Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,133,330	G→A	8.7%	A92V (GCC→GTC)	fimI ←	type I pili subunit FimI

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,133,330	0	G	A	8.7%	158.0 / 4.8	57	A92V (GCC→GTC)	fimI	type I pili subunit FimI
Reads supporting (aligned to +/- strand):  ref base G (30/22);  new base A (2/3);  total (32/25)
Fisher's exact test for biased strand distribution p-value = 6.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.84e-01

TAATCAACCGAGGTTCCACCGGGTTTGATCGATGCCTTGGACTTGTCCCTGATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTGGCAGCGGGGAATCGCCCCATGGGAATTTCGCCCATGGCGACGCGGTCACTGACATTGCCGTCAC  >  NC_002947/2133186‑2133471                                                                                                                                                 |                                                                                                                                              tAATCAACCGAGGTTCCACCGGGTTTGATCGATGCCTTGGACTTGTCCCTGATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCAtt                                                                                                                                           <  4:240379/149‑1 (MQ=255)       aCCGAGGTTCCACCGGGTTTGATCGATGCCTTGGACTTGTCCCTGATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTc                                                                                                                                     >  5:240461/1‑149 (MQ=255)          gAGGTTCCACCGGGTTTGATCGATGCCTTGGACTTGTCCCTGATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGACAATGCCTTCgtg                                                                                                                                  <  8:11460/149‑3 (MQ=255)              ttCCACCGGGTTTGATCGATGCCTTGGACTTGTCCCTGATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGAt                                                                                                                               >  5:165465/1‑148 (MQ=255)                 cACCGGGTTTGATCGATGCCTTGGACTTGTCCCTGATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGAtgctg                                                                                                                           <  6:240461/149‑1 (MQ=255)                  aCCGGGTTTGATCGATGCCTTGGACTTGTCCCTGATCACAATCGAGATGTTTTCTGCCGTGCAGGCACTGTTACCAATGCTGAAATAGTCGCAGCTGGCATCAGCGGCACCGACAAACTTCACGAAGGCAATGTATTCGCTGAagctg                                                                                                                           >  7:293508/1‑148 (MQ=255)                   ccGGGTTTGATCGATGCCTTGGACTTGTCCCTGATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCa                                                                                                                         <  6:165465/149‑1 (MQ=255)                   ccGGGTTTGATCGATGCCTTGGACTTGTCCCTGATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCa                                                                                                                         <  2:84396/149‑1 (MQ=255)                    cGGGTTTGATCGATGCCTTGGACTTGTCCCTGATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGAt                                                                                                                               >  1:251421/1‑142 (MQ=255)                    cGGGTTTGATCGATGCCTTGGACTTGTCCCTGATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGAt                                                                                                                               <  2:251421/142‑1 (MQ=255)                      ggTTTGATCGATGCCTTGGACTTGTCCCTGATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGAc                                                                                                                      >  4:161919/1‑149 (MQ=255)                           gATCGATGCCTTGGACTTGTCCCTGATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGttt                                                                                                                 >  8:206574/1‑149 (MQ=255)                            aTCGATGCCTTGGACTTGTCCCTGATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGtttt                                                                                                                >  7:119983/1‑149 (MQ=255)                             tCGATGCCTTGGACTTGTCCCTGATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTg                                                                                                               >  7:256750/1‑149 (MQ=255)                               gATGCCTTGGACTTGTCCCTGATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTc                                                                                                             <  8:119983/149‑1 (MQ=255)                               gATGCCTTGGACTTGTCCCTGATCACAATCGAGATGTTTTCTGCAGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCAACGTCAAACTTAACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTc                                                                                                             >  5:12791/1‑149 (MQ=255)                                   ccTTGGACTTGTCCCTGATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCggg                                                                                                          >  2:6425/1‑148 (MQ=255)                                    cTTGGACTTGTCCCTGATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTa                                                                                                        >  1:46665/1‑149 (MQ=255)                                           ttGTCCCTGATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGTACCGTCAAACTTCACGAAGACAATGCCTTCg                                                                                                                                    <  3:233516/114‑1 (MQ=255)                                           ttGTCCCTGATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGTACCGTCAAACTTCACGAAGACAATGCCTTCg                                                                                                                                    >  4:233516/1‑114 (MQ=255)                                             gtgccTGATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTCCCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATg                                                                                                <  8:277627/145‑1 (MQ=255)                                             gTCCCTGATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGACAATGCCTTCgtga                                                                                                                                 >  1:289567/1‑112 (MQ=255)                                             gTCCCTGATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGACAATGCCTTCgtga                                                                                                                                 <  2:289567/115‑4 (MQ=255)                                                   gATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCCGAGGCACCGTCAAACTTCACGAAGGCATTGTCTTAGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTaa                                                                                            >  4:261472/1‑146 (MQ=255)                                                           tCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCa                                                                                 >  5:99866/1‑149 (MQ=255)                                                              agaTGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACg                                                                               >  2:278416/1‑148 (MQ=255)                                                               gaTGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGa                                                                             >  4:260320/1‑149 (MQ=255)                                                                   ttttCTGCCGTGACTGAACTGTTACCAATGCTGAAATCGTCGCCGCTGGCATGAGCGGCACCGTCAAACTTCACGAAGGCTTTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACtt                                                                          <  8:293508/148‑1 (MQ=255)                                                                      tCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAAc                                                                      >  2:137163/1‑149 (MQ=255)                                                                           cgtgccgGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTgg                                                                 <  6:99866/149‑1 (MQ=255)                                                                           cgtgccgGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTgg                                                                 <  5:199270/149‑1 (MQ=255)                                                                            gtgccgGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTGGc                                                                <  3:161919/149‑1 (MQ=255)                                                                            gtgccgGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTAACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTgg                                                                 >  4:81377/1‑148 (MQ=255)                                                                                 ggCACTGTTACCAATGCTGAAATAGGCGCCGGTGGCCTCCGGGGCACCGTCAAACGTCCCGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTGGCAGCgg                                                           <  7:202143/149‑1 (MQ=255)                                                                                     cTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGa                                                                                        <  8:279794/116‑1 (MQ=255)                                                                                     cTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGa                                                                                        >  7:279794/1‑116 (MQ=255)                                                                                        ttACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTGGCAGCGGGGAATCg                                                    >  8:273068/1‑149 (MQ=255)                                                                                                   gAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTGGCAGCGGGGAATCGCCCCATgggc                                          >  6:209369/1‑147 (MQ=255)                                                                                                    aaaTAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATgc                                                                                     <  8:169542/104‑1 (MQ=255)                                                                                                    aaaTAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATgc                                                                                     >  7:169542/1‑104 (MQ=255)                                                                                                     aaTAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTGGCAGCGGGGAATCGCCCCATGGGAAt                                        <  3:81377/148‑1 (MQ=255)                                                                                                         gTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTGGCAGCGGGGAATCGCCCCATGGGAATTTCGc                                   <  7:273068/149‑1 (MQ=255)                                                                                                          tCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTGGCAGCGGGGAATCGCCCCATGGGaa                                         <  5:167332/142‑1 (MQ=255)                                                                                                          tCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTGGCAGCGGGGAATCGCCCCATGGGaa                                         >  6:167332/1‑142 (MQ=255)                                                                                                                        aGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTGGCAGCGGGGAATCGCCCCATGGGAATTTCGCCCATGGCGACGCGGt                    >  8:251732/1‑149 (MQ=255)                                                                                                                         gCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTGGCAGCGGGGAATCGCCCCATGGGAATTTCGCCCATGGCGACGCGGt                    >  8:61932/1‑148 (MQ=255)                                                                                                                             cACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTGGCAGCGGGGAATCGCCCCATGGGAATTTCGCCCATGGCGACGCGGTCACTg               <  1:6425/149‑1 (MQ=255)                                                                                                                                cGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTGGCAGCGGGGAATCGCCCCATGGGAATTTCGCCCATGGCGACGCGGTCACTGACa            >  3:7367/1‑149 (MQ=255)                                                                                                                                 gTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTGGCAGCGGGGAATCGCCCCATGGGAATTTCGCCCATGGCGACGCGGTCACTGACAt           >  2:187593/1‑149 (MQ=255)                                                                                                                                  tCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTGGCAGCGGGGAATCGCCCCATGGGAATTTCGCCCATGGCGACGCgg                     >  6:258485/1‑138 (MQ=255)                                                                                                                                  tCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTGGCAGCGGGGAATCGCCCCATGGGAATTTCGCCCATGGCGACGCgg                     <  5:258485/138‑1 (MQ=255)                                                                                                                                   cAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTGGCAGCGGGGAATCGCCCCATGGGAATTTCGCCCATGGCGAcgc                       >  3:217838/1‑135 (MQ=255)                                                                                                                                   cAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTGGCAGCGGGGAATCGCCCCATGGGAATTTCGCCCATGGCGAcgc                       <  4:217838/135‑1 (MQ=255)                                                                                                                                     aaCTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTg                                                                  <  7:182170/90‑1 (MQ=255)                                                                                                                                     aaCTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTg                                                                  >  8:182170/1‑90 (MQ=255)                                                                                                                                        ttCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTGGCAGCGGGGAATCGCCCCATGGGAATTTCGCCCATGGCGACGCGGTCACTGACATTGCCGt     >  3:3505/1‑148 (MQ=255)                                                                                                                                           aCGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTGGCAGCGGGGAATCGCCCCATGGGAATTTCGCCCATGGCGACGCGGTCACTGACATTGCCGTCAc  <  3:260320/148‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                              TAATCAACCGAGGTTCCACCGGGTTTGATCGATGCCTTGGACTTGTCCCTGATCACAATCGAGATGTTTTCTGCCGTGCCGGCACTGTTACCAATGCTGAAATAGTCGCCGCTGGCATCAGCGGCACCGTCAAACTTCACGAAGGCATTGTCTTCGCTGATGCTGCAGACTGTTTTGTCGGGTACGCGGATGTTAAAAGATGCGCCACGGACTTCAACGTTGGCAGCGGGGAATCGCCCCATGGGAATTTCGCCCATGGCGACGCGGTCACTGACATTGCCGTCAC  >  NC_002947/2133186‑2133471

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑