Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,478,260	C→T	Y32Y (TAC→TAT)	unknown →	Flp pilus assembly protein, pilin Flp

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	1,478,260	0	C	T	100.0%	68.9 / NA	27	Y32Y (TAC→TAT)	unknown	Flp pilus assembly protein, pilin Flp
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (15/12);  total (15/12)

TTTCAGGACTATAATGCCACTCGTTTATTTAATTCCACAAGATTATTAAATAAATGACATTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACCTTAATTACGAAAGCATACATCAAAGCAACCGAAGCAATCCGTTCTTTCAAAAAAAATCAAGCAGGTGTGACTGCAATTGAATACGGTTTGATCGCCATTGCTGTTGCCGTGTTAATCGTTGCTGTATTCTACAGCGACAATGGTTTTATTAAGGGCTTACAAAA  >  1/1478042‑1478340                                                                                                                                                                                                                           |                                                                                 tttCAGGACTAT‑ATACCGGTCGTTTATTTAATTCCACAAGCTTATTAAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCGTGTTAATc                                                 <  1:625438/251‑1 (MQ=255)         actatataccggtCGTTTATTTAATTCCACAAGCTTATTAAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTg                                                               >  1:664083/13‑230 (MQ=255)         actatataccggtCGTTTATTTAATTCCACAAGCTTATTAAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTg                                                               >  1:253314/13‑230 (MQ=255)         actatataccggtCGTTTATTTAATTCCACAAGCTTATTAAATAAATGACACTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACTTTAACTACTAAAGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCGTGTTAATCGTTGcag                                          >  1:468214/13‑249 (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)                                                                                                                                               ctaaaGCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCGTGTTAATCGTTGCAGTATTCTAc                                  <  1:834789/123‑1 (MQ=255)                                                                                                                                                    gCATACATCAAAGCAGCTGAAGCAATCCGTTCTTTCAGAGAAAATCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCGTGTTAATCGTTGCAGTATTCTACAGCAACAATGGtt                     >  1:830047/1‑133 (MQ=255)                                                                                                                                                                                              aaTCAAGCAGGTGTGACTGCAATTGAATATGGTTTGATCGCTATTGCTGTTGCCGTGTTAATc                                                 <  1:392590/63‑1 (MQ=255)                                                                                                                                                                                                                           |                                                                                 TTTCAGGACTATAATGCCACTCGTTTATTTAATTCCACAAGATTATTAAATAAATGACATTAAGTTCAAACTCAAGGATTCTTGAATTTTATTTTCTATAAACAACAAAGGAGCATTAAGACAATGTTAAATACCTTAATTACGAAAGCATACATCAAAGCAACCGAAGCAATCCGTTCTTTCAAAAAAAATCAAGCAGGTGTGACTGCAATTGAATACGGTTTGATCGCCATTGCTGTTGCCGTGTTAATCGTTGCTGTATTCTACAGCGACAATGGTTTTATTAAGGGCTTACAAAA  >  1/1478042‑1478340

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: ‑