Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP009273	104,031	G→T	intergenic (+70/‑161)	lpxC → / → secM	UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	104,031	0	G	T	100.0%	63.0 / NA	22	intergenic (+70/‑161)	lpxC/secM	UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (16/6);  total (16/6)

GTGACCTTCCAGGACGACGCAGAACTGCCGTTGGCCTTCAAAGCGCCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGTTTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTGGACTGCAGGCTTTAATGATAAGATTTGTGCGCTAAATACGTTTG  >  CP009273/103896‑104168                                                                                                                                        |                                                                                                                                          gtgACCTTCCAGGACGACGCAGAACTGCCGTTGGCCTTCAAAGCGCCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCTTTTTTTTTTGAAt                                                                                                                              <  1:561612/149‑1 (MQ=255) gggcccTGCCAGGACGACGCAGAGCGGCCGTTGGCCTTCAAAGCGCCTTCAGCTGTACTGGCATAACGACATTTATACTGTGGTATAAAATTCGACTGGCAAATCTGGCACTCTCGCCGGCCAGGTGAACCAGTCtttttttt                                                                                                                                    <  2:459523/139‑1 (MQ=255)      cTTCCAGGACGACGCAGAACTGCCGTTGGCCTTCAAAGCGCCTTCAGCTATACCGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAGTCTGGCACTCTGTCCGGCCACGTGAACCAGTCTGTTTTTTTTGaa                                                                                                                               >  2:310747/1‑143 (MQ=255)       ttCCAGGACGACGCAGAACTGCCGTTGGCCTTCAAAGCGCCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCTTTTTTTTTTGAATTTtata                                                                                                                        >  1:616849/1‑149 (MQ=255)                          tGCCGTTGGCCTTCAAAGCGCCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATCAAATTCGTCTGGCGAATCTGGCACTCTCTCCGGCCAGGTGTACCAGTCTTTTTTTTTTGAATTTTATAAGAGCCATAAAAAACGGTg                                                                                                     >  1:277637/1‑149 (MQ=255)                                                      tGTACTGGGAAAACGACCTCCTTCCTGTCGGATAAAATTCGCCTGGCAACTCTGGCACTCTCTCCGGCCAGGTGAACCAGTCTTTTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTcc                                                                         <  1:36341/149‑1 (MQ=255)                                                                     aCATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCAATCTCTCCGGCCAGGTGAACCAGTCTTTTTTTTTTTATTTTTATAAGTTCTATAAAAAACGGTGCGAAGGCTGTTTTATTAAGCACTTTTCTGCACAACtt                                                                >  2:342166/1‑143 (MQ=255)                                                                       aTTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCTTTTTTTTTTTTTTTTTTTATGTGCTTTAAACAACGGTGCGCAGGCGGTTTTCTTCACCACTTTTGCGAACAACtaac                                                              >  2:707718/1‑140 (MQ=255)                                                                       aTTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCTTTTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCCCAACTTATCTTCAt                                                        >  1:203210/1‑149 (MQ=255)                                                                               tGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCTTTTTTTTTTGAATTTTATAAGACCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTc                                                      >  2:156167/1‑143 (MQ=255)                                                                                     atatAATTCGACTGGCAAACCTGGCACTCTCTCCGGCCAGGTGATCCAGTCTTTTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTGGACt                                          <  1:506063/149‑1 (MQ=255)                                                                                         aaTTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCTTTTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTGGACTGccg                                      >  1:10162/1‑147 (MQ=255)                                                                                         aaTTCGACTGGCAAATCTGGCACCTTCTCCCGCCAGGCGAACCAGTCTTTTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTGGa                                            <  2:244910/143‑1 (MQ=255)                                                                                              gACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCTTTTTTTTTTGAATTTTTTAATAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTGGACTGCAGGCttt                                 >  1:708341/1‑149 (MQ=255)                                                                                                   gcagctCTGGGCCTCTCCCCGGCCAGGTGACCCAGTCTTTTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTGGACTGCAGGCTTTCATGa                            <  1:356333/144‑1 (MQ=255)                                                                                                     aaaTCTGGCACTCTCTCCGGCCAGGTGAACCAGTCTTTTTTTTTTGAAGTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTATCTTCAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTTTGGACTGCCGGCGTTa                                >  2:511744/1‑143 (MQ=255)                                                                                                       aTCTGGCACTCTCTCCGGCCAGGTGAACCAGTCTTTTTTTTTTGATTTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCCTTCTTGCTGTGGACTGCATGCTTTAAt                              >  2:129903/1‑143 (MQ=255)                                                                                                           ggCACTCTCTCCGGCCAGGTGAACCAGTCTTTTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTACTTCGTACTGTGAGCTGCAGGCTTTAATGATAAGAtct                    >  1:688762/1‑147 (MQ=255)                                                                                                                tctctcCGGCCAGGTGAACCAGTCTTTTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTGGACTGCAGGCTTTAATGATAAGATTTGTgcg               >  1:614567/1‑149 (MQ=255)                                                                                                                       ggCCAGGTGAACCAGTCTTTTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTGGACTGCAGGCTTTAATGATAAGATTTGTGCGCTAAATa        >  1:115126/1‑149 (MQ=255)                                                                                                                       ggCCAGGTGAACCAGTCTTTTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGGTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTTGACTGCAGGCTTTAATGATAAGTTTTGTGCGGTAAATa        >  1:115086/1‑149 (MQ=255)                                                                                                                           aGGTGGACCAGTCTTTTTTTTTTGAATTGTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTGGACTGCAGGCTTTAATGATAAGATTTGTGCGCTaaa          <  2:288568/143‑1 (MQ=255)                                                                                                                             gTGAACCAGTCTTTTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTGGACTGCAGGCTTTAATGATAAGATTTGTGCGCTAAATACGTTTg  >  1:728697/1‑149 (MQ=255)                                                                                                                                        |                                                                                                                                          GTGACCTTCCAGGACGACGCAGAACTGCCGTTGGCCTTCAAAGCGCCTTCAGCTGTACTGGCATAACGACATTTATACTGTCGTATAAAATTCGACTGGCAAATCTGGCACTCTCTCCGGCCAGGTGAACCAGTCGTTTTTTTTTGAATTTTATAAGAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTAAGCACTTTTCCGCACAACTTATCTTCATTCGTGCTGTGGACTGCAGGCTTTAATGATAAGATTTGTGCGCTAAATACGTTTG  >  CP009273/103896‑104168

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑