Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,343,821	0	C	A	38.5%	58.6 / 10.9	39	A117S (GCT→TCT)	yfaL	adhesin
Reads supporting (aligned to +/- strand):  ref base C (19/5);  new base A (0/15);  total (19/20)
Fisher's exact test for biased strand distribution p-value = 7.71e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGATGTTATTGCGAAACATGGCGTTAGTGACACGTAAATCGACGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTGGCGTTATTGGTCATATCCGAA  >  NC_000913/2343671‑2343969                                                                                                                                                       |                                                                                                                                                     cGATGTTATTGCGAAACATGGCGTTAGTGACACGTAAATCGACGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGc                                                                                                                                                      <  1:799657/151‑1 (MQ=255)  gATGTTATTGCGAAACATGGCGTTAGTGACACGTAAATCGACGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCa                                                                                                                                                     <  1:233638/151‑1 (MQ=255)   aTGTTATTGCGAAACATGGCGTTAGTGACACGTAAATCGACGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCaa                                                                                                                                                    <  1:704759/151‑1 (MQ=255)     gTTATTGCGAAACATGGCGTTAGTGACACGTAAATCGACGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCaaa                                                                                                                                                   <  2:482900/150‑1 (MQ=255)         ttGCGAAACATGGCGTTAGTGACACGTAAATCGACGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATgg                                                                                                                                              >  2:479174/1‑151 (MQ=255)         ttGCGAAACATGGCGTTAGTGACACGTAAATCGACGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATgg                                                                                                                                              >  2:727031/1‑151 (MQ=255)                  aTGGCGTTAGTGACACGTAAATCGACGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCGGCGTTGAGTTTTCTTTAGCAAATATGGCCCCGCCGt                                                                                                                                     >  2:271364/1‑151 (MQ=255)                   tGGCGTTAGTGACACGTAAATCGACGGCACCAGTATCTTTAGTACCAGAAAAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCTTTGAGTTTTCTTTAGCAAATATGGCCccgccg                                                                                                                                      <  1:563436/149‑1 (MQ=255)                           gTGACACGTAAATCGACGGCCCCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGACCCCGCCGTTATTATAtt                                                                                                                            >  2:563563/1‑151 (MQ=255)                             gACACTTAAATCGACGGCACCAGTATCGTTAGAACCAGAAGAGTAGATGGCGCCACAATAGCCGCCTGCCACGTTACCGGAAAAAATAATATCAGTAAGATTCAGCGTTGAGGTTTCTTTAGCAAATATCGCCCCGCCGTTATTATAtt                                                                                                                            >  2:768432/1‑149 (MQ=255)                                acGAAAATCCACGGCCCCATTATTGTTAGTACGAGAAAAATATATCGCCCCCCCATGGCCGCCTGGGGCGTTACAGAAAAAAATAACATCAGTAAAATTCAGCTTTGTTTTTTCTTTAAAAAATTGGGCCCCGCCGTTATTATATTCTCCt                                                                                                                       <  1:41184/151‑1 (MQ=255)                                     aaTCGACGCCACCAGTATCGTTAGCACAAGAAAAATAGTTTGCCCCCCAATCGCCGCCGGCGACTTTACAGAAAAAAATAACATCAGTAAGTTTCAGGTTTGTTTTTTTTTTAAAAAATAGGGCCCCGCCGTTATTATATTCTCCTGt                                                                                                                     <  1:924892/148‑1 (MQ=255)                                                ccAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTgg                                                                                                       >  1:782083/1‑151 (MQ=255)                                                    tATCGTTAGTGACAAAAAAATAGTTCGCCCCAACACCGCCGCCTGCAACGTTACCAAAAAAAAAACCATCAGTAAGATTCTCGGTTTATTTTTTGTTATAAATGATGCCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGc                                                                                                      <  2:183831/148‑1 (MQ=255)                                                          tAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGt                                                                                             >  1:351973/1‑151 (MQ=255)                                                               caaaaagaaTGGTCTGCGGCACCATCGCCGCCTGCCAGTTTACAGAAAAAAAAAACATCAGTAATATTGAGTTTTGTGTTTGCTTTAACAAATATGACCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCAt                                                                                          <  2:422376/145‑1 (MQ=255)                                                                 agaagaATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTcc                                                                                       >  1:332141/1‑150 (MQ=255)                                                                 aaaaaaaTAGTTGGCCCCCCCACACCCCCCGGCGATGTTAAAGAAAAAAAAAACATAAGTAAGATTCAGTGTTGATTTTTTTTTAAAAAATATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCa                                                                                      <  1:110776/146‑1 (MQ=255)                                                                   aaaaaaaGATTGCCCCCCCAGAGCCGCCGGCGACTTTACAGAAAAAAAAAACATAAGAAAGATTCAGCGTTGATTTTTCTTAAGAAAATTTGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGt                                                                                    <  1:406968/145‑1 (MQ=255)                                                                    agaaTAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGtt                                                                                   >  1:923928/1‑151 (MQ=255)                                                                      aaTAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTAAGCGTTGAGTTTTCTTTAGCAAATATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGttt                                                                                  >  2:168113/1‑150 (MQ=255)                                                                        tAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCAt                                                                               >  1:714905/1‑151 (MQ=255)                                                                            tggcccccccaacgcccccTGGGACGTTACAAAAAAAAAAAACACCAGTAAGATTCAGCTTTGTTTTTTTTTTAGAAAATTGGCCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCa                                                                                <  1:47987/133‑1 (MQ=255)                                                                             tgccaaacaagaGCCGCTTGCGTCTATACCAAAAAAAATAACACCAGTAATACTCATTGTTGATTTTTCTTTAAAAGAGACGCCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCAtt                                                                              <  2:235498/136‑1 (MQ=255)                                                                               ccccaccaAAGCCGCCTGCGACGTTACAAAAAAAAAAAACAACAGAAAGTTTCAGCTTGGTGTTTTCTTTAAAAAATAGGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTgg                                                                        <  1:289378/149‑1 (MQ=255)                                                                                    ccaTAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAAt                                                                    >  1:578954/1‑150 (MQ=255)                                                                                          ccgtcTGCGACGTTAACAAAAAAAATAACATCAGAAAGATTCATCGTTGTTTTTTCTTTAAAAAATATGCCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGaa                                                              <  2:777891/150‑1 (MQ=255)                                                                                                gcgactttccaaaaaaaaaaaACAACAGAAAGATTCAGTTTTGTTTTTTTTTAAAAAAATAGGCCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTcc                                                        <  2:886048/137‑1 (MQ=255)                                                                                                            gAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGc                                            >  1:69901/1‑150 (MQ=255)                                                                                                                aaaaaaCATAAGTAAGATTCAGGGTTGATTTTTTTTTAAAAAATATGCCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCaaaaa                                       <  1:59222/151‑1 (MQ=255)                                                                                                                    aaCATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACg                                   >  1:211904/1‑151 (MQ=255)                                                                                                                         aagaaaGATTGAGTGTTGTTTTTTTTTTAAAAAATATCGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACg                                   <  2:781642/142‑1 (MQ=255)                                                                                                                            aaggATTCGGGGTTGATTTTTTTTTAGAAAATAGGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCAcc                           <  1:597742/148‑1 (MQ=255)                                                                                                                              aGATTCAGCGTTGAGTTTTCTTTAGCAAATATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGc                         >  1:150175/1‑151 (MQ=255)                                                                                                                                   cAGTGTTGTTTTTTTTTTAGAAAATATGCCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTgg                      <  1:909763/149‑1 (MQ=255)                                                                                                                                        tttatttttttttAAAAAAACTGCCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTGGCGt                   <  2:189742/142‑1 (MQ=255)                                                                                                                                              tttCTTTAGCAAATATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTGGCGTTATTGGTCat         >  1:362461/1‑151 (MQ=255)                                                                                                                                                 cTTTAGCAAATATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTGGCGTTATAGGTCATATc      >  2:251005/1‑151 (MQ=255)                                                                                                                                                  tttAGCAAATATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTGGCGTTATTGGTCATATcc     >  1:546338/1‑151 (MQ=255)                                                                                                                                                     aacAAATATCCCACCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTGGCGTTATTGGTCATATCCGaa  <  2:301698/149‑1 (MQ=255)                                                                                                                                                     aGCAAATATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTGGCGTTATTGGTCATATCCGa   >  1:185918/1‑150 (MQ=255)                                                                                                                                                       cAAATATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACCGAGTCATTCCAGTTTCATTTTCTGGTAATAGCGAAAATTCCGCTCCTTGTTGCACAAATACTGCCCCACCGCTGGCGTTATTGGTCATATCCg    >  2:661629/1‑147 (MQ=255)                                                                                                                                                       |                                                                                                                                                     CGATGTTATTGCGAAACATGGCGTTAGTGACACGTAAATCGACGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTGGCGTTATTGGTCATATCCGAA  >  NC_000913/2343671‑2343969

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑