Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,481,562	C→T	Y56Y (TAC→TAT)	unknown →	Flp pilus assembly protein RcpB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	1,481,562	0	C	T	100.0%	83.7 / NA	33	Y56Y (TAC→TAT)	unknown	Flp pilus assembly protein RcpB
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (19/14);  total (19/14)

TCCATACGACTCCGTTAAAGAATGTTTATTACAAAACATTAACATCTAACTTCTTAAAAAATAGTGGGTTCATACAATGAGAAAATTAGTTATCACGGCCTCCATTGCATTGGCCTCAATTACCGCCCCGGTAACAACATTTGCAATCAGTGAATTTGTTAACGATACGACTGTTGCACAACCGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCGATCGTTATGTATTACCGGATTACTCTAATGTCAGTTATAGTAATTTATTTAATTCCGTTATTCGTGATATAGGTAGTAACAACCAAAAGCAAATCAATATAATTTGGCGTGATGCTACGGCAAAGAAAGCCGCAATGAAAATTCGTACAAAATTGATTAAAAATGGTATTACCTCTAAATCTATTTACTTAGAGAAAAAAGCACATAAAGCAAAAACATATCCAATCTATATTGAA  >  1/1481319‑1481775                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                      tcCATACGACTCCGTTAAAGAATGTTTATTACAAGACATTAACATCTAACTTCTTAAAGAATAGTGGGTTCATACAATGAGAAAATTAGTTATTACGGCCTCCATTGCATTGGCCTCAATTATCGTTCCGGCAAAAACATTTGCAATCAATGAATTTGTTGACGATACGACTGTTGCACAACCGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATg                                                                                                                                                                                                                <  1:438033/251‑1 (MQ=255)                        gTTTATTACAAGACATTAACATCTAACTTCTTAAAGAATAGTGGGTTCATACAATGAGAAAATTAGTTATTACGGCCTCCATTGCATTGGCCTCAATTATCGTTCCGGCAAAAACATTTGCAATCAATGAATTTGTTGACGATACGACTGTTGCACAACCGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATg                                                                                                                                                                                                                >  1:160/1‑228 (MQ=255)                        gTTTATTACAAGACATTAACATCTAACTTCTTAAAGAATAGTGGGTTCATACAATGAGAAAATTAGTTATTACGGCCTCCATTGCATTGGCCTCAATTATCGTTCCGGCAAAAACATTTGCAATCAATGAATTTGTTGACGATACGACTGTTGCACAACCGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGt                                                                                                                                                                                                               <  1:882225/229‑1 (MQ=255)                        gTTTATTACAAGACATTAACATCTAACTTCTTAAAGAATAGTGGGTTCATACAATGAGAAAATTAGTTATTACGGCCTCCATTGCATTGGCCTCAATTATCGTTCCGGCAAAAACATTTGCAATCAATGAATTTGTTGACGATACGACTGTTGCACAACCGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAAt                                                                                                                                                                                         >  1:801448/1‑251 (MQ=255)                             ttaCAAGACATTAACATCTAACTTCTTAAAGAATAGTGGGTTCATACAATGAGAAAATTAGTTATTACGGCCTCCATTGCATTGGCCTCAATTATCGTTCCGGCAAAAACATTTGCAATCAATGAATTTGTTGACGATACGACTGTTGCACAACCGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTAttct                                                                                                                                                                                                                    <  1:855606/219‑1 (MQ=255)                                                  cttcttAAAGAATAGTGGGTTCATACAATGAGAAAATTAGTTATTACGGCCTCCATTGCATTGGCCTCAATTATCGTTCCGGCAAAAACATTTGCAATCAATGAATTTGTTGACGATACGACTGTTGCACAACCGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTaa                                                                                                                                                               <  1:508324/251‑1 (MQ=255)                                                           gaaTAGTGGGTTCATACAATGAGAAAATTAGTTATTACGGCCTCCATTGCATTGGCCTCAATTATCGTTCCGGCAAAAACATTTGCAATCAATGAATTTGTTGACGATACGACTGTTGCACAACCGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCaaaa                                                                                                                                                      >  1:504045/2‑251 (MQ=255)                                                               aGTGGGTTCATACAATGAGAAAATTAGTTATTACGGCCTCCATTGCATTGGCCTCAATTATCGTTCCGGCAAAAACATTTGCAATCAATGAATTTGTTGACGATACGACTGTTGCACAACCGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCAAAAACaa                                                                                                                                                  >  1:211/1‑251 (MQ=255)                                                                                 gaAAATTAGTTATTACGGCCTCCATTGCATTGGCCTCAATTATCGTTCCGGCAAAAACATTTGCAATCAATGAATTTGTTGACGATACGACTGTTGCACAACCGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAg                                                                                                                                                                                                      >  1:121544/1‑181 (MQ=255)                                                                                               aCGGCCTCCATTGCATTGGCCTCAATTATCGTTCCGGCAAAAACATTTGCAATCAATGAATTTGTTGACGATACGACTGTTGCACAACCGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCAAAAACAAATCAATATCAttt                                                                                                                                     >  1:676897/1‑232 (MQ=255)                                                                                                  gCCTCCATTGCATTGGCCTCAATTATCGTTCCGGCAAAAACATTTGCAATCAATGAATTTGTTGACGATACGACTGTTGCACAACCGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCAAAAACAAATCAATATCATTTGGCGTGATGCTACGGCaaagaa                                                                                                               >  1:497763/1‑251 (MQ=255)                                                                                                   ccTCCATTGCATTGGCCTCAATTATCGTTCCGGCAAAAACATTTGCAATCAATGAATTTGTTGACGATACGACTGTTGCACAACCGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCAAAAACAAATCAATATCATTTGGCGTGATGCTACGGCaaagaa                                                                                                               <  1:767128/250‑1 (MQ=255)                                                                                                      ccATTGCATTGGCCTCAATTATCGTTCCGGCAAAAACATTTGCAATCAATGAATTTGTTGACGATACGACTGTTGCACAACCGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCAAAAACAAATCAATATCATTTGGCg                                                                                                                                 >  1:24003/1‑229 (MQ=255)                                                                                                      ccATTGCATTGGCCTCAATTATCGTTCCGGCAAAAACATTTGCAATCAATGAATTTGTTGACGATACGACTGTTGCACAACCGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCAAAAACAAATCAATATCATTTGGCGTGATGCTACGGCAAAGAAAGc                                                                                                            >  1:578163/1‑250 (MQ=255)                                                                                                        attgcattgGCCTCAATTATCGTTCCGGCAAAAACATTTGCAATCAATGAATTTGTTGACGATACGACTGTTGCACAACCGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCAAAAACAAATCAATATCATTTGGCGTGATGCTACGGCAAAGAAAGCCg                                                                                                          >  1:228237/1‑250 (MQ=255)                                                                                                           gcattgGCCTCAATTATCGTTCCGGCAAAAACATTTGCAATCAATGAATTTGTTGACGATACGACTGTTGCACAACCGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTaa                                                                                                                                                               <  1:222257/194‑1 (MQ=255)                                                                                                                                                       tGAATTTGTTGACGATACGACTGTTGCACAACCGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCAAAAACAAATCAATATCATTTGGCGTGATGCTACGGCAAAGAAAGCCGCAATGGAAATTCGTACAAAATTGATTAAAAATGGTATCGCCTCTAAAt                                                          <  1:467484/251‑1 (MQ=255)                                                                                                                                                                   cGATACGACTGTTGCACAACCGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAg                                                                                                                                                                                                      <  1:270385/99‑1 (MQ=255)                                                                                                                                                                   cGATACGACTGTTGCACAACCGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCAAAAACAAATCAATATCATTTGGCGTGATGCTACGGCAAAGAAAGCCGCAATGGAAATTCGTACAAAATTGATTAAAAATGGTATCGCCTCTAAATCCATTTAc                                                  <  1:90780/247‑1 (MQ=255)                                                                                                                                                                             gTTGCACAACCGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGatat                                                                                                                                                                        >  1:895490/1‑119 (MQ=255)                                                                                                                                                                             gTTGCACAACCGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCAAAAACAAATCAATATCATTTGGCGTGATGCTACGGCAAAGAAAGCCGCAATGGAAATTCGTACAAAATTGATTAAAAATGGTATCGCCTCTAAATCCATTTACTTAGAGAAAAAAg                                     >  1:240469/1‑250 (MQ=255)                                                                                                                                                                                      ccGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCAAAAACAAATCAATATCATTTGGCGTGATGCTACGGCAAAGAAAGCCGCAATGGAAATTCGTACAAAATTGATTAAAAATGGTATCGCCTCTAAATCCATTTACTTAGAGAAAAAAGCACATAAAGc                           <  1:625946/251‑1 (MQ=255)                                                                                                                                                                                         gTACAAAATAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCAAAAACAAATCAATATCATTTGGCGTGATGCTACGGCAAAGAAAGCCGCAATGGAAATTCGTACAAAATTGATTAAAAATGGTATCGCCTCTAAATCCATTTACTTAGAGAAAAAAGCACATAAAGCaaa                        >  1:107084/1‑251 (MQ=255)                                                                                                                                                                                                aTAGTGAATTTAATCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCAAAAACAAATCAATATCATTTGGCGTGATGCTACGGCAAAGAAAGCCGCAATGGAAATTCGTACAAAATTGATTAAAAATGGTATCGCCTCTAAATCCATTTACTTAGAGAAAAAAGCACATAAAGCAAAAatatat                 >  1:745632/1‑251 (MQ=255)                                                                                                                                                                                                            aTCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATGGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCAAAAACAAATCAATATCATTTGGCGTGATGCTACGGCAAAGAAAGCCGCAATGGAAATTCGTACAAAATTGATTAAAAATGGTATCGCCTCTAAATCCATTTACTTAGAGAAAAAAGCACATAAAGCAAAAATATATCCAATCTATAtt     >  1:470825/1‑251 (MQ=255)                                                                                                                                                                                                            aTCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCAAAAACAAATCAATATCATTTGGCGTGATGCTACGGCAAAGAAAGCCGCAATGGAAATTCGTACAAAATTGATTAAAAATGGTATCGCCTCTAAATCCATTTACTTAGAGAAAAAAGCACATAAAGCAAAAATATATCCAATCTATAtt     >  1:741021/1‑251 (MQ=255)                                                                                                                                                                                                            aTCGTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCAAAAACAAATCAATATCATTTGGCGTGATGCTACGGCAAAGAAAGCCGCAATGGAAATTCGTACAAAATTGATTAAAAATGGTATCGCCTCTAAATCCATTTACTTAGAGAAAAAAGCACATAAAGCAAAAATATATCCAATCTATAtt     <  1:331429/251‑1 (MQ=255)                                                                                                                                                                                                               gTACACAGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCAAAAACAAATCAATATCATTTGGCGTGATGCTACGGCAAAGAAAGCCGCAATGGAAATTCGTACAAAATTGATTAAAAATGGTATCGCCTCTAAATCCATTTACTTAGAGAAAAAAGCACATAAAGCAAAAATATATCCAATCTATATTGaa  >  1:530630/1‑251 (MQ=255)                                                                                                                                                                                                                    caGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCAAAAACAAATCAATATCATTTGGCGTGATGCTACGGCAAAGAAAGCCGCAATGGAAATTCGTACAAAATTGATTAAAAATGGTATCGCCTCTAAAt                                                          <  1:868739/190‑1 (MQ=255)                                                                                                                                                                                                                    caGTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCAAAAACAAATCAATATCATTTGGCGTGATGCTACGGCAAAGAAAGCCGCAATGGAAATTCGTACAAAATTGATTAAAAATGGTATCGCCTCTAAATCCATTTACTTAGAGAAAAAAGCACATAAAGCAAAAatatat                 >  1:832398/1‑231 (MQ=255)                                                                                                                                                                                                                      gTTAGTCAATCGTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCAAAAACAAATCAATATCATTTGGCGTGATGCTACGGCAAAGAAAGCCGCAATGGAAATTCg                                                                                             <  1:486569/153‑1 (MQ=255)                                                                                                                                                                                                                                 gTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCAAAAACAAATCAATATCATTTGGCGTGATGCTACGGCAAAGAAAGCCGCAATGGAAATTCGTACAAAATTGATTAAAAATGGTATCGCCTCTAAATCCATTTACTTAGAGAAAAAAGc                                    >  1:802737/1‑199 (MQ=255)                                                                                                                                                                                                                                 gTTATGTATTACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCAAAAACAAATCAATATCATTTGGCGTGATGCTACGGCAAAGAAAGCCGCAATGGAAATTCGTACAAAATTGATTAAAAATGGTATCGCCTCTAAATCCATTTACTTAGAGAAAAAAGc                                    <  1:163066/199‑1 (MQ=255)                                                                                                                                                                                                                                         ttACCGGATTATTCTAATGTCAGTTATAGTAATTTATTCAATTCTGTCATTCGTGATATAGGTAGTAACAACCAAAAACAAATCAATATCATTTGGCGTGATGCTACGGCAAAGAAAGCCGCAATGGAAATTCGTACAAAATTGATTAAAAATGGTATCGCCTCTAAATCCATTTACTTAGAGAAAAAAGCACATAAAGCAAAAATATATCCAATCTATATTGa   <  1:332138/224‑1 (MQ=255)                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                      TCCATACGACTCCGTTAAAGAATGTTTATTACAAAACATTAACATCTAACTTCTTAAAAAATAGTGGGTTCATACAATGAGAAAATTAGTTATCACGGCCTCCATTGCATTGGCCTCAATTACCGCCCCGGTAACAACATTTGCAATCAGTGAATTTGTTAACGATACGACTGTTGCACAACCGGTACAAAATAGTGAATTTAATCGTACACAGTTAGTCGATCGTTATGTATTACCGGATTACTCTAATGTCAGTTATAGTAATTTATTTAATTCCGTTATTCGTGATATAGGTAGTAACAACCAAAAGCAAATCAATATAATTTGGCGTGATGCTACGGCAAAGAAAGCCGCAATGAAAATTCGTACAAAATTGATTAAAAATGGTATTACCTCTAAATCTATTTACTTAGAGAAAAAAGCACATAAAGCAAAAACATATCCAATCTATATTGAA  >  1/1481319‑1481775

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: ‑