Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,343,829	0	G	C	40.0%	40.6 / 11.3	26	A114G (GCC→GGC)	yfaL	adhesin
Reads supporting (aligned to +/- strand):  ref base G (14/1);  new base C (0/10);  total (14/12)
Fisher's exact test for biased strand distribution p-value = 3.37e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTGCGAAACATGGCGTTAGTGACACGTAAATCGACGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAA‑TATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTGGCGTTATTGGTCATAT  >  NC_000913/2343679‑2343964                                                                                                                                                        |                                                                                                                                        ttGCGAAACATGGCGTTAGTGACACGTAAATCGACGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAA‑TATgg                                                                                                                                         >  2:657777/1‑151 (MQ=255)             gCGTTAGTGACACGTAAATCGACGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAA‑TATGGCCCCGCCGttat                                                                                                                             >  1:264262/1‑151 (MQ=255)                  aGTGACACGTAAATCGACGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAA‑TATGGCCCCGCCGTTATTatat                                                                                                                        >  1:306076/1‑151 (MQ=255)                          gTAAATCGACGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAA‑TATGGCCCCGCCGTTATTATATTCTCCTGt                                                                                                                >  2:527845/1‑151 (MQ=255)                            aaaCCGCCGGCACAAGTTTCTTTAGTACAAAAAAAAAATTTTGCCCCCCCATCCCCCCCGGCGACTTTACCAAAAAAAAAACCACAAATAATATTCGGCTTTGATTTTTCTTAACAAAA‑TAGGCCCCCGCCGTTATTATATTCTCCTGTaa                                                                                                              <  2:51050/151‑1 (MQ=255)                                  aCGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAA‑TATGGCCCCGCCGTTATTATATTCTCCTGTAACGgtgt                                                                                                        >  1:357867/1‑151 (MQ=255)                                          aGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAA‑TATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGc                                                                                                 >  1:532003/1‑150 (MQ=255)                                                      aCCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAA‑TATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCAtt                                                                                    >  2:294770/1‑151 (MQ=255)                                                        cAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAA‑TATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTcc                                                                                  >  1:389364/1‑151 (MQ=255)                                                               aTAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAA‑TATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTc                                                                            >  2:354946/1‑150 (MQ=255)                                                                       ccccccaacgccgcccTGCGCGGTTACAAAAAAAAATACCACAAGAAAATTTCAGTGTTGTTTTTTCTTAAGAAAA‑AGGGCCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCt                                                                     <  1:291721/135‑1 (MQ=255)                                                                                  ccgccTGCGACTTTACGAAAAAAAATAACATAAGAAAAATTCAGGTTTGTTTTTTTTTTAAAAAA‑TATGCCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGa                                                          <  2:20393/149‑1 (MQ=255)                                                                                        gCGACTTTACCGAAAAAAAAAACATAAGAAAGTTTCGGCTTTGTTTTTTCTTAAGAAAT‑TAGGCCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTcc                                                   <  2:291036/150‑1 (MQ=255)                                                                                          tacataacaaaaaaaaaaaACAATAGTAAGTTTCATTGTTTGTTTTTTTTAAGATAA‑AAGGCCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTcc                                                   <  1:365614/137‑1 (MQ=255)                                                                                                   ggAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAA‑TATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGc                                       >  2:47776/1‑151 (MQ=255)                                                                                                    aaaaaaaaaACATCAGAAAGTTTCGGCGTTGTTTTTTTTTAAGCAAA‑TATGCCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCa                                      <  2:507302/150‑1 (MQ=255)                                                                                                         aaTAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAA‑TATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAAt                                 >  2:113201/1‑151 (MQ=255)                                                                                                               aTCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAA‑TATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGcc                           >  1:1831/1‑151 (MQ=255)                                                                                                                tCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAA‑TATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGcc                           >  2:45792/1‑150 (MQ=255)                                                                                                                    tAAGATTCAGCGTTGAGTTTTCTTTAGCAAA‑TATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCAcc                      >  1:519233/1‑151 (MQ=255)                                                                                                                       tttcttagtttattttttCTTTATAAAT‑TGCGTCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGcccc                         <  1:391816/131‑1 (MQ=255)                                                                                                                           cAGCTTTGATTTTTCTTAACAAAA‑TATGCCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTGGc                <  2:686269/150‑1 (MQ=255)                                                                                                                                 ttttttttttttAAAAAATTATGCCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTGGCGTTAt           <  2:457294/146‑1 (MQ=255)                                                                                                                                 ttattttttttaaaaaaa‑TATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTGGCGTTAtt          <  2:441133/135‑1 (MQ=255)                                                                                                                                    tttttttTAAGAAAA‑TTGGCCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTGGCGTTAtt          <  2:551632/146‑1 (MQ=255)                                                                                                                                       tttttaaaaaaa‑aATGCCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTGGCGTTATTGGTCa     <  1:657689/140‑1 (MQ=255)                                                                                                                                        tCTTTAGCAAA‑TATGGCCCCGCCATTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTGGCGTTATTGGTCatat  >  2:544/1‑151 (MQ=255)                                                                                                                                                        |                                                                                                                                        TTGCGAAACATGGCGTTAGTGACACGTAAATCGACGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAA‑TATGGCCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTGGCGTTATTGGTCATAT  >  NC_000913/2343679‑2343964

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑