Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,298,363	0	G	A	21.5%	132.9 / 31.9	65	L162F (CTT→TTT)	yraR	putative nucleoside‑diphosphate‑sugar epimerase
Reads supporting (aligned to +/- strand):  ref base G (30/21);  new base A (5/9);  total (35/30)
Fisher's exact test for biased strand distribution p-value = 1.43e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.27e-01

AGGCCGCATCGACTCTGCCAGCATGACCCGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGTCAATTTCGGCCAGTTCTGGGCGATTAATGCTTCTTCCAT  >  NC_000913/3298268‑3298462                                                                                                |                                                                                                    aGGCCGCATCGACTCTGCCAGCATGACCCGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGtt                                                                                                 >  1:850999/1‑100 (MQ=255)    ccGCATCGACTCTGCCAGCATGACCCGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAACGTTTCg                                                                                              <  1:1228756/100‑1 (MQ=255)    ccGCATCGACTCTGCCAGCATGACCCGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAACGTTTCg                                                                                              <  1:660245/100‑1 (MQ=255)      gCATCGACTCTGCCAGCATGACCCGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGtt                                                                                            >  2:1284171/1‑100 (MQ=255)       cATCGACTCTGCCAGCATGACCCGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTc                                                                                           >  1:663313/1‑100 (MQ=255)        aTCGACTCTGCCAGCATGACCCGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCa                                                                                          >  2:1082316/1‑100 (MQ=255)         tCGACTCTGCCAGCATGACCCGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAACGTTTCGTTc                                                                                           <  2:626428/98‑1 (MQ=255)          ctaCTCTGCCAGAATGACCCGCGCCACGTCTCTCGAATCAATGGATTTCCAGTTACCTGGTAACAAACAAAAAAAAAAAAAAAAAAGCGTTTCGTTCATc                                                                                        <  2:373418/98‑1 (MQ=255)             ctctGCCAGCATGACCCGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGc                                                                                     >  2:513639/1‑100 (MQ=255)              tctGCCAGCATGACCCGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGTAAAAAAAACGCAAAAAGCGTTTCGTTCATCCGCt                                                                                    <  2:573751/100‑1 (MQ=255)              tctGCCAGCATGACCCGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCg                                                                                      >  2:711894/1‑98 (MQ=255)              tctGCCAGCATGACCCGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCt                                                                                    <  1:736379/100‑1 (MQ=255)               ctGCCAGCATGACCCGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTg                                                                                   <  1:833373/100‑1 (MQ=255)               ctGCCAGCATGACCCGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAACGTTTCGTTCATCCGCTg                                                                                   <  2:33977/100‑1 (MQ=255)                 gCCAGCATGACCCGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGtt                                                                                 >  2:747075/1‑100 (MQ=255)                  ccAGCATGACCCGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGttt                                                                                >  1:724667/1‑100 (MQ=255)                     gCAGGACCCGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAAAAAAAAAAAAAAAAGCGTTTCGTTCATCCGCTGTTTGc                                                                              <  2:55454/99‑1 (MQ=255)                      cATGACCCGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTa                                                                            <  2:847938/100‑1 (MQ=255)                      cATGACCCGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAACGTTTCGTTCATCCGCTGTTTGCTa                                                                            <  1:13951/100‑1 (MQ=255)                        tGACCCGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACg                                                                          <  1:680735/100‑1 (MQ=255)                          aCCCGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGAt                                                                        <  1:1284182/100‑1 (MQ=255)                           cccGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATc                                                                       >  1:722462/1‑100 (MQ=255)                           cccGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAAAAAAAAAAAAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATc                                                                       <  2:213494/100‑1 (MQ=255)                             cgcgCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGc                                                                     >  1:29977/1‑100 (MQ=255)                             cgcgCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAACGTTTCGTTCATCCGCTGTTTGCTACGATCGc                                                                     >  2:702835/1‑100 (MQ=255)                              gcgcCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGcc                                                                    <  2:664613/100‑1 (MQ=255)                                 ccACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAg                                                                 >  1:271051/1‑100 (MQ=255)                                 ccACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAg                                                                 <  1:811162/100‑1 (MQ=255)                                    cGTCTCTCGCATGAATGGATTTGCAGGTACCTGGTAACAAACGGAACAAAGGAGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTa                                                               <  2:1003371/99‑1 (MQ=255)                                    cGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTaa                                                              <  1:513643/100‑1 (MQ=255)                                     gTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAAc                                                             >  1:1094991/1‑100 (MQ=255)                                         ctcGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCg                                                         <  1:1155408/100‑1 (MQ=255)                                          tcGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGa                                                        >  1:217939/1‑100 (MQ=255)                                            gCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACg                                                      >  2:1101178/1‑100 (MQ=255)                                                cAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCg                                                  >  2:1224396/1‑100 (MQ=255)                                                cAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAACGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCg                                                  <  1:150887/100‑1 (MQ=255)                                                 aaTGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGc                                                   >  2:222694/1‑98 (MQ=255)                                                 aaTGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGa                                                 <  2:663309/100‑1 (MQ=255)                                                   tGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGc                                               >  2:618260/1‑100 (MQ=255)                                                   tGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAACGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGc                                               <  2:488579/100‑1 (MQ=255)                                                    ggATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCATTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCAAGCa                                              >  2:725104/1‑100 (MQ=255)                                                     gATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAACGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCaa                                             >  2:1073388/1‑100 (MQ=255)                                                        ttCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATgg                                          <  1:1082326/100‑1 (MQ=255)                                                         tCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGt                                         >  2:1271441/1‑100 (MQ=255)                                                         tCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGt                                         >  1:668270/1‑100 (MQ=255)                                                         tCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGt                                         <  2:29976/100‑1 (MQ=255)                                                         tCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGt                                         >  1:8821/1‑100 (MQ=255)                                                              ttACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGTCAAtt                                    >  2:1039290/1‑100 (MQ=255)                                                                 ccTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGTCAATTTCg                                 <  1:874114/100‑1 (MQ=255)                                                                  cTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGTCAATTTCgg                                >  1:596394/1‑100 (MQ=255)                                                                   tGGTAACAAACGGAACAGCGGCGCAAAAAACGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGTCAATTTCGGc                               >  2:877039/1‑100 (MQ=255)                                                                   tGGTAACAAACGGAACAGCGGCGCAAAAAACGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGTCAATTTCGGc                               >  2:1114749/1‑100 (MQ=255)                                                                    ggTAACAAACGGAACAGCGGCGCAAAAAACGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGTCAATTTCGGcc                              <  1:528846/100‑1 (MQ=255)                                                                      tAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGTCAATTTCGGCCAg                            >  2:34876/1‑100 (MQ=255)                                                                      tAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGTCAATTTCGGCCAg                            >  2:765914/1‑100 (MQ=255)                                                                         cAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGTCAATTTCGGCCAGtt                          >  1:1263950/1‑99 (MQ=255)                                                                         cAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGTCAATTTCGGCCAGTTc                         >  2:94186/1‑100 (MQ=255)                                                                          aaaCGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGTCAATTTCGGCCAGTTCt                        >  1:240841/1‑100 (MQ=255)                                                                              ggAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGTCAATTTCGGCCAGTTCTGGGc                    <  1:402571/100‑1 (MQ=255)                                                                              ggAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGTCAATTTCGGCCAGTTCTGGGc                    <  1:402500/100‑1 (MQ=255)                                                                               gAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGTCAATTTCGGCCAGTTCTGGGCg                   <  1:1271452/100‑1 (MQ=255)                                                                                 aCAGCGGCGCAAAAAACGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGTCAATTTCGGCCAGTTCTGGGCGAt                 <  1:516404/100‑1 (MQ=255)                                                                                  cAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGTCAATTTCGGCCAGTTCTGGGCGAtt                >  1:830442/1‑100 (MQ=255)                                                                                  cAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGTCAATTTCGGCCAGTTCTGGGCGAtt                >  2:617526/1‑100 (MQ=255)                                                                                  cAGCGGCGCAAAAAACGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAAGGGTCAATTTCGGCCAGTTCTGGGCGa                  >  2:395448/1‑98 (MQ=255)                                                                                                gCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGTCAATTTCGGCCAGTTCTGGGCGATTAATGCTTCTTCCAt  <  2:1158633/100‑1 (MQ=255)                                                                                                |                                                                                                    AGGCCGCATCGACTCTGCCAGCATGACCCGCGCCACGTCTCTCGCATCAATGGATTTCCAGTTACCTGGTAACAAACGGAACAGCGGCGCAAAAAGCGTTTCGTTCATCCGCTGTTTGCTACGATCGCCCAGTAACATCGACGGGCGAGCAATGGTCAATTTCGGCCAGTTCTGGGCGATTAATGCTTCTTCCAT  >  NC_000913/3298268‑3298462

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑