Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,482,564	T→C	P217P (CCT→CCC)	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	1,482,564	0	T	C	100.0%	69.5 / NA	27	P217P (CCT→CCC)	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 (10/17);  total (10/17)

AAGAGATACTGTTAAAATTGCTGTATTAAGTTGTAAAGGTGGTATTGGCGCAAGTTTAATTAGTTCACATATTGCTAATGAGATTGTGTCAAGTAAAAAAATTCCAGTGCTATTAGCCCAAGGCCCTAATGGTTCTCAAGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATACTCCGAATTTAGACAT‑ATTTAACGGGAGTCTATTTGAGCTAACACCTGCGGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATAATGTTAAGAAGGATAATTTCATTGGTTTTTTAGAAAACTATAATAGTTTCGTATTAGTTGTAGAAAGAAGAATTGGTTCGCTACGTTTAGCTAAGCAGTTCCTAGATGAATGCGAGCGCATCCGTGGCACTTCGAGAAAACCAATTCGTACTTTTGTCTGTATTTC  >  1/1482327‑1482779                                                                                                                                                                                                                                               |                                                                                                                                                                                                                        aaGAGATACTGTTAAAATTGCTGTATTAAGTTGTAAGGGCGGTATTGTCGCAAGTTTAATTAGTTCACATATTGCTAATGAGATTGTATCAAGTAAAAAAATTCCGGTGCTATTAGCCCAAGGTCCTAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGaaa                                                                                                                                                                                                            <  1:538659/251‑1 (MQ=255)      aTACTGTTAAAATTGCTGTATTAAGTTGTAAGGGCGGTATTGGCGCAAGTTTAATTAGTTCACATATTGCTAATGAGATTGTATCAAGTAAAAAAATTCCGGTGCTATTAGCCCAAGGTCCTAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATAc                                                                                                                                                                                                       <  1:407631/251‑1 (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                                                                                                                                                                      <  1:556451/249‑2 (MQ=255)                                        cggtATTGGCGCAAGTTTAATTAGTTCACATATTGCTAATGAGATTGTATCAAGTAAAAAAATTCCGGTGCTATTAGCCCAAGGTCCTAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATaac                                                                                                                                                                      <  1:817751/249‑2 (MQ=255)                                        cggtATTGGCGCAAGTTTAATTAGTTCACATATTGCTAATGAGATTGTATCAAGTAAAAAAATTCCGGTGCTATTAGCCCAAGGTCCTAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATaac                                                                                                                                                                      <  1:477338/249‑2 (MQ=255)                                        cggtATTGGCGCAAGTTTAATTAGTTCACATATTGCTAATGAGATTGTATCAAGTAAAAAAATTCCGGTGCTATTAGCCCAAGGTCCTAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATaac                                                                                                                                                                      <  1:711880/249‑2 (MQ=255)                                                gcgcAAGTTTAATTAGTTCACATATTGCTAATGAGATTGTATCAAGTAAAAAAATTCCGGTGCTATTAGCCCAAGGTCCTAATGGTTCCCAGGATTTAGATTTATTATTTGATAAAAAGTTATCAGGTAATGTTATTGAATATGCTCCTAATTTAGATAT‑ATTTAACGGGAGCTTATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTGCGATCAACCTATCTATaacgtcaaaaa                                                                                                                                                              <  1:158595/250‑10 (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)                                                                                                                                                                                                                               tATTTGAGCTAACACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATaac                                                                                                                                                                      <  1:673605/68‑2 (MQ=255)                                                                                                                                                                                                                                    gAGCTAAAACCCGCAGCGACTGAAAAATACAATTTTATTATCTACGATCAAcc                                                                                                                                                                                >  1:573312/1‑53 (MQ=255)                                                                                                                                                                                                                                               |                                                                                                                                                                                                                        AAGAGATACTGTTAAAATTGCTGTATTAAGTTGTAAAGGTGGTATTGGCGCAAGTTTAATTAGTTCACATATTGCTAATGAGATTGTGTCAAGTAAAAAAATTCCAGTGCTATTAGCCCAAGGCCCTAATGGTTCTCAAGATTTAGATTTATTATTTGATAAAAAGCTATCAGGTAATGTTATTGAATATACTCCGAATTTAGACAT‑ATTTAACGGGAGTCTATTTGAGCTAACACCTGCGGCGACTGAAAAATACAATTTTATTATCTACGATCAACCTATCTATAATGTTAAGAAGGATAATTTCATTGGTTTTTTAGAAAACTATAATAGTTTCGTATTAGTTGTAGAAAGAAGAATTGGTTCGCTACGTTTAGCTAAGCAGTTCCTAGATGAATGCGAGCGCATCCGTGGCACTTCGAGAAAACCAATTCGTACTTTTGTCTGTATTTC  >  1/1482327‑1482779

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: ‑