Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,343,821	0	C	A	53.3%	33.5 / 66.0	46	A117S (GCT→TCT)	yfaL	adhesin
Reads supporting (aligned to +/- strand):  ref base C (17/4);  new base A (0/24);  total (17/29)
Fisher's exact test for biased strand distribution p-value = 5.43e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.66e-08

GATGTTATTGCGAAACATGGCGTTAGTGACACGTAAATCGACGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGG‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTGGCGTTATTGGTCATATCCG  >  NC_000913/2343672‑2343967                                                                                                                                                      |                                                                                                                                                    gATGTTATTGCGAAACATGGCGTTAGTGACACGTAAATCGACGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCa                                                                                                                                                    <  2:10671/151‑1 (MQ=255)      tATTGCGAAACATGGCGTTAGTGACACGTAAATCGACGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAatat                                                                                                                                               >  2:469531/1‑151 (MQ=255)         tGCGAAACATGGCGTTAGTGACACGTAAATCGACGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATgg                                                                                                                                             <  2:897996/150‑1 (MQ=255)                 aTGGCGTTAGTGACACGTAAATCGACGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGG‑CCCCGCCGt                                                                                                                                   >  2:73623/1‑151 (MQ=255)                          gTGACACGTAAATCGACGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGG‑CCCCGCCGTTATTATAtt                                                                                                                          >  1:308065/1‑151 (MQ=255)                             acacGAAAACCGCCGCCCCCTTTATCTTTATCACTAAAAAAATAGTTTCCCCCACAATCGCCGCTTGCGTCTTTCCAGAAAAAAATAACATCAGTATTTTTCTTTGTTGTTTTTTTTTTACAAAATACGC‑CCCCGCCGTTATTATATtct                                                                                                                        <  1:129183/150‑1 (MQ=255)                                   aaaTCGACGCCACAAGTGTCGTTAGTACAAAAAAAAGAGATTCCGCCACCATGCCCGCCTGCGCCGTTACCAAAAAAAATAACATCAAAAAGATTCAGCTTTGATTTTTCTTAAGAAAATATGG‑CCCCGCCGTTATTATATTCTCCTGTa                                                                                                                  <  2:682132/150‑1 (MQ=255)                                   aaaCCGACGCCACCAGTATTGTTATTACAAGAAAAATAGATTGCCCCACCATAGCCGCCTGCGACTTTACAGAAAAAAAAAACATAAGAAAGATTCAGCGTTGATTTTTTTTTAGAAAATAGGC‑CCCCGCCGTTATTATATTCTCCTGTa                                                                                                                  <  2:89282/150‑1 (MQ=255)                                       cGACGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGG‑CCCCGCCGTTATTATATTCTCCTGTAACGgt                                                                                                             >  2:477652/1‑151 (MQ=255)                                               ccATTATCGTTAGTAAAAAAAAAATAGTTTCCCCAACCATACCCGCCTGCGTCTTTACCGAAAAAAATAACATCAGTAAGATTCGGTTTTGTTTTTTTTTTAGAAAATATGC‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTAt                                                                                                        <  1:880979/148‑1 (MQ=255)                                               ccAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGG‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTgg                                                                                                     >  2:13173/1‑151 (MQ=255)                                                        ttAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGG‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACag                                                                                              >  1:831765/1‑149 (MQ=255)                                                        ttAGTACAAGAAAAAAAGATGCCCCCACCATGCCCGCCTGCGACTTTCCCAAAAAAAAAAACACCAGTAAAATTCTGGTTTGATTTTTCTTTAAAAATTGTGC‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAAc                                                                                                <  1:568091/147‑1 (MQ=255)                                                          aGTACAAAAAGAATAGATTGCCCCCCCATACCCGCCTGCGACGTTCCGGAAAAAAATAACATCAGAAAGATTCGGCGTTGATTTTTCTTTAGAAAATAGGC‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTc                                                                                          <  2:512593/151‑1 (MQ=255)                                                                aaaaaaaaagtttGCCCCCCCATAGCCGCCGGCGACTTTACCGAAAAAAAAAACATCAGAAAGTTTCGGCGTTGTTTTTTCTTTAAAAAATAGGG‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCAtt                                                                                       <  2:318131/137‑1 (MQ=255)                                                                 gaagaaTAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGG‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTcc                                                                                     >  2:727320/1‑149 (MQ=255)                                                                          aTTCCGCCCCAAAAGCCGCCGGCGTTTTTACGGAAAAAAAAAACAACAGAAATATTCGGTTTTGTTTTTTTTTTAAAAAATGGGG‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCAttt                                                                           <  1:672116/150‑1 (MQ=255)                                                                           ttGCGCCCCAATGGCCGCCTGGGACGTTCCGAAAAAAAAAAACATAAGAAAGATTCAGTTTTGATTTTTCTTAAAAAAATATGG‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCAttt                                                                           <  2:917431/149‑1 (MQ=255)                                                                              cgcCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGG‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTgg                                                                      >  2:563699/1‑151 (MQ=255)                                                                                   caatgccccccggCGACTTTCCGGAAAAAAATAACATCAGTAAGTTTCGGTTTTGTTTTTTTTTTAGAAAATAGGC‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAAt                                                                  <  2:103133/138‑1 (MQ=255)                                                                                         ccgccgGCGACTTTACAAAAAAAAAAAACATAAGTAATATTCAGTTTTGATTTTTTTTAAAAAAATATGG‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGaa                                                            <  1:274785/150‑1 (MQ=255)                                                                                         ccgccTGCGACTTTACAAAAAAAAAAAACATAAGAAATTTTCAGGTTTGTTTTTTCTTTAAAAAATATGC‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTg                                                              <  1:133892/148‑1 (MQ=255)                                                                                           gccTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGG‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAAt                                                         >  1:455275/1‑151 (MQ=255)                                                                                              tGCGATGTTACCAAAAAAAATAACACAAGAAATTTTCGGGTTTGATTTTTTTTTAAAAAATGTGC‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAAtt                                                        <  1:780979/149‑1 (MQ=255)                                                                                               gCGACGTTACGGAAAAAAAAAACATAAGTAAGATTCAGCTTTGATTTTTTTTTAGAAAATATGG‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTcc                                                      <  2:742348/150‑1 (MQ=255)                                                                                               gCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGG‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCg                                                     >  1:306682/1‑151 (MQ=255)                                                                                                 gactttccgaaaaaaaaaaACATCAGTAATATTCGGCTTGGTTTTTTTTTAAAAAAATAGGC‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGc                                                    <  2:581920/139‑1 (MQ=255)                                                                                                   cgtccgggaaaaaaaTAACGAGATAAAGATTAATGGTTGTTTTTTTTTAAGAAATTAGGC‑GCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCt                                                   <  2:599619/140‑1 (MQ=255)                                                                                                     ttACCAAAAAAAAAAACATCAGTAATATTCAGCGTTGTTTTTTTTTAAGCAAATATGC‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCt                                                <  2:657093/150‑1 (MQ=255)                                                                                                       aCCGAAAAAAAAAACATCATTAAGATTCAGTTTTGTTTTTTCTTTAGCAATTATGC‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCttgt                                             <  2:130478/151‑1 (MQ=255)                                                                                                        ccGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGG‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCttgtt                                            >  1:424513/1‑151 (MQ=255)                                                                                                          ggAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGG‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGc                                          >  1:171126/1‑151 (MQ=255)                                                                                                          aaaaaaaaaaACATCAGTAATATTCAGTGTTTGTTTTTTTTTAAAAAATATGC‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCttgttg                                           <  1:716280/148‑1 (MQ=255)                                                                                                           aaaaaaaaaACATAAGAAAGATTCAGTGTTGTTTTTTTTTTACAAAATAGGC‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCttgt                                             <  1:835766/146‑1 (MQ=255)                                                                                                             aaaaaaaaCATCAGTAAGTTTCAGTTTTGTTTTTTTTTTATAAAATAGGC‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCaaa                                       <  1:433244/151‑1 (MQ=255)                                                                                                             aaaaaTAACTACTATAATTTTCAGCTTTTTTTTTTCTTCAG‑AAATTTGGTCGCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCGCCTTGTTGCaaa                                       <  1:223424/151‑1 (MQ=255)                                                                                                              aaaaaaACATCAGAAAGATTCGGTGTTGTTTTTTTTTAAGAAATTATGG‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCaaaa                                      <  2:513834/151‑1 (MQ=255)                                                                                                                aacaaCATCAGAAAGATTCTTTGTTATGTTTTATTTAAAAAATTTGG‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAAt                                    <  1:251907/148‑1 (MQ=255)                                                                                                                    aCATCAGAAAGATTCAGCTTTGATTTTTCTTAAGAAAATATGC‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACg                                 <  1:630361/150‑1 (MQ=255)                                                                                                                              gATTCAGCGTTGAGTTTTCTTTAGCAAATATGG‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCt                      >  2:706356/1‑151 (MQ=255)                                                                                                                                ttaggcttttttttttCTTAAAAAAATTCGG‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTg                     <  1:624399/138‑1 (MQ=255)                                                                                                                                ttCAGCGTTGAGTTTTCTTTAGCAAATATGG‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTgg                    >  1:105240/1‑151 (MQ=255)                                                                                                                                     cGTTGAGTTTTCTTTAGCAAATATGG‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTGGCGtt                >  2:817236/1‑150 (MQ=255)                                                                                                                                       ttGAGTTTTCTTTAGCAAATATGG‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTGGCGTTAtt             >  2:312355/1‑151 (MQ=255)                                                                                                                                            ttttCTTAAGAAAATTGGC‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTGGCGTTa               <  2:818676/144‑1 (MQ=255)                                                                                                                                                cTTTAGCAAATATGG‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTGGCGTTATTGGTCATATc    >  2:244000/1‑151 (MQ=255)                                                                                                                                                     acAAATATGC‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTGGCGTTATTGGTCATATCCg  <  1:166161/147‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                    GATGTTATTGCGAAACATGGCGTTAGTGACACGTAAATCGACGGCACCAGTATCGTTAGTACCAGAAGAATAGATTGCGCCACCATAGCCGCCTGCGACGTTACCGGAAAAAATAACATCAGTAAGATTCAGCGTTGAGTTTTCTTTAGCAAATATGG‑CCCCGCCGTTATTATATTCTCCTGTAACGGTGTTATTGGCAAACAGAGTCATTCCAGTTTCATTTTCTGGTAATAGTGAAAATTCCGCTCCTTGTTGCAAAAATACGGCCCCACCGCTGGCGTTATTGGTCATATCCG  >  NC_000913/2343672‑2343967

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: ‑