Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,549,000	T→C	C65R (TGC→CGC)	fimH →	minor component of type 1 fimbriae

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,549,000	0	T	C	100.0%	199.6 / NA	56	C65R (TGC→CGC)	fimH	minor component of type 1 fimbriae
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (25/31);  total (25/31)

TAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTA  >  NC_000913/4548879‑4549126                                                                                                                            |                                                                                                                               tAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGTGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCg                                                                                                               <  1:1026276/139‑1 (MQ=255)   aaaCCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGa                                                                                                             <  1:94939/139‑1 (MQ=255)     aCCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATTTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGaaa                                                                                                           <  1:1114138/139‑1 (MQ=255)      ccGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGaa                                                                                                            >  2:1021698/1‑139 (MQ=255)      ccGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGTCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAAc                                                                                                          <  2:734409/139‑1 (MQ=255)      ccGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAAc                                                                                                          <  1:1095755/139‑1 (MQ=255)          cAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCAtt                                                                                                      >  2:393010/1‑139 (MQ=255)           aaTGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTa                                                                                                     >  2:398993/1‑139 (MQ=255)             tGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACa                                                                                                   <  1:137578/139‑1 (MQ=255)                 aCCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTTTATATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGa                                                                                                 <  1:1021698/139‑1 (MQ=255)                       aTCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTca                                                                                         >  2:872174/1‑139 (MQ=255)                       aTCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTca                                                                                         <  1:185860/139‑1 (MQ=255)                        tCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTcac                                                                                        >  1:312714/1‑139 (MQ=255)                        tCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTcac                                                                                        >  2:26601/1‑139 (MQ=255)                                   ggTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTACGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGAAACGAg                                                                             >  2:774550/1‑139 (MQ=255)                                    gTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCg                                                                                                               <  2:543527/104‑1 (MQ=255)                                    gTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCg                                                                                                               >  1:543527/1‑104 (MQ=255)                                           cgcCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCt                                                                     >  2:51896/1‑139 (MQ=255)                                              cAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACg                                                                                                                       >  2:892718/1‑86 (MQ=255)                                              cAATGTT‑‑TATGTAAACCGTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACg                                                                                                                       <  1:892718/86‑1 (MQ=255)                                                  gTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATggcg                                                              <  1:393010/139‑1 (MQ=255)                                                              aCCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCAt                                                                                                                           <  1:171023/68‑1 (MQ=255)                                                              aCCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCAt                                                                                                                           >  2:171023/1‑68 (MQ=255)                                                              aCCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTa                                                                   >  2:1012596/1‑124 (MQ=255)                                                              aCCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTa                                                                   <  1:1012596/124‑1 (MQ=255)                                                              aCCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATc                                                    >  1:975177/1‑139 (MQ=255)                                                                  tGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAAt                                                >  2:979140/1‑139 (MQ=255)                                                                   gcgcCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGAt                                                                                                                     <  1:947642/69‑1 (MQ=255)                                                                   gcgcCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGAt                                                                                                                     >  2:947642/1‑69 (MQ=255)                                                                   gcgcCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATggcg                                                              <  1:777608/124‑1 (MQ=255)                                                                   gcgcCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATggcg                                                              >  2:777608/1‑124 (MQ=255)                                                                          tcgtGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCgg                                        <  1:872174/139‑1 (MQ=255)                                                                          tcgtGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCgg                                        <  2:886680/139‑1 (MQ=255)                                                                            gtGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGa                                      <  1:398993/139‑1 (MQ=255)                                                                            gtGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGa                                      <  1:541182/139‑1 (MQ=255)                                                                            gtGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGa                                      <  1:51896/139‑1 (MQ=255)                                                                            gtGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGa                                      <  2:312714/139‑1 (MQ=255)                                                                              gAATGTGGGGCAAAACCTGGTCGTGGATCTTACGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGAcc                                    <  1:774550/139‑1 (MQ=255)                                                                                 tgtgGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTa                                 <  1:979140/139‑1 (MQ=255)                                                                                 tgtgGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTa                                 <  1:507636/139‑1 (MQ=255)                                                                                     gggCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAAc                                                                                                          >  1:105527/1‑62 (MQ=255)                                                                                     gggCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAAc                                                                                                          <  2:105527/62‑1 (MQ=255)                                                                                     gggCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCg                                                                        <  2:286576/96‑1 (MQ=255)                                                                                     gggCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCg                                                                        >  1:286576/1‑96 (MQ=255)                                                                                        cAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAAtata                          <  2:958100/139‑1 (MQ=255)                                                                                           aaCCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTg                       >  1:444860/1‑139 (MQ=255)                                                                                           aaCCTGGTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTg                       >  1:178916/1‑139 (MQ=255)                                                                                                ggTCGTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGt                  >  1:762204/1‑139 (MQ=255)                                                                                                    gTGGATCTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCt              <  2:975177/139‑1 (MQ=255)                                                                                                          cTTTCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCAt        <  1:26601/139‑1 (MQ=255)                                                                                                            ttCGACGCAAATCTTTCGCCATAACGATTATCCGGaaa                                                                                                           >  2:1056866/1‑38 (MQ=255)                                                                                                            ttCGACGCAAATCTTTCGCCATAACGATTATCCGGaaa                                                                                                           <  1:1056866/38‑1 (MQ=38)                                                                                                            ttCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGa                                      >  2:350175/1‑107 (MQ=255)                                                                                                            ttCGACGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGa                                      <  1:350175/107‑1 (MQ=255)                                                                                                             tCGACGCAAATCATTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTc     >  2:1068487/1‑139 (MQ=255)                                                                                                                aCGCAAATCTTTCGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTa  >  1:583401/1‑139 (MQ=255)                                                                                                                            |                                                                                                                               TAAAACCGCCAATGGTACCGCTATCCCTATTGGCGGTGGCAGCGCCAATGTT‑‑TATGTAAACCTTGCGCCCGTCGTGAATGTGGGGCAAAACCTGGTCGTGGATCTTTCGACGCAAATCTTTTGCCATAACGATTATCCGGAAACCATTACAGACTATGTCACACTGCAACGAGGCTCGGCTTATGGCGGCGTGTTATCTAATTTTTCCGGGACCGTAAAATATAGTGGCAGTAGCTATCCATTTCCTA  >  NC_000913/4548879‑4549126

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑