Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,482,546	2 bp→CT	coding (633‑634/1125 nt)	unknown →	Type II/IV secretion system ATPase TadZ/CpaE, associated with Flp pilus assembly

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	1,482,546	0	T	C	100.0%	82.5 / NA	30	S211S (AGT→AGC)	unknown	Type II/IV secretion system ATPase TadZ/CpaE, associated with Flp pilus assembly
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (10/20);  total (10/20)
*	1	1,482,547	0	C	T	100.0%	76.6 / NA	30	L212L (CTA→TTA)	unknown	Type II/IV secretion system ATPase TadZ/CpaE, associated with Flp pilus assembly
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (10/20);  total (10/20)

TTTAGGTGCTGATATCCCTCGCTTAAGAGATACTGTTAAAATTGCTGTATTAAGTTGTAAAGGTGGTATTGGCGCAAGTTTAATTAGTTCACATATTGCTAATGAGATTGTGTCAAGTAAAAAAATTCCAGTGCTATTAGCCCAAGGCCCTAATGGTTCTCAAGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATACTCCGAATTTAGACAT‑ATTTAACGGGAGTCTATTTGAGCTAACACCTGCGGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATAATGTTAAGAAGGATAATTTCATTGGTTTTTTAGAAAACTATAATAGTTTCGTATTAGTTGTAGAAAGAAGAATTGGTTCGCTACGTTTAGCTAAGCAGTTCCTAGATGAATGCGAGCGCATCCGTGGCACTTCGAGAAAACCAATTCGTACTTTTGTCTGTATTTC  >  1/1482303‑1482779                                                                                                                                                                                                                                                     ||                                                                                                                                                                                                                                         tttAGGTGTTGATATACCTCGTTTAAGAGATACTGTTAAAATTGCTGTATTAAGTTGTAAGGGCGGTATTGGCGCAAGTTTAATTAGTTCACATATTGCTAATGAGATTGTATCAAGTAAAAAAATTCCGGTGCTATTAGCCCAAGGTCCTAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTg                                                                                                                                                                                                                                    <  1:21137/251‑1 (MQ=255)                         aaGAGATACTGTTAAAATTGCTGTATTAAGTTGTAAGGGCGGTATTGTCGCAAGTTTAATTAGTTCACATATTGCTAATGAGATTGTATCAAGTAAAAAAATTCCGGTGCTATTAGCCCAAGGTCCTAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGaaa                                                                                                                                                                                                            <  1:538659/251‑1 (MQ=255)                              aTACTGTTAAAATTGCTGTATTAAGTTGTAAGGGCGGTATTGGCGCAAGTTTAATTAGTTCACATATTGCTAATGAGATTGTATCAAGTAAAAAAATTCCGGTGCTATTAGCCCAAGGTCCTAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATAc                                                                                                                                                                                                       <  1:407631/251‑1 (MQ=255)                                          ttGCTGTATTAAGTTGTAAGGGCGGTATTGGCGCAAGTTTAATTAGTTCACATATTGCTAATGAGATTGTATCAAGTAAAAAAATTCCGGTGCTATTAGCCCAAGGTCCTAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCt                                                                                                                                                                                                                                >  1:347677/1‑214 (MQ=255)                                               gTATTAAGTTGTAAGGGCGGTATTGGCGCAAGTTTAATTAGTTCACATATTGCTAATGAGATTGTATCAAGTAAAAAAATTCCGGTGCTATTAGCCCAAGGTCCTAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGc                                                                                                                                                                                                                                 <  1:748852/208‑1 (MQ=255)                                                      gTTGTAAGGGCGGTATTGGCGCAAGTTTAATTAGTTCACATATTGCTAATGAGATTGTATCAAGTAAAAAAATTCCGGTGCTATTAGCCCAAGGTCCTAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAAc                                                                                                                                                                                 >  1:252111/1‑249 (MQ=255)                                                           aagggcggtATTGGCGCAAGTTTAATTAGTTCACATATTGCTAATGAGATTGTATCAAGTAAAAAAATTCCGGTGCTATTAGCCCAAGGTCCTAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAACctatcta                                                                                                                                                                          <  1:367582/245‑1 (MQ=255)                                                              ggcggtATTGGCGCAAGTTTAATTAGTTCACATATTGCTAATGAGATTGTATCAAGTAAAAAAATTCCGGTGCTATTAGCCCAAGGTCCTAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAACctatctat                                                                                                                                                                         <  1:7724/246‑1 (MQ=255)                                                                cggtATTGGCGCAAGTTTAATTAGTTCACATATTGCTAATGAGATTGTATCAAGTAAAAAAATTCCGGTGCTATTAGCCCAAGGTCCTAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATaac                                                                                                                                                                      <  1:817751/249‑2 (MQ=255)                                                                cggtATTGGCGCAAGTTTAATTAGTTCACATATTGCTAATGAGATTGTATCAAGTAAAAAAATTCCGGTGCTATTAGCCCAAGGTCCTAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATaac                                                                                                                                                                      <  1:711880/249‑2 (MQ=255)                                                                cggtATTGGCGCAAGTTTAATTAGTTCACATATTGCTAATGAGATTGTATCAAGTAAAAAAATTCCGGTGCTATTAGCCCAAGGTCCTAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATaac                                                                                                                                                                      <  1:556451/249‑2 (MQ=255)                                                                cggtATTGGCGCAAGTTTAATTAGTTCACATATTGCTAATGAGATTGTATCAAGTAAAAAAATTCCGGTGCTATTAGCCCAAGGTCCTAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATaac                                                                                                                                                                      <  1:477338/249‑2 (MQ=255)                                                                        gcgcAAGTTTAATTAGTTCACATATTGCTAATGAGATTGTATCAAGTAAAAAAATTCCGGTGCTATTAGCCCAAGGTCCTAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGTTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTGCGATCAACCTATCTATaacgtcaaaaa                                                                                                                                                              <  1:158595/250‑10 (MQ=255)                                                                                            caTATTGCTAATGAGATTGTATCAAGTAAAAAAATTCCGGTGCTATTAGCCCAAGGTCCTAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTg                                                                                                                                                                                                                                    <  1:154381/160‑1 (MQ=255)                                                                                                          gaTTGTATCAAGTAAAAAAATTCCGGTGCTATTAGCCCAAGGTCCTAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTg                                                                                                                                                                                                                                    <  1:861778/146‑1 (MQ=255)                                                                                                          gaTTGTATCAAGTAAAAAAATTCCGGTGCTATTAGCCCAAGGTCCTAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGAt                                                                                                                                                                                     >  1:637905/1‑193 (MQ=255)                                                                                                                                     gCTATTAGCCCAAGGTCCTAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATAACGTCAAAAAGGATAATTTCATTAGTTTTTTAGAAAACTATAATAATTTCGTATTAGTTGTagaaagaaaaa                                                                                                >  1:496521/1‑248 (MQ=255)                                                                                                                                                       tAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGAt                                                                                                                                                                                     >  1:470018/1‑148 (MQ=255)                                                                                                                                                                       ttagatttaTTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATAACGTCAAAAAGGATAATTTCATTAGTTTTTTAGAAAACTATAATAATTTCGTATTAGTTGTAGAAAGAAAAATCGGTTCTCTACGTTTAGCTAAACAGTTTCTAGa                                                              <  1:32018/251‑1 (MQ=255)                                                                                                                                                                                 tattTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAGCCTATCTATAACGTCAAAAAGGATAATTTCATTAGTTTTTTAGAAAACTATAATAATTTCGTATTAGTTGTAGAAAGAAAAATCGGTTCTCTACGTTTAGCTAAACAGTTTCTAGATGAATGTGAg                                                    <  1:26506/251‑1 (MQ=255)                                                                                                                                                                                      gATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATATAATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATaac                                                                                                                                                                      <  1:467729/133‑2 (MQ=255)                                                                                                                                                                                              gCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATaac                                                                                                                                                                      <  1:634047/124‑2 (MQ=255)                                                                                                                                                                                              gCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATAACGTCAAAAAGGATAATTTCATTAGTTTTTTAGAAAACTATAATAATTTCGTATTAGTTGTAGAAAGAAAAATCGGTTCTCTACGTTTAGCTAAACAGTTTCTAGATGAATGTGAgcgtattcgcagta                                       >  1:504066/1‑240 (MQ=255)                                                                                                                                                                                                 aTCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATAACGTCAAAAAGGATAATTTCATTAGTTTTTTAGAAAACTataataa                                                                                                                          <  1:573624/165‑2 (MQ=255)                                                                                                                                                                                                             tATTGAATATGCTCCTAATTTAGATAT‑ATTTAACAGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATAACGTCAAAAAGGATAATTTCATTAGTTTTTTAGAAAACTATAATAATTTCGTATTAGTTGTAGAAAGAAAAATCGGTTCTCTACGTTTAGCTAAACAGTTTCTAGATGAATGTGAGCGTATTCGCAGTACTTCGAGAAAACCaa                        >  1:206159/1‑251 (MQ=255)                                                                                                                                                                                                             caTTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATAACGTCAAAAAGGATAATTTCATTAGTTTTTTAGAAAACTATAATAATTTCGTATTAGTTGTAGAAAGAAAAATCGGTTCTCTACGTTTAGCTAAACAGTTTCTAGATGAATGTGAGCGTATTCGCAGTACTTCGAGAAAACCaa                        >  1:206128/2‑251 (MQ=255)                                                                                                                                                                                                                       gcTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATaac                                                                                                                                                                      >  1:306341/2‑98 (MQ=255)                                                                                                                                                                                                                             aaTTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATaac                                                                                                                                                                      <  1:261018/93‑2 (MQ=255)                                                                                                                                                                                                                                    atat‑atTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATAACGTCAAAAAGGATAATTTCATTAGTTTTTTAGAAAACTATAATAATTTCGTATTAGCTGTAGAAAGAAAAATCGGTTCTCTACGTTTAGCTAAACAGTTTCTAGATGAATGTGAGCGTATTCGCAGTACTTCGAGAAAACCAATTCGCACTTTTGTATGTATTTc  <  1:860437/248‑1 (MQ=255)                                                                                                                                                                                                                                       t‑atTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATAACGTCAAAAAGGATAATTTCATTAGTTTTTTAGAAAACTATAATAATTTCGTATTAGTTGTAGAAAGAAAAAtcg                                                                                             >  1:424188/1‑154 (MQ=255)                                                                                                                                                                                                                                                     ||                                                                                                                                                                                                                                         TTTAGGTGCTGATATCCCTCGCTTAAGAGATACTGTTAAAATTGCTGTATTAAGTTGTAAAGGTGGTATTGGCGCAAGTTTAATTAGTTCACATATTGCTAATGAGATTGTGTCAAGTAAAAAAATTCCAGTGCTATTAGCCCAAGGCCCTAATGGTTCTCAAGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATACTCCGAATTTAGACAT‑ATTTAACGGGAGTCTATTTGAGCTAACACCTGCGGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATAATGTTAAGAAGGATAATTTCATTGGTTTTTTAGAAAACTATAATAGTTTCGTATTAGTTGTAGAAAGAAGAATTGGTTCGCTACGTTTAGCTAAGCAGTTCCTAGATGAATGCGAGCGCATCCGTGGCACTTCGAGAAAACCAATTCGTACTTTTGTCTGTATTTC  >  1/1482303‑1482779

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑