Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,274,353	G→T	A190A (GCG→GCT)	ychO →	putative invasin YchO

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,274,353	0	G	T	97.6%	140.3 / ‑2.7	42	A190A (GCG→GCT)	ychO	putative invasin YchO
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base T (23/18);  total (24/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.28e-01

AGCCAGCTTGGTCTTACTCAGCAGGATAATGGGTTGGTGAGCAATGTGGGCGTTGGGCAACGCTGGGCGCGCGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCGGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTGCATGGCATGAACAGACAGCCACGCAGGAACAACGGATGGCGCGCGGGTACGACCTGACAGCTCGG  >  NC_000913/1274216‑1274485                                                                                                                                          |                                                                                                                                     aGCCAGCTTGGTCTTACTCAGCAGGATAATGGGTTGGTGAGCAATGTGGGCGTTGGGCAACGCTGGGCGCGCGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCtgg                                                                                                                                    >  2:101024/1‑140 (MQ=255)    caacTTGGTCTTACTCAGCAGGATAATGGGTTGGTGAGCAATGTGGGCGTTGGGCAACGCTGGGCGCGCGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCtt                                                                                                                                 <  1:219708/137‑1 (MQ=255)    cAGCTTGGTCTTACTCAGCAGGATAATGGGTTGGTGAGCAATGTGGGCGTTGGGCAACGCTGGGCGCGCGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCtt                                                                                                                                 <  1:575710/140‑1 (MQ=255)     aGCTTGGTCTTACTCAGCAGGATAATGGGTTGGTGAGCAATGTGGGCGTTGGGCAACGCTGGGCGCGCGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCttt                                                                                                                                >  2:165161/1‑140 (MQ=255)       cTTGGTCTTACTCAGCAGGATAATGGGTTGGTGAGCAATGTGGGCGTTGGGCAACGCTGGGCGCGCGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTgg                                                                                                                              >  2:668344/1‑140 (MQ=255)         tGGTCTTACTCAGCAGGATAATGGGTTGGTGAGCAATGTGGGCGTTGGGCAACGCTGGGCGCGCGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTg                                                                                                                            <  1:693953/140‑1 (MQ=255)                aCTCAGCAGGATAATGGGTTGGTGAGCAATGTGGGCGTTGGGCAACGCTGGGCGCGCGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGc                                                                                                                     >  1:27258/1‑140 (MQ=255)                 cTCAGCAGGATAATGGGTTGGTGAGCAATGTGGGCGTTGGGCAACGCTGGGCGCGCGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCg                                                                                                                    >  1:733281/1‑140 (MQ=255)                  tCAGCAGGATAATGGGTTGGTGAGCAATGTGGGCGTTGGGCAACGCTGGGCGCGCGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGt                                                                                                                   <  2:716822/140‑1 (MQ=255)                    agcagGATAATGGGTTGGTGAGCAATGTGGGCGTTGGGCAACGCTGGGCGCGCGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTgg                                                                                                                 >  2:515066/1‑140 (MQ=255)                      cagGATAATGGGTTGGTGAGCAATGTGGGCGTTGGGCAACGCTGGGCGCGCGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTgggg                                                                                                               >  1:278550/1‑140 (MQ=255)                      cagGATAATGGGTTGGTGAGCAATGTGGGCGTTGGGCAACGCTGGGCGCGCGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTgggg                                                                                                               >  1:515764/1‑140 (MQ=255)                         gATAATGGGTTGGTGAGCAATGTGGGCGTTGGGCAACGCTGGGCGCGCGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGa                                                                                                            >  1:183974/1‑140 (MQ=255)                              tGGGTTGGTGAGCAATGTGGGCGTTGGGCAACGCTGGGCGCGCGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATAtt                                                                                                       >  1:521260/1‑140 (MQ=255)                                    ggTGAGCAATGTGGGCGTTGGGCAACGCTGGGCGCGCGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGAt                                                                                                 >  1:147471/1‑140 (MQ=255)                                          cAATGTGGGCGTTGGGCAACGCTGGGCGCGCGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCgg                                                                                           >  1:461908/1‑140 (MQ=255)                                           aaTGTGGGCGTTGGGCAACGCTGGGCGCGCGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGc                                                                                          <  2:461908/140‑1 (MQ=255)                                            aTGTGGGCGTTGGGCAACGCTGGGCGCGCGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCa                                                                                         <  1:222209/140‑1 (MQ=255)                                               tgGGCGTTGGGCAACGCTGGGCGCGCGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAAc                                                                                      >  1:612033/1‑140 (MQ=255)                                                gggCGTTGGGCAACGCTGGGCGCGCGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACt                                                                                     >  1:405450/1‑140 (MQ=255)                                                     ttGGGCAACGCTGGGCGCGCGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTAt                                                                                >  2:478763/1‑140 (MQ=255)                                                                   gcgcgcGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGGAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTtgctgc                                                                  <  1:304653/140‑1 (MQ=255)                                                                       gcgGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTgcatgg                                                              >  2:632068/1‑140 (MQ=255)                                                                        cgGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTgcatggc                                                             <  2:612033/140‑1 (MQ=255)                                                                        cgGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTgcatggc                                                             >  2:179031/1‑140 (MQ=255)                                                                         ggCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTgcatggca                                                            <  2:728474/140‑1 (MQ=255)                                                                          gCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTgcatggcat                                                           <  2:744103/140‑1 (MQ=255)                                                                               tggctggTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTGCATGGCATGAaca                                                      <  2:733281/140‑1 (MQ=255)                                                                                     gtggGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTGCATGGCATGAACAGACAGc                                                <  1:117473/140‑1 (MQ=255)                                                                                            ataACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTGCATGGCATGAACAGACAGCCACGCAg                                         <  2:679854/140‑1 (MQ=255)                                                                                              aaCACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTGCATGGCATGAACAGACAGCCACGCAGGa                                       <  1:165161/140‑1 (MQ=255)                                                                                                  cTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTGCATGGCATGAACAGACAGCCACGCAGGaacaa                                   >  1:239711/1‑140 (MQ=255)                                                                                                  cTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTGCATGGCATGAACAGACAGCCACGCAGGaacaa                                   >  2:569599/1‑140 (MQ=255)                                                                                                   tttttATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTGCATGGCATGAACAGACAGCCACGCAGGaacaac                                  >  1:58113/1‑140 (MQ=255)                                                                                                    ttttATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTGCATGGCATGAACAGACAGCCACGCAGGAACAACg                                 >  2:241800/1‑140 (MQ=255)                                                                                                    ttttATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTGCATGGCATGAACAGACAGCCACGCAGGAACAACg                                 >  2:36818/1‑140 (MQ=255)                                                                                                    ttttATGACAACTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTGCATGGCATGAACAGACAGCCACGCAGGAACAACg                                 >  2:393001/1‑140 (MQ=255)                                                                                                    ttttATGACAACTTGCTGGACGAAAATCTTCAGCGAGCGGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTGCATGGCATGAACAGACAGCCACGCAGGAACAACg                                 >  2:2560/1‑140 (MQ=255)                                                                                                             aaCTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTGCATGGCATGAACAGACAGCCACGCAGGAACAACGGATGgcgcg                        <  1:393001/140‑1 (MQ=255)                                                                                                               cTTGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTGCATGGCATGAACAGACAGCCACGCAGGAACAACGGATGGcgcgcg                      >  2:352933/1‑140 (MQ=255)                                                                                                                 tGCTGGACGAAAATCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTGCATGGCATGAACAGACAGCCACGCAGGAACAACGGATGGCGCGCggg                    <  1:515066/140‑1 (MQ=255)                                                                                                                              tCTTCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTGCATGGCATGAACAGACAGCCACGCAGGAACAACGGATGGCGCGCGGGTACGACCTGACAg       <  1:93900/140‑1 (MQ=255)                                                                                                                                ttCAGCGAGCTGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTGCATGGCATGAACAGACAGCCACGCAGGAACAACGGATGGCGCGCGGGTACGACCTGACAGCt     <  1:424782/140‑1 (MQ=255)                                                                                                                                   agcgagctGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTGCATGGCATGAACAGACAGCCACGCAGGAACAACGGATGGCGCGCGGGTACGACCTGACAGCTCgg  <  1:179031/140‑1 (MQ=255)                                                                                                                                          |                                                                                                                                     AGCCAGCTTGGTCTTACTCAGCAGGATAATGGGTTGGTGAGCAATGTGGGCGTTGGGCAACGCTGGGCGCGCGGCAACTGGCTGGTGGGTTATAACACTTTTTATGACAACTTGCTGGACGAAAATCTTCAGCGAGCGGGCTTTGGTGCCGAAGCGTGGGGCGAATATTTGCGATTATCGGCAAACTTTTATCAGCCGTTTGCTGCATGGCATGAACAGACAGCCACGCAGGAACAACGGATGGCGCGCGGGTACGACCTGACAGCTCGG  >  NC_000913/1274216‑1274485

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑