Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	562,665	G→A	Q110Q (CAG→CAA)	sfmH →	putative fimbrial adhesin protein SfmH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	562,665	0	G	A	100.0%	119.7 / NA	34	Q110Q (CAG→CAA)	sfmH	putative fimbrial adhesin protein SfmH
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (19/15);  total (19/15)

CTCAAATATCTTTAATAGCACCAATAACCAGCCAGGGCAGATTGTTGTTTTACCGGAAAAATCCGGCTGGGTAGGTGTCTCAGCAATTTGTCCACCCGGTACGCTGGTGAATTATACATACCGTAGTTATGTCACCAACTTTATTGTTCAGGAAACTATCGATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAGTTCCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGTTTCGCAAAACCTTCCATTCGGGGTGATGGATTCTCGTTTAATATTTCGTTTAAAGGTTATTCGTCCCTTTATTAACATGGTGGAGATCCCCAGACAGGTGATGTTTACCGTGTATGTGACATCAACGCCTTACGATCCGTTGGTTACACCTGTTTATACCATTAGTTTTGGTGGCCGGGTTGAAGTACCGCA  >  NC_000913/562428‑562901                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                             ctcAAATATCTTTAATAGCACCAATAACCAGCCAGGGCAGATTGTTGTTTTACCGGAAAAATCCGGCTGGGTAGGTGTCTCAGCAATTTGTCCACCCGGTACGCTGGTGAATTATACATACCGTAGTTATGTCACCAACTTTATTGTTCAGGAAACTATCGATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCa                                                                                                                                                                                                                                   <  2:276493/249‑1 (MQ=255)   cAAATATCTTTAATAGCACCAATAACCAGCCAGGGCAGATTGTTGTTTTACCGGAAAAATCCGGCTGGGTAGGTGTCTCAGCAATTTGTCCACCCGGTACGCTGGTGAATTATACATACCGTAGTTATGTCACCAACTTTATTGTTCAGGAAACTATCGATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAAt                                                                                                                                                                                                                               >  1:170217/1‑251 (MQ=255)         tCTTTAATAGCACCAATAACCAGCCAGGGCAGATTGTTGTTTTACCGGAAAAATCCGGCTGGGTAGGTGTCTCAGCAATTTGTCCACCCGGTACGCTGGTGAATTATACATACCGTAGTTATGTCACCAACTTTATTGTTCAGGAAACTATCGATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATAtt                                                                                                                                                                                                                         >  2:79525/1‑251 (MQ=255)             tAATAGCACCAATCACCAGCCAGGGCAGATTGTTGTTTTAACGGAAAAATCCGGCTGGGTAGGTGTCTCAGCAATTTGTCCACCCGGTACGCTGGTGAATTATACATACCGTAGTTATGTCACCAACTTTATTGTTCAGGAAACTATCGATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCgg                                                                                                                                                                                                                      >  2:185365/1‑250 (MQ=255)              aatagcagcgaaaccaagcccaggCAGATTGTAGTTTTACGGGAAAAAACCGCCTGGGTAGGTGTCTCAGCAATTTATCCACCCGGTACGCTGGTGCATTATACATACCGTAGTTATGTCACCAACTTTATTGTTGCGGAAACTATCGATAATTATAAATATATGCACTTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCggct                                                                                                                                                                                                                    >  2:373018/23‑249 (MQ=255)              aaTAGCACCAATAACCAGCCAGGGCAGATTGTTGTTTTACCGGAAAAATCCGGCTGGGTAGGTGTCTCAGCAATTTGTCCACCCGGTACGCTGGTGAATTATACATACCGTAGTTATGTCACCAACTTTATTGTTCAGGAAACTATCGATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCGGAt                                                                                                                                                                                                                    <  1:376325/251‑1 (MQ=255)                    aCCAATAACCAGCCAGGGCAGATTGTTGTTTTCCCGGAAAAATCCGGATGGGTAGGTGTCTCAGCAATTTGTCCACCCGGTACGCTGGTGAATTATACATACCGTAGTTATGTCACCAACTTTATTGTTCAGGAAACTATCGATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCGGATGGGAAc                                                                                                                                                                                                              >  2:26362/1‑251 (MQ=255)                                ccagGGCAGATTGCTGTTTTACCGGAAAAATCCGGCTGGGTAGGTGTCTCAGCAATTTGTCCACCCGGTACGCTGGTGAATTATACATACCGTAGTTATGTCACCAACTTTATTGTTCAGGAAACTATCGATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTTCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGt                                                                                                                                                                                                  >  2:4427/1‑251 (MQ=255)                                    ggCAGATTGTTGTTTTACCGGAAAAATCCGGCTGGGTAGGTGTCTCAGCAATTTGTCCACCCGGTACGCTGGTGAATTATACATACCGTAGTTATGTCACCAACTTTATTGTTCAGGAAACTATCGATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGTTTCg                                                                                                                                                                                              >  1:95788/1‑251 (MQ=255)                                                        gAAAAATCCGGCTGGGTAGGTGTCTCAGCAATTTGTCCACCCGGTACGCTGGTGAATTATACATACCGTAGTTATGTCACCAACTTTATTGTTCAGGAAACTATCGATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGTTTCGCAAAACCTTCCATTCGGGGt                                                                                                                                                                          <  1:155267/251‑1 (MQ=255)                                                         aaaaaTCCGGCTGGGTAGGTGTCTCAGCAATTTGTCCACCCGGTACGCTGGTGAATTATACATACCGTAGTTATGTCACCAACTTTATTGTTCAGGAAACTATCGATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGTTTCGCAAAACCTTCCATTCGGGGTg                                                                                                                                                                         <  2:178523/251‑1 (MQ=255)                                                                                                ccGGTACGCTGGTGAATTATACATACCGTAGTTATGTCACCAACTTTATTGTTCAGGAAACTATCGATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATGCGGATGGGAACAGATCCTAACGTGTCGCAAAACCTTCCATTCGGGGTGATGGATTCTCGTTTAATATTTCGTTTAAAGGTTATTCGt                                                                                                                                  <  1:25125/251‑1 (MQ=255)                                                                                                   gTACGCTGGTGAATTATACATACCGTAGTTATGTCACCAACTTTATTGTTCAGGAAACTATCGATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGTTTCGCAAAACCTTCCATTCGGGGTGATGGATTCTCGTTTAATATTTCGTTTAAAGGTTATTCGTccc                                                                                                                               >  1:325177/1‑251 (MQ=255)                                                                                                      cGCTGGTGAATTATACATACCGTAGTTATGTCACCAACTTTATTGTTCAGGAAACTATCGATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATACTCGGATGGGAACAGATCCTAACGTTTCGCAAAACCTTCCATTCGGGGTGATGGATTCTCGTTTAATATTTCGTTTAAAGGTTATTCGTCCCttt                                                                                                                            <  1:6518/251‑1 (MQ=255)                                                                                                          ggTGAATTATACATACCGTAGTTATGTCACCAACTTTATTGTTCAGGAAACTATCGATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGTTTCGCAAAACCTTCCATTCGGGGTGATGGATTCTCGTTTAATATTTCGTTTAAAGGTTATTCGTCCCTttat                                                                                                                          <  2:300443/249‑1 (MQ=255)                                                                                                                 tataCATACCGTAGTTATGTCACCAACTTTATTGTTCAGGAAACTATCGATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGTTTCGCAAAACCTTCCATTCGGGGTGATGGATTCTCGTTTAATATTTCGTTTAAAGGTTATTCGTCCCTTTATTAACAtgg                                                                                                                  <  1:124186/250‑1 (MQ=255)                                                                                                                  atacatacCGTAGTTATGTCACCAACTTTATTGTTCAGGAAACTATCGATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGTTTCGCAAAACCTTCCATTCGGGGTGATGGATTCTCGTTTAATATTTCGTTTAAAGGTTATTCGTCCCTTTATTAACAtggtg                                                                                                                >  1:309952/1‑251 (MQ=255)                                                                                                                  acacatacCGTAGTTATGTCACCAACTTTATTGTTCAGGAAACTATCGATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGTTTCGCAAAACCTTCCATTCAGGGTGATGGATTCTCGTTTAATATTTCGTTTAAAGGTTATTCGTCCCTTTATTAACAtggtg                                                                                                                >  1:309961/3‑251 (MQ=255)                                                                                                                         ccGTAGTTATGTCACCAACTTTATTGTTCAGGAAACTATCGATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGTTTCGCAAAACCTTCCATTCGGGGTGATGGATTCTCGTTTAATATTTCGTTTAAAGGTTATTCGTCCCTTTATTAACATGGTGGAGATcc                                                                                                         <  1:379439/251‑1 (MQ=255)                                                                                                                                 aTGTCACCAACTTTATTGTTCAGGAAACTATCGATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGTTTCGCAAAACCTTCCATTCGGGGTGATGGATTCTCGTTTAATATTTCg                                                                                                                                                  <  2:29336/202‑1 (MQ=255)                                                                                                                                 aTGTCACCAACTTTATTGTTCAGGAAACTATCGATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGTTTCGCAAAACCTTCCATTCGGGGTGATGGATTCTCGTTTAATATTTCg                                                                                                                                                  >  1:29336/1‑202 (MQ=255)                                                                                                                                 aTGTCACCAACTTTATTGTTCAGGAAACTATCGATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGTTTCGCAAAACCTTCCATTCGGGGTGATGGATTCTCGTTTAATATTTCGTTTAAAGGTTATTCGTCCCTTTATTAACATGGTGGATATCCCCAGACAg                                                                                                 <  2:216031/251‑1 (MQ=255)                                                                                                                                                   ttCAGGAAACTATCGATAATTATAAATATATGCAATTACCTGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGTTTCGCAAAACCTTCCATTCGGGGTGATGGATTCTCGTTTAATATTTCGTTTAAAGGTTATTCGTCCCTTTATTAACATGGTGGAGATCCCCAGACAGGTGATGTTTACCGTGTAt                                                                               >  1:152787/1‑251 (MQ=255)                                                                                                                                                                 gATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGTTTCGCAAAACCTTCCATTCGGGGTGATGGATTCTCGTTTAATATTTCGTTTAAAGGTTATTCGTCCCTTTATTAACATGGTGGAGATCCCCAGACAGGTGATGTTTACCGTGTATGTGACATCAACGcc                                                                 >  2:168666/1‑251 (MQ=255)                                                                                                                                                                     aTTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGTTTCGCAAAACCTTCCATTCGGGGTGATGGATTCTCGTTTAATATTTCGTTTAAAGGTTATTCGTCCCTTTATTAACATGGTGGAGATCCCCAGACAGGTGATGTTTACCGTGTATGTGACATCAACGCCTTAc                                                             <  1:366987/251‑1 (MQ=255)                                                                                                                                                                           aaTATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGTTTCGCAAAACCTTCCATTCGGGGTGATGGATTCTCGTTTAATAGTTCGTTTAAAGGTTATTCGTCCCTTTATTAACATGGTGGAGATCCCCAGACATGTGATGTTTACCGTGTATGTGACATCAACGCCTTACGATCCg                                                       <  1:59374/251‑1 (MQ=255)                                                                                                                                                                            atatatGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGTTTCGCAAAACCTTCCATTCGGGGTGATGGATTCTCGTTTAATATTTCGTTTAAAGGTTATTCGTCCCTTTATTAACATGGTGGAGATCCCCAGACAGGTGATGTTTACCGTGTATGTGACATCAACGCCTTACGATCCGt                                                      >  2:331725/1‑251 (MQ=255)                                                                                                                                                                                   cAATTACATGATTATCTATTAGGCGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCTCCGCAAAATTATATTCGGATGGGAACAGCTCCTAACGTTTCGCAAAACCTTCCTTTCGGGGCGATGGATTCTCGTTTAATATTTCGTTTAAAGGTTATTCGTCCCTTTATTAACATGGTGGAGATCCTCAGACAGGTGATGTTTAGCGTGTATGTGACATCAACGCATTACGATCCGTTGGTTac                                               >  2:340362/1‑251 (MQ=255)                                                                                                                                                                                         cATGATTATCTACTAGGTGCGATGAGTCTGGTCCATACTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTAGGATGGGAACAGATCCTAACGTTTCGCACAACCTTCCATTCGGGGTGATGGATTCTCGTTTGATATTTCGTTTAAAGGTTATTCGTCCCTTTATTCACATGGTGGAGATCCCAAGACAGGTGATGTTTACCGTGTATGTGACATAAACGCCTTACGATCCGTTGGTTACACCTGt                                         >  2:377132/1‑251 (MQ=255)                                                                                                                                                                                           tGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGTTTCGCAAAACCTTCCATTCGGGGTGATGGATtct                                                                                                                                                                <  1:78849/130‑1 (MQ=255)                                                                                                                                                                                           tGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGTTTCGCAAAACCTTCCATTCGGGGTGATGGATtct                                                                                                                                                                >  2:78849/1‑130 (MQ=255)                                                                                                                                                                                             aTTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGTTTCGCAAAACCTTCCATTCGGGGTGATGGATTCTCGTTTAATATTTCGTTTAAAGGTTATTCGTCCCTTTATTAACATGGTGGAGATCCCCAGACAGGTGATGTTTACCGTGTATGTGACATCAACGCCTTACGATCCGTTGGTTACACCTGTTtat                                     >  2:96943/1‑251 (MQ=255)                                                                                                                                                                                                                      tgTTGATAGTGTGATGGATATTCAATTCCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGTTTCGCAAAACCTTCCATTCGGGGTGATGGTTTCTCGTTTAATATTTCGTTGAAAGGTTGTTCGTCCCTTTATTAACATCGTGGAGATCCCGAGACAGGTTATTGTTACCGTGTATGTGACAGCAACGCCTCACGTTCCGTTGGGTATACCTGTTTATGGCATTGGTGTTGTTGGCCgg                <  2:36852/246‑1 (MQ=255)                                                                                                                                                                                                                                 agATGGATATTCAATACCCCCCGAAAAAGAATATTCCGATGGAGACAGATCCTAAAGTTTCGAACAACCTTCCATTCTGAGTGATGGCTCCTAGTTTAATATGTAGTTTAAAGGTTATTCGTCCCTTTATTAACATGGAGTAGTTCCACAGACATGTGAGGTTTACAGTGTATGTGCCATTACAGCATTACGATCCGTTGGTTAAAACTGTTTTTATCATTAGTTTTGGTAGCGTGGTTGAAgatcgtca  >  2:209397/2‑243 (MQ=255)                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                             CTCAAATATCTTTAATAGCACCAATAACCAGCCAGGGCAGATTGTTGTTTTACCGGAAAAATCCGGCTGGGTAGGTGTCTCAGCAATTTGTCCACCCGGTACGCTGGTGAATTATACATACCGTAGTTATGTCACCAACTTTATTGTTCAGGAAACTATCGATAATTATAAATATATGCAATTACATGATTATCTATTAGGTGCGATGAGTCTGGTTGATAGTGTGATGGATATTCAGTTCCCCCCGCAAAATTATATTCGGATGGGAACAGATCCTAACGTTTCGCAAAACCTTCCATTCGGGGTGATGGATTCTCGTTTAATATTTCGTTTAAAGGTTATTCGTCCCTTTATTAACATGGTGGAGATCCCCAGACAGGTGATGTTTACCGTGTATGTGACATCAACGCCTTACGATCCGTTGGTTACACCTGTTTATACCATTAGTTTTGGTGGCCGGGTTGAAGTACCGCA  >  NC_000913/562428‑562901

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑