Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,478,181	T→C	I6T (ATT→ACT)	unknown →	Flp pilus assembly protein, pilin Flp

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	1,478,181	0	T	C	100.0%	80.4 / NA	29	I6T (ATT→ACT)	unknown	Flp pilus assembly protein, pilin Flp
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (18/11);  total (18/11)

TACAATAACCCTTAACATACTGTTAATTAAAAA‑TTTTCGCAATCACAATACATACATATACGTAGTGAATTTATTATTCT‑AAAAAACTTGCATTTTAATTTTTCAGGACTATAATGCCACTCGTTTATTTAATTCCACAAGATTATTAAATAAATGACATTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACCTTAATTACGAAAGCATACATCAAAGCAACCGAAGCAATCCGTTCTTTCAAAAAAAATCAAGCAGGTGTGACTGCAATTGAATACGGTTTGATCGCCATTGCTGTTGCCGTGTTAATCGTTGCTGTATTCTACAGCGACAATGGTTTTATTAAGGGCTTACAAAA  >  1/1477942‑1478340                                                                                                                                                                                                                                                  |                                                                                                                                                                tACAATAACCCTTAACATACTGTTAATTAAAAAGTTTTCGCAATCACAATACGTACATATACATAGTGAATTTATTATTCTAAAAAAACTTGCATTTTAATTTTTCAGGACTAT‑ATACCGGTCGTTTATTTAATTCCACAAGCTTATTAAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCa                                                                                                                                                       >  1:484344/1‑251 (MQ=255)                                                        cataTACATAGTGAATTTATTATTCTAAAAAAACTTGCATTTTAATTTTTCAGGACTAT‑ATACCGGTCGTTTATTTAATTCCACAAGCTTATTAAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGa                                                                                                >  1:110562/1‑251 (MQ=255)                                                                                                       tttCAGGACTAT‑ATACCGGTCGTTTATTTAATTCCACAAGCTTATTAAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGc                                                                                                                                   <  1:424453/169‑1 (MQ=255)                                                                                                       tttCAGGACTAT‑ATACCGGTCGTTTATTTAATTCCACAAGCTTATTAAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCGTGTTAATc                                                 <  1:625438/251‑1 (MQ=255)                                                                                                               actatataccggtCGTTTATTTAATTCCACAAGCTTATTAAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTg                                                                                             >  1:17186/13‑200 (MQ=255)                                                                                                               actatataccggtCGTTTATTTAATTCCACAAGCTTATTAAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTg                                                               >  1:253314/13‑230 (MQ=255)                                                                                                               actatataccggtCGTTTATTTAATTCCACAAGCTTATTAAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTg                                                               >  1:664083/13‑230 (MQ=255)                                                                                                               actatataccggtCGTTTATTTAATTCCACAAGCTTATTAAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCGTGTTAATCGTTGcag                                          >  1:468214/13‑249 (MQ=255)                                                                                                                ctatataccggtCGTTTATTTAATTCCACAAGCTTATTAAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGc                                                                                                                                            >  1:411900/12‑152 (MQ=255)                                                                                                                  atataccggtCGTTTATTTAATTCCACAAGCTTATTAAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGAt                                                                          <  1:318791/207‑1 (MQ=255)                                                                                                                  atataccggtCGTTTATTTAATTCCACAAGCTTATTAAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCGTGTTAATCGTTGCAGTAt                                       >  1:884156/10‑251 (MQ=255)                                                                                                                  atataccggtCGTTTATTTAATTCCACAAGCTTATTAAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCGTGTTAATCGTTGCAGTAt                                       >  1:706114/10‑251 (MQ=255)                                                                                                                  atataccggtCGTTTATTTAATTCCACAAGCTTATTAAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCGTGTTAATCGTTGCAGTAt                                       >  1:627293/10‑251 (MQ=255)                                                                                                                    ataccggtCGTTTATTTAATTCCACAAGCTTATTAAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCGTGTTAATCGTTGCAGTATTc                                     <  1:28335/244‑1 (MQ=255)                                                                                                                       ccggtCGTTTATTTAATTCCACAAGCTTATTAAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCGTGTTAATCGTTGCAGTATTCTAc                                  <  1:558000/247‑1 (MQ=255)                                                                                                                                        tCCACAAGCTTATTAAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCGTGTTAATCGTTGCAGTATTCTACAGCAACAATGGTTttat                 <  1:714491/251‑1 (MQ=255)                                                                                                                                         ccACAAGCTTATTAAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCGTGTTAATCGTTGCAGTATTCTACAGCAACAATGGttt                    <  1:488632/247‑1 (MQ=255)                                                                                                                                              agcttattaAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCGTGTTAATCGTTGCAGTATTCTACAGCAACAATGGTTttatcgctaa           >  1:164569/4‑245 (MQ=255)                                                                                                                                                cttattaAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGc                                                                 >  1:16545/2‑195 (MQ=255)                                                                                                                                                 ttattaAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGAt                                                                          >  1:54615/1‑185 (MQ=255)                                                                                                                                                      aaataaatGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCGTGTTAATCGTTGCAGTATTCTACAGCAACAATGGTTttatcgctaacttacaaa   >  1:528346/1‑237 (MQ=255)                                                                                                                                                               acactAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCGTGTTAATCGTTGCAGTATTCTACAGcaa                             >  1:773810/5‑214 (MQ=255)                                                                                                                                                                                                                    ggAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCg                                                         >  1:237902/1‑135 (MQ=255)                                                                                                                                                                                                                    ggAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCGTGTTAATCGTTGCAGTAt                                       <  1:110319/153‑1 (MQ=255)                                                                                                                                                                                                                    ggAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCGTGTTAATCGTTGCAGTATTCTACAg                                >  1:522868/1‑160 (MQ=255)                                                                                                                                                                                                                        cATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCGTGTTAATCGTTGCAGTATTCTACAGCAACAATGGTTttatcgctaacttacaaaa  <  1:169879/186‑16 (MQ=255)                                                                                                                                                                                                                                  aTGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCGTGTTAATCGTTGCAGTATTCTAc                                  <  1:792921/144‑1 (MQ=255)                                                                                                                                                                                                                                  aTGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCGTGTTAATCGTTGCAGTATTCTACAGCAACAATGGTTttatcgctaacttacaaaa  >  1:625432/1‑161 (MQ=255)                                                                                                                                                                                                                                    gTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCGTGTTAATCGTTGCAGTATTCTAc                                  <  1:432152/142‑1 (MQ=255)                                                                                                                                                                                                                                                  |                                                                                                                                                                TACAATAACCCTTAACATACTGTTAATTAAAAA‑TTTTCGCAATCACAATACATACATATACGTAGTGAATTTATTATTCT‑AAAAAACTTGCATTTTAATTTTTCAGGACTATAATGCCACTCGTTTATTTAATTCCACAAGATTATTAAATAAATGACATTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACCTTAATTACGAAAGCATACATCAAAGCAACCGAAGCAATCCGTTCTTTCAAAAAAAATCAAGCAGGTGTGACTGCAATTGAATACGGTTTGATCGCCATTGCTGTTGCCGTGTTAATCGTTGCTGTATTCTACAGCGACAATGGTTTTATTAAGGGCTTACAAAA  >  1/1477942‑1478340

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑