Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,248,431	0	A	C	44.2%	76.4 / 16.3	52	G34G (GGT→GGG)	lysP	lysine transporter
Reads supporting (aligned to +/- strand):  ref base A (20/9);  new base C (0/23);  total (20/32)
Fisher's exact test for biased strand distribution p-value = 8.15e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGCAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGTAGCA  >  NC_000913/2248284‑2248575                                                                                                                                                      |                                                                                                                                                 ggCAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCt                                                                                                                                               <  2:528501/151‑1 (MQ=255) ggCAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCt                                                                                                                                               <  2:347040/151‑1 (MQ=255)   cAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGt                                                                                                                                             <  2:970006/151‑1 (MQ=255)             ggAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGaa                                                                                                                                   <  1:239799/151‑1 (MQ=255)               aaaCCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAAcc                                                                                                                                 <  2:753918/151‑1 (MQ=255)                 aCCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGc                                                                                                                               <  2:925875/151‑1 (MQ=255)                        tatatGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGc                                                                                                                        >  1:859153/1‑151 (MQ=255)                         atatGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGc                                                                                                                        >  2:900137/1‑150 (MQ=255)                           atGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAat                                                                                                                     >  2:398352/1‑151 (MQ=255)                                   aGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTc                                                                                                              >  2:608878/1‑150 (MQ=255)                                     tccccggagaGTGGTCATCAGGAAGAAACCCACCAGGCAAATCAGCATATACGAGAG‑AAATCCCCCGCCCGGCCCTGCCTG‑AGAAATCGTTGCGCAAGAGGCAAAAAAAAGCCCTGTACCGATGAAACCGCCAATGGCAATCATCGTc                                                                                                              <  1:418340/142‑1 (MQ=255)                                          cgatccTGGTAAGCAGGAAGAAAACCACCGGCCCAATCAGAACATACG‑GAGCCACTGCCCCCCCGGTACCGCCCTG‑AAAAATCGTGCCCCCAGACGCAACAAAAAGCCCTGTCCCGAGGGACCCGCCAATGGCAATCATCGTCAgg                                                                                                           <  2:430793/141‑1 (MQ=255)                                           gagaCTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGAcgc                                                                                                     >  1:258154/1‑151 (MQ=255)                                             gaCTGTTCACCAGAAAGAAAACCATCAGGCAAATCAGCATATACGAGAG‑CAATCCCCCGCCCGGCCCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAAAAAAAAGCCCTGTCCCGATGGAACCGCCAATGGCAATCATCGTCAGGTGAcgcg                                                                                                    <  1:312145/150‑1 (MQ=255)                                             gaCTGGTCATCAGGAAGAAACCCATCAGGCAAATCAGCATATCCGAGAG‑CAACCCCCCGCCCGGCCCTGCCTG‑AAAAATCGTGGCGCCAGGGGCAAAAAAAAGCCCTGTCCCGAGGGAACCGCCAATGGCAATCATCGTCAGGTGAcgcg                                                                                                    <  2:930147/150‑1 (MQ=255)                                              aCTGGTCATCAGGAAGAAAACCATCAGGCCAACCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTG‑AAAAATCGTTGCGCCAGAGGCAACAAAAAGCCCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGAcgcg                                                                                                    <  1:91722/149‑1 (MQ=255)                                               cTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCt                                                                                                 >  2:885865/1‑151 (MQ=255)                                                 gttaagcaGAAAGAAAACCACCGGCCCAATCAGCATATAGGAAAC‑CAATGCCCCGCCCGG‑CCCGCCGGAAGAAATCGTTGCGCAAGAGGCAAAAAAAAGCCCTGCACCGAGGAAACCGCCAATGGCAATCATCGTCAGGTGACgcgc                                                                                                   <  2:400999/141‑1 (MQ=255)                                                  gTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGCCCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTa                                                                                              <  1:698159/151‑1 (MQ=255)                                                     atcaGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAAtt                                                                                           >  1:443288/1‑151 (MQ=255)                                                      taagaaaGAAAACCATAAGGCAACTCAGAAAATACGAGAG‑AAACCCCCCCCCCGGCCCTCCAGG‑AGAAATCGTGGCGCCAGAGGCAACAAAAAGACCTGCCCCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCtt                                                                                                <  2:747306/140‑1 (MQ=255)                                                           aaGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCCTTAATTCACGGc                                                                                     >  2:307949/1‑151 (MQ=255)                                                           aaGAAAACCATCAGCCCAATCAGCATATACGAGAG‑CAATGCCCCCCCCGGCCCTGCCGG‑AAAAATCGTGGCGCCAGAGGCAAAAAAAAGCCCTGTCCCGAGGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACg                                                                                       <  2:178350/149‑1 (MQ=255)                                                                   cATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGccc                                                                             >  2:769280/1‑151 (MQ=255)                                                                        ggCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGgcgc                                                                        >  1:302887/1‑151 (MQ=255)                                                                        ggCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGgcgc                                                                        >  1:364235/1‑151 (MQ=255)                                                                        ggCAAATCAGCATATACGAGAG‑AAACGCCCCCCCCGGCCCGGCCTG‑AAAAATCGTGGCGCAAGAGGCAAAAAAAAGCCCTGTACGGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGgc                                                                          <  2:982488/149‑1 (MQ=255)                                                                              tCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCtgt                                                                  >  2:348802/1‑151 (MQ=255)                                                                                   atatACGAGAG‑CAAGGCCCCGCCGGGCCCTGCCTG‑AGAAATCGTGGCGCCAGAGGCAAAAAAAAGCCCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGt                                                               <  1:553478/149‑1 (MQ=255)                                                                                     ataCGAGAG‑CAATGCCCCCCCCGGACCTGCCTG‑AAAAATCGTTGCGCCAGAGGCAACAAAAAGCCCTGTACCGAGGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGttt                                                             <  1:622871/149‑1 (MQ=255)                                                                                        cGAGAG‑CAATCCCCCGCCCGGCCCTGCCTA‑AAAATGCGTGGCGCCAGAGGCAAAAAAAAGACCTGTCCCGATGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTa                                                           <  1:777425/148‑1 (MQ=255)                                                                                         gagag‑aAATCCCCCGCCCGGACCTGCCGG‑AAAAATCGTGGCGCCAGAGGCAAAAAAAAGCCCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGttt                                                       <  1:38914/151‑1 (MQ=255)                                                                                         gagaG‑CAATGCCCCGCCCGGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGttt                                                       >  1:305302/1‑151 (MQ=255)                                                                                          agag‑CAATGCCCCGCCCGGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTc                                                      >  2:206358/1‑151 (MQ=255)                                                                                                    ccccGCCCGGCCCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGCCCTGTCCCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCAt                                             <  1:59500/151‑1 (MQ=255)                                                                                                      ccgcccgGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATAc                                           >  2:316774/1‑151 (MQ=255)                                                                                                         cccgGCCCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAAAAAAAAGCCCTGTCCCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACaaa                                        <  1:667685/151‑1 (MQ=255)                                                                                                            ggccctgcctg‑AAAAATCGTTGCGCAAGAGGCAAAAAAAAGCCCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACaaaaa                                      <  2:721172/147‑1 (MQ=255)                                                                                                            ggACCTCCCTG‑AAAAATCGTGGCGCCAGAGGCAAAAAAAAGCCCTGTCCCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAAt                                     <  2:43406/151‑1 (MQ=255)                                                                                                                ctgcctg‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCt                                  >  1:254097/1‑150 (MQ=255)                                                                                                                 tgcctg‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTAt                                >  1:829987/1‑151 (MQ=255)                                                                                                                        aaaaaTCGTGGCGCCAGAGGAAAAAAAAAGCCCTGTACCGAGGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCAt                            <  1:713801/147‑1 (MQ=255)                                                                                                                          aaaTCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCtt                         >  2:634579/1‑150 (MQ=255)                                                                                                                           aaTGGTTGCGCCAGAGGAAAAAAAAAGCCCTTTACGGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTaa                       <  1:440438/151‑1 (MQ=255)                                                                                                                                  gcgcCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATg                  >  1:47949/1‑149 (MQ=255)                                                                                                                                   cgcCAGAGGCAAAAAAAAGCCCTGTCCCGAGGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTaaa                      <  2:993842/144‑1 (MQ=255)                                                                                                                                   ccccggggcaaaaaaaaaGCCCTGTCCCGAGGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAg                <  2:855288/137‑1 (MQ=255)                                                                                                                                          ggCAAAAAAAAGCCCTGTACCGAGGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGgcg             <  1:330504/146‑1 (MQ=255)                                                                                                                                              aaaaaaaGCCCTGTACCGAGGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGTAg    <  1:47801/149‑1 (MQ=255)                                                                                                                                                aaaaaGCCCTGTCCCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGTAGCa  <  1:900245/151‑1 (MQ=255)                                                                                                                                                 aaaaGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGTAGc   >  1:995378/1‑149 (MQ=255)                                                                                                                                                  aaaGACCTTTGCCGATGAACCCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGt      <  2:942530/145‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                 GGCAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAG‑CAATGCCCCGCCCGGACCTGCCTG‑AGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGTAGCA  >  NC_000913/2248284‑2248575

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑