACGAGATGGCTGGTTGACCATTCAACATGGC  >  NC_000913/1234942‑1235135                                                                                                  |                                                                                                 tCATTAAGGCGCAAAGCCCGGCGGGTTTCGCGGAAGAGTACATTATTGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACg                                                                                                >  2:1117208/1‑100 (MQ=255)  cATTAAGGCGCAAAGCCCGGCGGGTTTCGCGGAAGAGTACATTATTGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAGCGt                                                                                               <  1:1190912/100‑1 (MQ=255)  cATTAAGGCGCAAAGCCCGGCGGGTTTCGCGGAAGAGTACATTATTGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGt                                                                                               >  2:1250302/1‑100 (MQ=255)   aTTAAGGCGCAAAGCCCGGCGGGTTTCGCGGAAGAGTACATTATTGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTg                                                                                              <  1:1040715/100‑1 (MQ=255)   aTTAAGGCGCAAAGCCCGGCGGGGTTCGCGGAAGAGTACATTATTGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAGCGt                                                                                               <  2:514700/99‑1 (MQ=255)      aaGGCGCAAAGCCCGGCGGGTTTCGCGGAAGAGTACATTATTGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAAc                                                                                           <  1:988128/100‑1 (MQ=255)       aGGCGCAAAGCCCGGCGGGTTTCGCGGAAGAGTACATTATTGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAGCGTGAACt                                                                                          <  1:556090/100‑1 (MQ=255)        ggCGCAAAGCCCGGCGGGTTTCGCGGAAGAGTACATTATTGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACtt                                                                                         >  1:1196599/1‑100 (MQ=255)          cgcAAAGCCCGGCGGGTTTCGCGGAAGAGTACATTATTGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAGCGTGAACTTTc                                                                                       <  2:479585/100‑1 (MQ=255)           gcAAAGCCCGGCGGGTTTCGCGGAAGAGTACATTATTGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACTTTCa                                                                                      <  2:449739/100‑1 (MQ=255)            cAAAGCCCGGCGGGTTTCGCGGAAGAGTACATTATTGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACTTTCAg                                                                                     <  2:235245/100‑1 (MQ=255)            cAAAGCCCGGCGGGTTTCGCGGAAGAGTACATTATTGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACTTTCAg                                                                                     <  1:29666/100‑1 (MQ=255)              aaGCCCGGCGGGTTTCGCGGAAGAGTACATTATTGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAGCGTGAACTTTCAGaa                                                                                   >  2:632693/1‑100 (MQ=255)               aGCCCGGCGGGTTTCGCGGAAGAGTACATTATTGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAGCGTGAACTTTCAGaat                                                                                  <  2:961726/100‑1 (MQ=255)                  ccGGCGGGTTTCGCGGAAGAGTACATTATTGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACTTTCAGaattaa                                                                               <  1:586071/100‑1 (MQ=255)                    ggcggGTTTCGCGGAAGAGTACATTATTGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACTTTCAGaattaatt                                                                             <  1:1018985/100‑1 (MQ=255)                     gcggGTTTCGCGGAAGAGTACATTATTGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACTTTCAGAATTAATTg                                                                            <  2:385127/100‑1 (MQ=255)                        ggTTTCGCGGAAGAGTACATTATTGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAGCGTGAACTTTCAGAATTAATTGGCg                                                                         <  2:60926/100‑1 (MQ=255)                              gcgGAAGAGTACATTATTGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACTTTCAGAATTAATTGGCGTAAcgc                                                                   <  2:691429/100‑1 (MQ=255)                                ggAAGAGTACATTATTGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGt                                                                 >  2:226913/1‑100 (MQ=255)                                      gTACATTATTGAGAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTTCCTGCAGAACGTGAACTTTCATAATTAATTGGCGTAACGCGtactcc                                                            >  2:723175/1‑97 (MQ=255)                                      gTACATTATTGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCCGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACtacg                                                           >  1:1041124/1‑100 (MQ=255)                                           ttattGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACtacgttacg                                                      <  1:1117218/100‑1 (MQ=255)                                            tattGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACtacgttacgt                                                     <  1:380030/100‑1 (MQ=255)                                                gAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAg                                                 >  2:1100152/1‑100 (MQ=255)                                                   aGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAgtgt                                              <  2:962390/100‑1 (MQ=255)                                                      aTCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTAc                                           >  2:217081/1‑100 (MQ=255)                                                       tCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAGCGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTACa                                          <  1:386296/100‑1 (MQ=255)                                                       tCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAGCGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTACa                                          <  1:632697/100‑1 (MQ=255)                                                       tCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTACa                                          <  1:806461/100‑1 (MQ=255)                                                        cTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTACAg                                         >  2:36957/1‑100 (MQ=255)                                                          ggAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTACAGCg                                       <  1:1250313/100‑1 (MQ=255)                                                          ggAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTACAGCg                                       <  1:153474/100‑1 (MQ=255)                                                             aTAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACTTTCAGAATTAATTGGCCTAACGCGTACTACGTTACGTGAAGTGTTACAGCGTCt                                    <  2:699434/100‑1 (MQ=255)                                                                aCCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTACAGCGTCTGGc                                 <  1:1216061/100‑1 (MQ=255)                                                                  cGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTACAGCGTCTGGCAc                               >  2:19175/1‑100 (MQ=255)                                                                     ttCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTACAGCGTCTGGCACgag                            <  1:230634/100‑1 (MQ=255)                                                                        cctcccGGGACTATTTTGCCCGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGTGTACTACGTTACGTGAAGTGTTACAGCGTCTGGCACGAGATg                         >  1:431451/1‑100 (MQ=255)                                                                             cGGGACTATTTTGCCCGCAGAGCGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTACAGCGTCTGGCACGAGATGGCTgg                    >  2:45509/1‑100 (MQ=255)                                                                               ggACTATTTTGCCCGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTACAGCGTCTGGCACGAGATGGCTGGtt                  <  1:289649/100‑1 (MQ=255)                                                                                 aCTATTTTGCCCGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTACAGCGTCTGGCACGAGATGGCTGGTTGa                <  1:666731/100‑1 (MQ=255)                                                                                    aTTTTGCCCGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTACAGCGTCTGGCACGAGATGGCTGGTTGACCa             >  1:988499/1‑100 (MQ=255)                                                                                       ttGCCCGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTACAGCGTCTGGCACGAGATGGCTGGTTGACCATTc          <  2:573351/100‑1 (MQ=255)                                                                                        ctcccGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTACAGCGTCTGGCACGAGATGGCTGGTTGACCATTCa         <  1:200924/98‑1 (MQ=255)                                                                                          cccGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTACAGCGTCTGGCACGAGATGGCTGGTTGACCATTCaag       >  2:200922/1‑99 (MQ=255)                                                                                          cccGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTACAGCGTCTGGCACGAGATGGCTGGTTGACCATTCAAc       >  1:406881/1‑100 (MQ=255)                                                                                            cGCAGAGCGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTACAGCGTCTGGCACGAGATGGCTGGTTGACCATTCAACAt     >  1:1150411/1‑100 (MQ=255)                                                                                            cGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTACAGCGTCTGGCACGAGATGGCTGGTTGACCATTCAACAt     >  1:446811/1‑100 (MQ=255)                                                                                              cAGAACGTGTACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTACAGCGTTTGTCACGAGATGGCTGGTTGACCATTCAACATg    <  2:856370/99‑1 (MQ=255)                                                                                               aGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTACAGCGTCTGGCACGAGATGGCTGGTTGACCATTCAACATGGc  <  1:36958/100‑1 (MQ=255)                                                                                                  |                                                                                                 TCATTAAGGCGCAAAGCCCGGCGGGTTTCGCGGAAGAGTACATTATTGAAAGTATCTGGAATAACCGCTTCCCTCCCGGGACTATTTTGCCCGCAGAACGTGAACTTTCAGAATTAATTGGCGTAACGCGTACTACGTTACGTGAAGTGTTACAGCGTCTGGCACGAGATGGCTGGTTGACCATTCAACATGGC  >  NC_000913/1234942‑1235135

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑