Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,487,335	2 bp→AC	coding (488‑489/576 nt)	unknown →	Flp pilus assembly membrane protein TadE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	1,487,335	0	G	A	100.0%	24.9 / NA	11	S163N (AGT→AAC)	unknown	Flp pilus assembly membrane protein TadE
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (2/9);  total (2/9)
*	1	1,487,336	0	T	C	100.0%	23.2 / NA	11	S163N (AGT→AAC)	unknown	Flp pilus assembly membrane protein TadE
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (2/9);  total (2/9)

AAATGGCGGTTACAAGATTGATGTTAAATATGTTGATTGTGGTAGTGAGAGTTCTTGTGTTAAGTCTTTATTGGATGGTAGGTTTAGACGGCCTACTAAAGATAGAGACGGTAAGATTATACCCCCCAATGGTCGGTTAGCAACATTGGCTGTATATTCATTGACCTACAATTATGAGTTTCTGGTTTCACTGCCATTTTTACCTAAGGATAGTGTTGGCGGTTTATTGTCACGTAAGTTTGTAGCCGTACAGGAATTTAATAGATCTAAATTCCAATATCCCGGCAGGTCAAATAAATAATCAGGCAATTTACAATTATTTAAAGCATAAATAATATAATCACAGATGGCTAATCACTGGTATAAAAACATGAAAAAAAACATTCTCACTAATACTAAAAAATTTTTTCATAATAAAAGGGGCGCAGTTAGTCTTGAGT  >  1/1487123‑1487562                                                                                                                                                                                                                     ||                                                                                                                                                                                                                                   aaaTGGCGGTTATGAAATTGATGTTAAATATGTTGATTGTGGTAGTGAGAGCTCTTGTATTAAATCTTTATTAGATGGTAAGTTTAGGCAGCCTACAAAAGACAGAAACGGTAATATTATACCCCCCAATGGTAGGTTAGCAACATTGGCTGTGTATTCATTAACCTACAAGTATGAATTTTTGGTTTCGCTGCCATTTTTACCTAGGGATAACGTTAGCAGTTTGTTGTCACGTAAGt                                                                                                                                                                                                           <  1:392231/239‑1 (MQ=255)       cggttatgaaaTTGATGTTAAATATGTTGATTGTGGTAGTGAGAGCTCTTGTATTAAATCTTTATTAGATGGTAAGTTTAGGCAGCCTACAAAAGACAGAAACGGTAATATTATACCCCCCAATGGTAGGTTAGCAACATTGGCTGTGTATTCATTAACCTACAAGTATGAATTTTTGGTTTCGCTGCCATTTTTACCTAGGGATAACGTTAGCAGTTTGTTGTCACGTAAGTTTGTAGCCGTACAAGaa                                                                                                                                                                                          <  1:164474/240‑1 (MQ=255)            atgaaaTTGATGTTAAATATGTTGATTGTGGTAGTGAGAGCTCTTGTATTAAATCTTTATTAGATGGTAAGTTTAGGCAGCTTACAAAAGACAGAAACGGTAATATTATACCCCCCAATGGTAGGTTAGCAACATTGGCTGTGTATTCATTAACCTACAAGTATGAATTTTTGGTTTCGCTGCCATTTTTACCTAGGGATAACGTTAGCAGTTTGTTGTCACGTAAGTTTGTAGCCGTACAAGAATTTAAt                                                                                                                                                                                    <  1:424603/246‑1 (MQ=255)                                      tgtgGTAGTGAGAGCTCTTGTATTAAATCTTTATTAGATGGTAAGTTTAGGCAGCCTACAAAAGACAGAAACGGTAATATTATACCCCCCAATGGTAGGTTAGCAACATTGGCTGTGTATTCATTAACCTACAAGTATGAATTTTTGGTTTCGCTGCCATTTTTACCTAGGGATAACGTTAGCAGTTTGTTGTCACGTAAGTTTGTAGCCGTACAAGAATTTAATAGATCTAAAtttcagcatccaggtag                                                                                                                                                          <  1:462618/251‑16 (MQ=255)                                       gtgGTAGTGAGAGCTCTTGTATTAAATCTTTATTAGATGGTAAGTTTAGGCAGCCTACAAAAGACAGAAACGGTAATATTATACCCCCCAATGGTAGGTTAGCAACATTGGCTGTGTATTCATTAACCTACAAGTATGAATTTTTGGTTTCGCTGCCATTTTTACCTAGGGATAACGTTAGCAGTTTGTTGTCACGTAAGTTTGTAGCCGTACAAGAATTTAATAGATCTAAAtttcagcatccaggtagg                                                                                                                                                         >  1:355380/1‑235 (MQ=255)                                       gtgGTAGTGAGAGCTCTTGTATTAAATCTTTATTAGATGGTAAGTTTAGGCAGCCTACAAAAGACAGAAACGGTAATATTATACCCCCCAATGGTAGGTTAGCAACATTGGCTGTGTATTCATTAACCTACAAGTATGAATTTTTGGTTTCGCTGCCATTTTTACCTAGGGATAACGTTAGCAGTTTGTTGTCACGTAAGTTTGTAGCCGTACAAGAATTTAATAGATCTAAAtttcagcatccaggtagg                                                                                                                                                         >  1:38067/1‑235 (MQ=255)                                                                                  gTTTAGGCAGCCTACAAAAGACAGAAACGGTAATATTATACCCCCCAATGGTAGGTTAGCAACATTGGCTGTGTATTCATTAACCTACAAGTATGAATTTTTGGTTTCGCTGCCATTTTTACCTAGGGATAACGTTAGCAGTTTGTTGTCACGTAAGTTTGTAGCCGTACAAGAATTTAATAGATCTAAATTTCAGCATCCAGGTAGGTCAAACAaataattaattcatga                                                                                                                                  <  1:768933/231‑11 (MQ=255)                                                                                           gCCTACAAAAGACAGAAACGGTAATATTATACCCCCCAATGGTAGGTTAGCAACATTGGCTGTGTATTCATTAACCTACAAGTATGAATTTTTGGTTTCGCTGCCATTTTTACCTAGGGATAACGTTAGCAGTTTGTTGTCACGTAAGTTTGTAGCCGTACAAGAATTTAATAGATCTAAAt                                                                                                                                                                          <  1:129261/182‑1 (MQ=255)                                                                                               acaaaaGACAGAAACGGTAATATTATACCCCCCAATGGTAGGTTAGCAACATTGGCTGTGTATTCATTAACCTACAAGTATGAATTTTTGGTTTCGCTGCCATTTTTACCTAGGGATAACGTTAGCAGTTTGTTGTCACGTAAGTTTGTAGCCGTACAAGAATTTAATAGATCTAAATTTCAGCATCCAGGTAGGTCaaaca                                                                                                                                                  <  1:502462/199‑3 (MQ=255)                                                                                                                                                             ttCATTAACCTACAAGTATGAATTTTTGGTTTCGCTGCCATTTTTACCTAGGGATAACGTTAGCAGTTTGTTGTCACGTAAGTTTGTAGCCGTACAAGAATTTAATAGATCTAAATTTCAGCATCCAGGTAGGTCAaacaaata                                                                                                                                              <  1:78544/144‑1 (MQ=255)                                                                                                                                                                                          tttCGCTGCCATTTTTACCTAGGGATAACGTTAGCAGTTTGTTGTCACGTAAGTTTGTAGCCGTACAAGAATTTAATAGATCTAAATTTCAGCATCCAGGTAGGTCAAACAAATAAT‑‑‑‑TAATTCATGATTATTTAAAGCACGAGTAATATAATTGCAAATGGTTAATCACCGGTATAAAAACATGAAAAAAAATATCATCACTAGTATTAAAAAATTTTTTCGTAATAAAAAGGGCGCAGTTACGCTTGAgc  <  1:267921/251‑2 (MQ=255)                                                                                                                                                                                                                     ||                                                                                                                                                                                                                                   AAATGGCGGTTACAAGATTGATGTTAAATATGTTGATTGTGGTAGTGAGAGTTCTTGTGTTAAGTCTTTATTGGATGGTAGGTTTAGACGGCCTACTAAAGATAGAGACGGTAAGATTATACCCCCCAATGGTCGGTTAGCAACATTGGCTGTATATTCATTGACCTACAATTATGAGTTTCTGGTTTCACTGCCATTTTTACCTAAGGATAGTGTTGGCGGTTTATTGTCACGTAAGTTTGTAGCCGTACAGGAATTTAATAGATCTAAATTCCAATATCCCGGCAGGTCAAATAAATAATCAGGCAATTTACAATTATTTAAAGCATAAATAATATAATCACAGATGGCTAATCACTGGTATAAAAACATGAAAAAAAACATTCTCACTAATACTAAAAAATTTTTTCATAATAAAAGGGGCGCAGTTAGTCTTGAGT  >  1/1487123‑1487562

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑