Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,540,785	C→T	intergenic (‑1284/‑172)	nanC ← / → fimB	N‑acetylnuraminic acid outer membrane channel protein/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	4,540,785	0	C	T	100.0%	183.6 / NA	56	intergenic (‑1284/‑172)	nanC/fimB	N‑acetylnuraminic acid outer membrane channel protein/tyrosine recombinase/inversion of on/off regulator of fimA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (31/25);  total (31/25)

TTGTTACAGAACATATCACATGATATATAGATAAGATTAGTTGCATTAATGATGAGGGTTATTATTAGATTCGTATCCGATTGATAAATATATAAAGGTACATAGCATGCAAGAGCATGGCGTTTGTATGGCAACGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGTTCGCTTTTATAAACATAATCAGGATAAAAATGTTGGATTATTGCTAAC  >  NC_000913/4540651‑4540914                                                                                                                                       |                                                                                                                                  ttGTTACAGAACATATCACATGATATATAGATAAGATTAGTTGCATTAATGATGAGGGTTATTATTAGATTCGTATCCGATTGATAAATATATAAAGGTACATAGCATGCAAGAGCATGGCGTTTGTATGGCAATGtta                                                                                                                               <  1:54942/139‑1 (MQ=255)               atCACATGATATATAGATAAGATTAGTTGCATTAATGATGAGGGTTATTATTAGATTCGTATCCGATTGATAAATATATAAAGGTACATAGCATGCAAGAGCATGGCGTTTGTATGGCAATGtta                                                                                                                               <  1:1080115/125‑1 (MQ=255)               atCACATGATATATAGATAAGATTAGTTGCATTAATGATGAGGGTTATTATTAGATTCGTATCCGATTGATAAATATATAAAGGTACATAGCATGCAAGAGCATGGCGTTTGTATGGCAATGtta                                                                                                                               >  2:1080115/1‑125 (MQ=255)                      gATATATAGATAAGATTAGTTGCATTAATGATGAGGGTTATTATTAGATTCGTATCCGATTGATAAATATATAAAGGTACATAGCATGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACt                                                                                                          >  2:56901/1‑139 (MQ=255)                              gATAAGATTAGTTGCATTAATGATGAGGGTTATTATTAGATTCGTATCCGATTGATAAATATATAAAGGTACATAGCATGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTAc                                                                                                           >  1:252248/1‑130 (MQ=255)                              gATAAGATTAGTTGCATTAATGATGAGGGTTATTATTAGATTCGTATCCGATTGATAAATATATAAAGGTACATAGCATGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTAc                                                                                                           <  2:252248/130‑1 (MQ=255)                                tAAGATTAGTTGCATTAATGATGAGGGTTATTATTAGATTCGTATCCGATTGATAAATATATAAAGGTACATAGCATGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGt                                                                                                <  2:33642/139‑1 (MQ=255)                                                       aGGGTTATTATTAGATTCGTATCCGATTGATAAATATATAAAGGTACATAGCATGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCAtt                                                                                                     >  2:408897/1‑111 (MQ=255)                                                       aGGGTTATTATTAGATTCGTATCCGATTGATAAATATATAAAGGTACATAGCATGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCAtt                                                                                                     <  1:408897/111‑1 (MQ=255)                                                           ttattattaGATTCGTATCCGATTGATAAATATATAAAGGTACATAGCATACAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACt                                                                                                          <  1:804285/102‑1 (MQ=255)                                                           ttattattaGATTCGTATCCGATTGATAAATATATAAAGGTACAGAGCATACAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACt                                                                                                          >  2:804285/1‑102 (MQ=255)                                                             attattaGATTCGTATCCGATTGATAAATATATAAAGGTACATAGCATGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACgtt                                                                   >  2:351984/1‑139 (MQ=255)                                                                attaGATTCGTATCCGATTGATAAATATATAAAGGTACATAGCATGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACgttagt                                                                <  1:351984/139‑1 (MQ=255)                                                                      ttCGTATCCGATTGATAAATATATAAAGGTACATAGCATGCAAGAGCATGGCATTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTaa                                                          >  1:765594/1‑139 (MQ=255)                                                                                 ttGATAAATATATAAAGGTACATAGCATGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCaga                                                                                       >  1:469557/1‑99 (MQ=255)                                                                                 ttGATAAATATATAAAGGTACATAGCATGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCaga                                                                                       <  2:469557/99‑1 (MQ=255)                                                                                   gATAAATATATAAAGGTACATAGCATGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGTTCGCt                                             >  2:192005/1‑139 (MQ=255)                                                                                                   tACATAGCATGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGTTCGCTTTta                                         >  2:1000140/1‑127 (MQ=255)                                                                                                   tACATAGCATGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGTTCGCTTTta                                         <  1:1000140/127‑1 (MQ=255)                                                                                                     cATAGCATGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGTTCGCTTTTATAAACATAAt                               <  2:725507/135‑1 (MQ=255)                                                                                                     cATAGCATGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGTTCGCTTTTATAAACATAAt                               >  1:725507/1‑135 (MQ=255)                                                                                                     cATAGCATGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGTTCGCTTTTATAAACATAATCAgg                           >  1:899123/1‑139 (MQ=255)                                                                                                        aGCATGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCa                                                                           >  1:772898/1‑88 (MQ=255)                                                                                                        aGCATGCAAGAGCATGGCGTTTCTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCa                                                                           <  2:772898/88‑1 (MQ=255)                                                                                                         gCATGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGTTCGCTTTTATAAACATAATCAGGATaa                       <  1:56901/139‑1 (MQ=255)                                                                                                          cATGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGTTCGCTTTTATAAACATAATCAGGATaaa                      >  1:6591/1‑139 (MQ=255)                                                                                                            tGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACt                                                                         >  1:307529/1‑86 (MQ=255)                                                                                                            tGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACt                                                                         <  2:307529/86‑1 (MQ=255)                                                                                                            tGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGTTCg                                               >  2:58043/1‑112 (MQ=255)                                                                                                            tGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGTTCg                                               <  1:58043/112‑1 (MQ=255)                                                                                                            tGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGTTCGCTTTta                                         >  1:1075466/1‑118 (MQ=255)                                                                                                            tGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGTTCGCTTTta                                         <  2:1075466/118‑1 (MQ=255)                                                                                                            tGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGTTCGCTTTTATAAACATAATCAGGATaaaaa                    >  2:559259/1‑139 (MQ=255)                                                                                                            tGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGTTCGCTTTTATAAACATAATCAGGATaaaaa                    >  1:315352/1‑139 (MQ=255)                                                                                                            tGCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTCCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGTTCGCTTTTATAAACATAATCAGGATaaaaa                    >  2:738504/1‑139 (MQ=255)                                                                                                             gCAAGAGCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGTTCGCTTTTATAAACATAATCAGGATAAAAAt                   >  1:193849/1‑139 (MQ=255)                                                                                                                agagCATGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGTTCGCTTTTATAAACATAATCAGGATAAAAATGtt                <  2:315352/139‑1 (MQ=255)                                                                                                                     aTGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGTTCGCTTTTATAAACATAATCAGGATAAAAATGTTGGatt           >  2:585511/1‑139 (MQ=255)                                                                                                                      tGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCa                                                                                             <  1:503499/56‑1 (MQ=255)                                                                                                                      tGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCa                                                                                             >  2:503499/1‑56 (MQ=255)                                                                                                                      tGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTcc                                                                            <  1:406692/73‑1 (MQ=255)                                                                                                                      tGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTcc                                                                            >  2:406692/1‑73 (MQ=255)                                                                                                                      tGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGTTCGCTTTTATAAACATAATCAGGATAAAAATGTTGGatt           <  2:802876/138‑1 (MQ=255)                                                                                                                      tGGCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGTTCGCTTTTATAAACATAATCAGGATAAAAATGTTGGatt           >  1:802876/1‑138 (MQ=255)                                                                                                                       ggCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTa                                                                                                            >  2:626854/1‑40 (MQ=255)                                                                                                                       ggCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTa                                                                                                            <  1:626854/40‑1 (MQ=255)                                                                                                                       ggCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCAc                                                                          <  1:1065193/74‑1 (MQ=255)                                                                                                                       ggCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCAc                                                                          >  2:1065193/1‑74 (MQ=255)                                                                                                                       ggCGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTACGCAAACGTTCGCTTTTATAAACATAATCAGGATAAAAATGTTGGattat         >  2:887457/1‑139 (MQ=255)                                                                                                                         cGTTTGTATGGCAATGTTATTATAATTAACAGTTGCTa                                                                                                            >  1:655004/1‑38 (MQ=255)                                                                                                                         cGTTTGTAAGGCAATGTTATTATAATTAACAGTTGCTa                                                                                                            <  2:655004/38‑1 (MQ=255)                                                                                                                             tGTATGGCAATGTTATTATAATTAACAGTTGCTAc                                                                                                           <  2:1119023/35‑1 (MQ=255)                                                                                                                             tGTATGGCAATGTTATTATAATTAACAGTTGCTAc                                                                                                           >  1:1119023/1‑35 (MQ=255)                                                                                                                              gTATGGCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGTTCGCTTTTATAAACATAATCAGGATAAAAATGTTGGATTATTGCTAAc  <  1:887457/139‑1 (MQ=255)                                                                                                                                   gCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGtt                                                 <  2:757396/87‑1 (MQ=255)                                                                                                                                   gCAATGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGtt                                                 >  1:757396/1‑87 (MQ=255)                                                                                                                                       |                                                                                                                                  TTGTTACAGAACATATCACATGATATATAGATAAGATTAGTTGCATTAATGATGAGGGTTATTATTAGATTCGTATCCGATTGATAAATATATAAAGGTACATAGCATGCAAGAGCATGGCGTTTGTATGGCAACGTTATTATAATTAACAGTTGCTACTCCATTTAAGTTCACTCAGAAGAACTGGTCCACTTACGTTAGTTATTAAGCAAACGTTCGCTTTTATAAACATAATCAGGATAAAAATGTTGGATTATTGCTAAC  >  NC_000913/4540651‑4540914

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: ‑