Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,541,559	G→A	*201* (TAG→TAA)	fimB →	tyrosine recombinase/inversion of on/off regulator of fimA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,541,559	0	G	A	100.0%	207.9 / NA	64	*201* (TAG→TAA)	fimB	tyrosine recombinase/inversion of on/off regulator of fimA
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (29/35);  total (29/35)

GATACGCGACTTATCCAGGATTATCTTGGGCATCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAGAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAATTGATGTTATTGTAAGTGTGATTCTTAATTATCATAATAAACATTAAGT  >  NC_000913/4541425‑4541687                                                                                                                                       |                                                                                                                                 gATACGCGACTTATCAAGGATTATCTTGGGCATCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGAt                                                                                                                              <  1:377410/139‑1 (MQ=255)    aCGCGACTTATCCAGGATTATCTTGGGCATCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGt                                                                                                                           >  1:448410/1‑139 (MQ=255)         aCTTATCCAGGATTATCTTGGGCATCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTgaga                                                                                                                      <  2:273212/139‑1 (MQ=255)                  ggATTATCTTGGGCATCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGa                                                                                                             <  2:448410/139‑1 (MQ=255)                             ggCATCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTg                                                                                                                         >  1:492891/1‑116 (MQ=255)                             ggCATCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACACTGTTTTATAAAGATAGTTg                                                                                                                         <  2:492891/116‑1 (MQ=255)                               cATCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATg                                                                                                           >  2:815946/1‑128 (MQ=255)                               cATCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATg                                                                                                           <  1:815946/128‑1 (MQ=255)                                 tCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTa                                                                                              <  2:308852/139‑1 (MQ=255)                                    cAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACat                                                                                           <  1:438772/139‑1 (MQ=255)                                                   tGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTaaaaa                                                                                                 >  1:252395/1‑118 (MQ=255)                                                   tGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTaaaaa                                                                                                 <  2:252395/118‑1 (MQ=255)                                                     tCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATc                                                                          >  2:742608/1‑139 (MQ=255)                                                            taCCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGa                                                                                                             <  2:535172/97‑1 (MQ=255)                                                            taCCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGa                                                                                                             >  1:535172/1‑97 (MQ=255)                                                             aCCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTaaaaa                                                                                                 >  1:80677/1‑108 (MQ=255)                                                             aCCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTaaaaa                                                                                                 <  2:80677/108‑1 (MQ=255)                                                               cGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATAc                                                                                                                   <  2:790799/88‑1 (MQ=255)                                                               cGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATAc                                                                                                                   >  1:790799/1‑88 (MQ=255)                                                               cGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGAt                                                                                                            <  1:164077/95‑1 (MQ=255)                                                               cGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGAt                                                                                                            >  2:164077/1‑95 (MQ=255)                                                               cGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACatt                                                                                          <  2:768735/113‑1 (MQ=255)                                                               cGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACatt                                                                                          >  1:768735/1‑113 (MQ=255)                                                               cGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGAtt                                                                >  1:696898/1‑139 (MQ=255)                                                               cGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGAtt                                                                >  2:223408/1‑139 (MQ=255)                                                               cGCCAGCAATGCAGAGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGa                                                                                                             <  1:365906/94‑1 (MQ=255)                                                               cGCCAGCAATGCAGAGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGa                                                                                                             >  2:365906/1‑94 (MQ=255)                                                                    gCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTg                                                                                                                         <  2:456905/77‑1 (MQ=255)                                                                    gCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTg                                                                                                                         >  1:456905/1‑77 (MQ=255)                                                                    gCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGGTGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAAc                                                             >  1:414925/1‑137 (MQ=255)                                                                    gCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGGTGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAAc                                                             <  2:414925/137‑1 (MQ=255)                                                                    gCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCa                                                           >  1:448371/1‑139 (MQ=255)                                                                     cAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTgag                                                                                                                       <  1:691531/78‑1 (MQ=255)                                                                     cAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTgag                                                                                                                       >  2:691531/1‑78 (MQ=255)                                                                        tGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATtta                                                       >  2:593201/1‑139 (MQ=255)                                                                        tGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATtta                                                       <  1:223408/139‑1 (MQ=255)                                                                             ggCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAAt                                                  <  1:742608/139‑1 (MQ=255)                                                                                  ttttACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTga                                                                                                                        >  2:266328/1‑64 (MQ=255)                                                                                  ttttACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTga                                                                                                                        <  1:266328/64‑1 (MQ=255)                                                                                   tttACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACat                                                                                           >  2:515318/1‑92 (MQ=255)                                                                                   tttACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACat                                                                                           <  1:515318/92‑1 (MQ=255)                                                                                       cGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAATTGATGTTAtt                                        >  2:133673/1‑139 (MQ=255)                                                                                         gCATCTGGGATAGATCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTgag                                                                                                                       >  1:509789/1‑58 (MQ=255)                                                                                         gCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTgag                                                                                                                       <  2:509789/58‑1 (MQ=255)                                                                                               gggATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAATTGATGTTATTGTAAgtgt                                <  1:593201/139‑1 (MQ=255)                                                                                                  aTAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAATTGATGTTATTGTAAGTGTGAt                             <  1:322583/139‑1 (MQ=255)                                                                                                      agCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGa                                                                                                             <  2:795997/55‑1 (MQ=255)                                                                                                      agCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGa                                                                                                             >  1:795997/1‑55 (MQ=255)                                                                                                      agCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATgg                                                                                                          >  2:320229/1‑58 (MQ=255)                                                                                                      agCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATgg                                                                                                          <  1:320229/58‑1 (MQ=255)                                                                                                      agCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACatta                                                                                         >  2:770466/1‑75 (MQ=255)                                                                                                      agCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACatta                                                                                         <  1:770466/75‑1 (MQ=255)                                                                                                      agCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTa                                                                                   <  1:31463/81‑1 (MQ=255)                                                                                                      agCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTa                                                                                   >  2:31463/1‑81 (MQ=255)                                                                                                      agCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAATTGATGTTATTGt                                      >  2:220206/1‑126 (MQ=255)                                                                                                      agCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAATTGATGTTATTGt                                      <  1:220206/126‑1 (MQ=255)                                                                                                      agCCAGAGGACGACAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAATTGATGTTATTGTAAGTGTGATTCtt                         >  1:98056/1‑139 (MQ=255)                                                                                                               acgacAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTa                                                                                              >  2:398350/1‑61 (MQ=255)                                                                                                               acgacAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTa                                                                                              <  1:398350/61‑1 (MQ=255)                                                                                                                   cAGCGTCACGCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAATTGATGTTATTGTAAGTGTGATTCTTAATTATCataata            <  2:448371/139‑1 (MQ=255)                                                                                                                            gCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAATTGATGTTATTGTAAGTGTGATTCTTAATTATCATAATAAACATTAAg   <  1:101634/139‑1 (MQ=255)                                                                                                                            gCTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAATTGATGTTATTGTAAGTGTGATTCTTAATTATCATAATAAACATTAAg   <  1:5788/139‑1 (MQ=255)                                                                                                                             cTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAATTGATGTTATTGTAAGTGTGATTCTTAATTATCATAATAAACATTAAGt  <  2:47319/139‑1 (MQ=255)                                                                                                                             cTGTTTTATAAAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAATTGATGTTATTGTAAGTGTGATTCTTAATTATCATAATAAACATTAAGt  <  2:98056/139‑1 (MQ=255)                                                                                                                                       |                                                                                                                                 GATACGCGACTTATCCAGGATTATCTTGGGCATCGCAATATTCGTCATACTGTCTGGTATACCGCCAGCAATGCAGGGCGTTTTTACGGCATCTGGGATAGAGCCAGAGGACGACAGCGTCACGCTGTTTTATAGAGATAGTTGAGATACCAGGGATGGTGTTAAAAACTACATTATTCTTACGATATATCAAAAATGATTAACCATTTATTAATTGATGTTATTGTAAGTGTGATTCTTAATTATCATAATAAACATTAAGT  >  NC_000913/4541425‑4541687

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑