Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,248,424	0	C	A	40.6%	47.9 / 20.9	32	V37F (GTT→TTT)	lysP	lysine transporter
Reads supporting (aligned to +/- strand):  ref base C (15/4);  new base A (0/13);  total (15/17)
Fisher's exact test for biased strand distribution p-value = 7.15e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGTGGCAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTG‑TACCGATGG‑AACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCG  >  NC_000913/2248281‑2248566                                                                                                                                                |                                                                                                                                                 aGTGGCAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACaaaa                                                                                                                                              >  1:659614/1‑148 (MQ=255)       aaaCGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTG‑Ta                                                                                                                                    <  1:529382/151‑1 (MQ=255)            aaCCGGAAACCGGCATATATGCAGCCAGTTCCCCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTG‑TACCGAt                                                                                                                               <  1:220878/151‑1 (MQ=255)            aaCCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTG‑TACCGAt                                                                                                                               <  1:6744/151‑1 (MQ=255)             aCCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTG‑TACCGATg                                                                                                                              >  1:296184/1‑151 (MQ=255)                ggAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTG‑TACCGATGG‑aa                                                                                                                          <  1:345792/151‑1 (MQ=255)                                gCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTG‑TACCGATGG‑AACCGCCAATGGCAatc                                                                                                           >  2:233404/1‑150 (MQ=255)                                      aGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTG‑TACCGATGG‑AACCGCCAATGGCAATCATCGTc                                                                                                     >  1:103732/1‑150 (MQ=255)                                               tgaCTGGTCATCAGGAAGTAAACCATCAGTCCAATCAGCATATACGTGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTG‑TACCGATGG‑AACCGCCAATGGCAATCATCGTCAGGAGAcg                                                                                             >  1:107227/2‑149 (MQ=255)                                               agaCTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTG‑TACCGATGG‑AACCGCCAATGGCAATCATCGTCAGGTGAcgcg                                                                                           >  1:124243/1‑151 (MQ=255)                                                       catcaGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTG‑TACCGATGG‑AACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAAt                                                                                   >  2:90473/1‑151 (MQ=255)                                                               aGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTG‑TACCGATGG‑AACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCg                                                                           >  2:131513/1‑151 (MQ=255)                                                                  aaaCCTTCAGACCAATCACCATATAGAAGATCATTCCCCCGCCCGGCCCTGCCGAAAAAAGCTTCGCCCGAGAGACAAAAAAAAGCCTTG‑CACCGATAG‑ATCCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTa                                                                         <  2:2282/150‑1 (MQ=255)                                                                  aaaCCATCAGCCCAATCACCATATACGAGAGCAATCCCCCCCCCGGCCCTGCCTGAGAATTCGTTGCGCCAGAGACAAAAAAAAGCCCTG‑TCCGGAGGG‑AACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGt                                                                          <  2:688339/149‑1 (MQ=255)                                                                     ccATCAGCCCAATCAGCTTAGACGAGAGAAAGGCCCCGCCCGGCCCGTCGTAAAAAATCGTTGCCCCAGGGGCAAAAAAAAGACCTG‑TCCCGAGGG‑AACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGcc                                                                     <  2:232179/151‑1 (MQ=255)                                                                          aGGCCACTCACCAAATCGGAGAACAACCCCCCGCCGGGACCTCCTAGAGAAATCGTGGCGCCAGAGGAAAAAAAAAGCCCTG‑TACCGAGGG‑AACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCg                                                                   <  1:17240/148‑1 (MQ=255)                                                                             ccAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTG‑TACCGATGG‑AACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCtt                                                             >  2:135674/1‑151 (MQ=255)                                                                             ccAAACAGCATATACGAGAGAAATCCCCCCCCCGTCCCGCCCGGAAAAATCTTGGCGCCAGAGGCAAAAAAAAGCCCTG‑TCCCGAGGA‑AACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGgc                                                                 <  2:533226/147‑1 (MQ=255)                                                                                 acAGCATAAACGAAACAAACCCCCCGCCCGGCCCGCCCGAAAAAATCGTGGCGCGAGCACCAAAAAAAAAACCGC‑TCCGGATGA‑AACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCgg                                                                  <  2:49038/141‑1 (MQ=255)                                                                                      atatACGGGAGCAATCCCCCCCCCGGCCCTCCCGGAGAAATCGTGGCGCGAGAGGCAAAAAAAAGCCCTG‑TCCCGATGG‑AACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGtt                                                     <  1:465141/150‑1 (MQ=255)                                                                                      ataaACGAAAGAAACCCCCCGCCCGGACCTGCCGGAAAAATCGTGGCGCAAGAGGAAAAAAAAAGCCCTG‑TACAGATGG‑AACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGtt                                                     <  1:641603/150‑1 (MQ=255)                                                                                            gagaACAACGCCCCGCCCCGCCGTGCCTGAAAAATTTTTGCACCAGGAGCAAAAAAAACACCTG‑CCCAGAGGA‑AACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGtt                                               <  1:329069/150‑1 (MQ=255)                                                                                             agagCAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTG‑TACCGATGG‑AACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTc                                             >  1:210569/1‑151 (MQ=255)                                                                                              gaccAACGCCCCGCCGGCCCCTGCCTAAAAAACCGTGGCGCAAGGGGAAAAAAAAAGCCCTT‑TACGGAGGG‑AACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGtt                                               <  1:366997/145‑1 (MQ=255)                                                                                               agCAACCCCCCGCCCGTCCCTCCCGGAAAAATCGTGGCGCC‑GGGGAAAAAAAAAACCCTGTTCCCGATGA‑AACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGttt                                              <  1:54426/148‑1 (MQ=255)                                                                                                     gCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTG‑TACCGATGG‑AACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAAcc                                      >  2:372807/1‑150 (MQ=255)                                                                                                                 cctgcctgAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTG‑TACCGATGG‑AACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCt                         >  2:536486/1‑151 (MQ=255)                                                                                                                            aaTCGTTGCGCAAGAGGCAAAAAAAAGCCCTG‑TCCCGAGGG‑AACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTaa              <  2:235015/151‑1 (MQ=255)                                                                                                                               cGTTGCGCCAGAGGCAACAAAAAGACCTG‑TACCGATGG‑AACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTaaaa            >  2:501539/1‑150 (MQ=255)                                                                                                                                    cgcAAGAGGAAAAAAAAAGATCT‑‑TCCCGAAGGCATCCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGTTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTaaaatg          <  1:678647/147‑3 (MQ=255)                                                                                                                                     gcCAGAGGCAACAAAAAGACCTG‑TACCGATGG‑AACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGgc     >  2:16337/1‑151 (MQ=255)                                                                                                                                        agagGCAACAAAAAGACCTG‑TACCGATGG‑AACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGcgcg  >  1:467507/1‑151 (MQ=255)                                                                                                                                                |                                                                                                                                                 AGTGGCAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTG‑TACCGATGG‑AACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCG  >  NC_000913/2248281‑2248566

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑