Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	REL606	3,910,119	0	G	A	22.2%	140.5 / 34.3	63	W78* (TGG→TGA)	yifE	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (18/31);  new base A (8/6);  total (26/37)
Fisher's exact test for biased strand distribution p-value = 2.23e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.97e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TGGATCTTGGCAAACGCGAGCCGGTTACCGAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGAAGGTGCTGAAGACTACACCGATTCTGACG  >  REL606/3910019‑3910219                                                                                                     |                                                                                                     tGGATCTTGGCAAACGCGAGCCGGTTACCGAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTgg                                                                                                      >  1:1239187/1‑101 (MQ=255) tGGATCTTGGCAAACGCGAGCCGGTTACCGAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTgg                                                                                                      <  1:1242860/101‑1 (MQ=255)     tCTTGGCAAACGCGAGCCGGTTACCGAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCa                                                                                                  <  2:1010717/101‑1 (MQ=255)      cTTGGCAAACGCGAGCCGGTTACCGAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCGaa                                                                                                 >  1:72703/1‑101 (MQ=255)      cTTGGCAAACGCGAGCCGGTTACCGAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCaa                                                                                                 >  1:1489974/1‑101 (MQ=255)       ttGGCAAACGCGAGCCGGTTACCGAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAg                                                                                                <  2:1571134/101‑1 (MQ=255)         ggCAAACGCGAGCCGGTTACCGAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGta                                                                                              >  2:378533/1‑101 (MQ=255)         ggCAAACGCGAGCCGGTTACCGAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGATTCAAGta                                                                                              >  1:93851/1‑101 (MQ=255)             aaCGCGAGCCGGTTACCGAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATg                                                                                          <  1:205242/101‑1 (MQ=255)               cgcgAGCCGGTTACCGAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGAc                                                                                        <  2:390709/101‑1 (MQ=255)               cgcgAGCCGGTTACCGAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGAc                                                                                        <  1:463272/101‑1 (MQ=255)                gcgAGCCGGTTACCGAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGAct                                                                                       <  2:435862/101‑2 (MQ=255)                   aGCCGGTTACCGAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGt                                                                                    <  1:1092374/101‑1 (MQ=255)                       ggTTACCGAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTa                                                                                <  2:1277607/101‑1 (MQ=255)                        gTTACCGAGGCAGAGAACCTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGCCGCGTATTaa                                                                               <  2:1616111/101‑1 (MQ=255)                        gTTACCGAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTaa                                                                               <  1:1073700/101‑1 (MQ=255)                        gTTACCGAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTaa                                                                               <  2:1692658/101‑1 (MQ=255)                         ttACCGAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATG‑CGCGTATTAAGc                                                                             <  2:1059642/101‑1 (MQ=255)                           aCCGAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCg                                                                            >  2:188833/1‑101 (MQ=255)                            ccGAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGt                                                                           <  2:457179/101‑1 (MQ=255)                            ccGAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGATCCAAGTATATGACGCGTATTAAGCGt                                                                           >  1:518082/1‑101 (MQ=255)                             cGAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTc                                                                          >  2:241527/1‑101 (MQ=255)                              gAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTcc                                                                         <  2:783263/101‑1 (MQ=255)                               aGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCa                                                                        <  2:319584/101‑1 (MQ=255)                                 gAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCaaa                                                                      >  1:28873/1‑101 (MQ=255)                                  aaGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGATCCAAGTATATGACGCGTATTAAGCGTCCaaaa                                                                     >  1:1627453/1‑101 (MQ=255)                                  aaGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGATCCAAGTATATGACGCGTATTAAGCGTCCaaaa                                                                     >  2:583339/1‑101 (MQ=255)                                    gagaAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACg                                                                   <  2:1014317/101‑1 (MQ=255)                                     agaAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGt                                                                  >  1:580659/1‑101 (MQ=255)                                     agaAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGt                                                                  >  1:365239/1‑101 (MQ=255)                                        accttttCGTAGCAGTATGACGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGTGTGTGGTACAAGTATATGACGCGTATTAAACGTCCAAAACGtttt                                                               <  2:829591/96‑1 (MQ=255)                                        aaCTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGtttt                                                               <  1:613979/101‑1 (MQ=255)                                         aCTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTc                                                              <  1:187270/101‑1 (MQ=255)                                          ctctTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTca                                                             >  1:397111/1‑101 (MQ=255)                                          ctctTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTca                                                             >  1:195943/1‑101 (MQ=255)                                          ctctTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGATCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTca                                                             <  2:631044/101‑1 (MQ=255)                                            ctTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATG‑CGCGTATTAAGCGTCCAAAACGTTTTCacac                                                          <  1:1654397/101‑1 (MQ=255)                                             ttCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCacac                                                          <  2:707259/101‑1 (MQ=255)                                             ttCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCacac                                                          <  2:567822/101‑1 (MQ=255)                                             ttCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCacac                                                          >  1:6884/1‑101 (MQ=255)                                                gTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGATCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCt                                                       >  2:252031/1‑101 (MQ=255)                                                 tAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCtt                                                      <  1:348740/101‑1 (MQ=255)                                                   gCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTc                                                    <  2:445890/101‑1 (MQ=255)                                                   gCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTc                                                    <  2:43857/101‑1 (MQ=255)                                                        aTGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCcggcg                                               >  2:56966/1‑101 (MQ=255)                                                               ggCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAAcc                                        >  1:1103750/1‑101 (MQ=255)                                                                      gTGAGCCAGTGACAGAAGCAGAACGCGTGTGATCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGtt                                 >  1:1518055/1‑101 (MQ=255)                                                                         aGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGaa                              <  2:661588/101‑1 (MQ=255)                                                                           ccAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGAAgg                            >  2:17672/1‑101 (MQ=255)                                                                            cAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGAAGGt                           <  2:72703/101‑1 (MQ=255)                                                                            cAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGAAGGt                           >  2:1189906/1‑101 (MQ=255)                                                                              gTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGAAGGTGc                         >  2:247060/1‑101 (MQ=255)                                                                               tGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGAAGGTGCt                        <  2:1439434/101‑1 (MQ=255)                                                                                gACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGAAGGTGCTg                       <  2:1339810/101‑1 (MQ=255)                                                                                gACAGAAGCAGAACGCGTGTGATCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGAAGGTGCTg                       <  1:535037/101‑1 (MQ=255)                                                                                  cAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGAAGGTGCTGaa                     >  1:26026/1‑101 (MQ=255)                                                                                    gAAGCAGAACGCGTGTGATCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGAAGGTGCTGAAGa                   >  1:1207580/1‑101 (MQ=255)                                                                                     aaGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGAAGGTGCTGAAGAc                  <  2:6884/101‑1 (MQ=255)                                                                                      aGCAGAACGCGTGTGATCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGAAGGTGCTGAAGACt                 >  2:1376634/1‑101 (MQ=255)                                                                                        cAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGAAGGTGCTGAAGACTac               >  1:352685/1‑101 (MQ=255)                                                                                        cAGAACGCGTGTGATCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGAAGGTGCTGAAGACTac               <  2:1461922/101‑1 (MQ=255)                                                                                         aGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGAAGGTGCTGAAGACTaca              <  1:424417/101‑1 (MQ=255)                                                                                          gAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGAAGGTGCTGAAGACTacac             >  1:164841/1‑101 (MQ=255)                                                                                          gAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGAAGGTGCTGAAGACTacac             <  2:195943/101‑1 (MQ=255)                                                                                             cgcgTGTGATCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGAAGGTGCTGAAGACTACACCGa          <  2:1342684/101‑1 (MQ=255)                                                                                             cgcgTGTGATCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGAAGGTGCTGAAGACTACACCGa          <  2:1189673/101‑1 (MQ=255)                                                                                                 tgtgATCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGAAGGTGCTGAAGACTACACCGATTCt      <  2:984557/101‑1 (MQ=255)                                                                                                    ggTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGAAGGTGCTGAAGACTACACCGATTCTGAc   <  1:378538/101‑1 (MQ=255)                                                                                                     gTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGAAGGTGCTGAAGACTACACCGATTCTGACg  <  1:851056/101‑1 (MQ=255)                                                                                                     |                                                                                                     TGGATCTTGGCAAACGCGAGCCGGTTACCGAGGAAGAGAAACTCTTCGTAGCAGTATGCCGTGGCGAACGTGAGCCAGTGACAGAAGCAGAACGCGTGTGGTCCAAGTATATGACGCGTATTAAGCGTCCAAAACGTTTTCACACCCTTTCCGGCGGTAAACCGCAGGTTGAAGGTGCTGAAGACTACACCGATTCTGACG  >  REL606/3910019‑3910219

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑