Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,207,739	A→C	100%	D445A (GAT→GCT)	rpoD →	RNA polymerase, sigma 70 (sigma D) factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,207,739	0	A	C	100.0%	119.1 / ‑6.7	36	D445A (GAT→GCT)	rpoD	RNA polymerase, sigma 70 (sigma D) factor
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base C (17/18);  total (17/19)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GTTAAAGATATCAACCGTCGTATGTCCATCGGTGAAGCGAAAGCCCGCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGATCCGCAAAGTGCTGAAGATCGCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGA  >  CP009273/3207477‑3207979                                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                 gTTAAAGATATCATCCGTCGTATTTCCATCGGTGAAGCGAAAGCCCGCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCAc                                                                                                                                                                                                                                      <  1:305986/275‑1 (MQ=255) gTTAAAGATATCAACCGTCGTATGTCCATCGGTGAAGCGAAAGCCCGCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGgcgcg                                                                                                                                                                                                                                         <  1:195136/272‑1 (MQ=255) gTTAAAGATATCAACCGTCGTATGTCCATCGGTGAAGCGAAAGCCCGCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGgcgcg                                                                                                                                                                                                                                         >  2:195133/1‑272 (MQ=255)    aaaGTTATCATCCGTCGTATGTCCATCGGTGAAGCGAAAGCCCGCCGTGCTAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGTTAAGAAATACTCCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGGCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCAt                                                                                                                                                                                                                                   <  1:390199/275‑1 (MQ=255)           tCAACCGTCGTATGTCCATCGGTGAAGCGAAAGCCCGCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTNTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTAtt                                                                                                                                                                                                                            >  1:614654/1‑275 (MQ=255)                 gtcgtATGTCCATCGGTGAAGCGAAAGCCCGCCGTTGGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGTTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCTATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGt                                                                                                                                                                                                                       <  1:432073/274‑1 (MQ=255)                    gtttgtcgttaggTGAAGCGGAAGCCCGACGTGCGAAGAAAGAGATGGTTGAAGCGAACTTATGTCTTGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCCTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAAGTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCat                                                                                                                                                                                                                   <  2:81198/264‑1 (MQ=255)                    gtATGTCCAGCGGTGAAGCGAAAGGCCGCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTACTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCat                                                                                                                                                                                                                   <  2:667657/275‑1 (MQ=255)                            aTCGGTGAAGCGAAAGCCCGCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGAtt                                                                                                                                                                                                             >  2:654940/1‑273 (MQ=255)                              cGGTGAAGCGAAAGCCCGCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCAACCGCTCTATCACGGCCCAAGCGCGCAACATCCGTATTCCGGTGCATATGCTTgag                                                                                                                                                                                                          >  1:308486/1‑274 (MQ=255)                                   aaGCGAAAGCCCGCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCCCAGGCGCGCACCATCCGt                                                                                                                                                                                                                               >  2:326754/1‑248 (MQ=255)                                       gAAAGCCCGCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTc                                                                                                                                                                                                                           <  1:326760/248‑1 (MQ=255)                                                                  ggtgtaaGCGGACTTACGTCTTGTTATTTCTATCGCGAAGAAATACACCAACCGTTGCTTGCAGTTCATTGACCTGATTCAGGAAGGCAACATCGGTCGGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCCACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGa                                                                                                                                                                        <  2:691105/267‑1 (MQ=255)                                                                                       ggTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCa                                                                                                                                                                                                                                       >  2:63394/1‑188 (MQ=255)                                                                                           aTTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCAt                                                                                                                                                                                                                                   <  1:63395/188‑1 (MQ=255)                                                                                           aTTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGAc                                                                                                                                            <  1:654949/275‑1 (MQ=255)                                                                                                         aaaaaACACCACTAGTGGGTTGCTGTTCCTTGACCGGATTCAGGAAGGCAACATTGGTCTGATGAACGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGgacggacgat                                                                                                                              <  2:614645/274‑9 (MQ=255)                                                                                                                     ccGTGGCTTGCAGTTCCTTGTCCTGATTCAGGAAGGCAACATCGATCTGATGAAAGCGGTTGATAAATTCGAATACAGCCGTGGTTACAAGTTCTACACCTCCGCAACCTGGTGGATCCGTCAGGCGATCACACGCGCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGCGCATATGAtgg                                                                                                                                                                                                            >  1:324271/1‑183 (MQ=255)                                                                                                                                       tGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATcaacaa                                                                                                                                                                                               >  1:201556/1‑180 (MQ=255)                                                                                                                                           cTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTc                                                                                                                                                                                           <  2:201553/180‑1 (MQ=255)                                                                                                                                                   ggAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGt                                                                                                                                                                                                                               >  2:626120/1‑136 (MQ=255)                                                                                                                                                       ggCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTc                                                                                                                                                                                                                           <  1:626129/136‑1 (MQ=255)                                                                                                                                                        gCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCAGAACGTATGCTGATGCCGGAAGACAAGATCCGAAAAGTGCTGAAg                                                                               >  1:146663/1‑275 (MQ=255)                                                                                                                                                            cATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACACGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGAtgctgc                                                                                                                                                                  <  1:98951/188‑1 (MQ=255)                                                                                                                                                               cGGTCTGATAACGCCGGTTGCTAACTTCGCATCCCGCCGTGTTTCCCATTTCTCCACCTCCGCAACTTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGATCCGCAAAGTGCTGAAGATCGCCa                                                                        <  2:146662/275‑1 (MQ=255)                                                                                                                                                                                ttGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTc                                                                                                                                                                                                                           >  2:324121/1‑111 (MQ=255)                                                                                                                                                                                    tAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGt                                                                                                                                                                                                                       <  1:324127/111‑1 (MQ=255)                                                                                                                                                                                                 cgccgTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCCCCCGCTCTATCGCGGCTCCGGCGCGCACCATCCGTATTCCGGTTCATATGATTGAGACCAt                                                                                                                                                                                                     >  1:261157/1‑116 (MQ=255)                                                                                                                                                                                                                  ctcCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGgcgc                                                                                                                                                                                                                                          >  1:78501/1‑62 (MQ=255)                                                                                                                                                                                                                      aCCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCAc                                                                                                                                                                                                                                      <  2:78500/62‑1 (MQ=255)                                                                                                                                                                                                                          aCGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGACTGCACGTATGCTGATGCCGGACGACAAGGTCCg                                                                                            >  1:124016/1‑196 (MQ=255)                                                                                                                                                                                                                                     tggATCCGTCAGGCGATCACGCGCTCTATCGCGGCTCATGCGCGCACGATCCGTATTCCGGTGCATATGATTGAGACGATCAACAAGCTCAACCGTATTTGTCGCCAGATCCTGCAAGAGATTTGCCGTGAACCGACGCGGGAAGAAc                                                                                                                                 >  2:543333/1‑148 (MQ=255)                                                                                                                                                                                                                                     tggATCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCACCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGATCCGCAAAGTGCTGAAGATCGCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGAGGGATATCATCGAGGa  >  1:353255/1‑275 (MQ=255)                                                                                                                                                                                                                                         tCCGTCAGGCGATCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGc                                                                                                                             <  1:543342/148‑1 (MQ=255)                                                                                                                                                                                                                                                    aTCACCCGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATcaaca                                                                                                                                                                                                >  2:351950/1‑70 (MQ=255)                                                                                                                                                                                                                                                        cccGCTCTATCGCGGCTCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCt                                                                                                                                                                                            <  1:351956/70‑1 (MQ=255)                                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                 GTTAAAGATATCAACCGTCGTATGTCCATCGGTGAAGCGAAAGCCCGCCGTGCGAAGAAAGAGATGGTTGAAGCGAACTTACGTCTGGTTATTTCTATCGCTAAGAAATACACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGCTCTATCGCGGATCAGGCGCGCACCATCCGTATTCCGGTGCATATGATTGAGACCATCAACAAGCTCAACCGTATTTCTCGCCAGATGCTGCAAGAGATGGGCCGTGAACCGACGCCGGAAGAACTGGCTGAACGTATGCTGATGCCGGAAGACAAGATCCGCAAAGTGCTGAAGATCGCCAAAGAGCCAATCTCCATGGAAACGCCGATCGGTGATGATGAAGATTCGCATCTGGGGGATTTCATCGAGGA  >  CP009273/3207477‑3207979

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑