Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,400,254	C→T	intergenic (+52/‑34)	miaA → / → hfq	tRNA dimethylallyltransferase/RNA‑binding protein Hfq

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,400,254	0	C	T	100.0%	112.1 / NA	33	intergenic (+52/‑34)	miaA/hfq	tRNA dimethylallyltransferase/RNA‑binding protein Hfq
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (19/14);  total (19/14)

TGTGGTCTTACCTTGAAGGCGAAATCTCATACGATGAAATGGTTTATCGAGGTGTTTGCGCCACGAGACAGTTGGCGAAGCGGCAGATAACCTGGCTGCGTGGTTGGGAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCAC  >  NC_000913/4400012‑4400500                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                       tgtgGTCTTACCTTGAAGGCGAAATCTCATACGATGAAATGGTTTATCGAGGTGTTTGCGCCACGAGACAGTTGGCGAAGCGGCAGATAACCTGGCTGCGTGGTTGGGAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTTAAAGTAc                                                                                                                                                                                                                                                 >  1:216125/1‑250 (MQ=255)        ttACCTTGAAGGCGAAATCTCATACGATGAAATGGTTTGTCGAGGGGATTGCGCCACTAGACAGTTGGCGAAGCGGCAGATAACCTGGATGCGTAGTTGGCAAGGGGTTCACTAGCTTAACAGTGAAAAACCAGAACAGGCGCGTGACGACGTATTAAAGGTTGGTGGTGCTATCGAAGGATGAATGTGTACAATTGAGACTTATCATGCGCGATTTTTTCAGAATCGAAAGGTTTAAAGTACAATTAAGc                                                                                                                                                                                                                                         >  1:138096/1‑251 (MQ=255)         tACCTTGAAGGCGAAATCCCATACGATGAAATGGTTTATCGAGGTGTTTGCGCCACGAGACAGTTGGCGAAGCGGCAGATAATCCGGCTGCGTGGTTGGGAAGGGGTTCACTGTCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTACTATCGCAGGCTGAATGTGTTCAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGTAAGGTTTAAAGTACAAATAAGc                                                                                                                                                                                                                                         <  2:298415/250‑1 (MQ=255)            cTTGAAGGCGAAATCTCATACGATGAAATGGTTTATCGAGGTGTTTGCGCCACGAGACAGTTGGCGAAGCGGCAGATAACCTGGCTGCGTGGTTGGGAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTTAAAGTACAAATAAGCatat                                                                                                                                                                                                                                     >  2:132749/1‑251 (MQ=255)              tGAAGGCGAAATCTCATACGATGAAATGGTTTATCGAGGTGTTTGCGCCACGAGACAGTTGGCGAAGCGGCAGATAACCTGGCTGCGTGGTTGGGAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTTAAAGTACAAATAAGCAtata                                                                                                                                                                                                                                    >  2:177015/1‑250 (MQ=255)                                cGATGAAATGGTTTATCGAGGTGTTTGCGCCACGAGACAGTTGGCGAAGCGGCAGATAACCTGGCTGCGTGGTTGGGAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTTAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCt                                                                                                                                                                                                                 >  1:167115/1‑251 (MQ=255)                                 gATGAAATGGTTTATCGAGGTGTTTGCGCCACGAGACAGTTGGCGAAGCGGCAGATAACCTGGCTGCGTGGTTGGGAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGCATCGAAAGGGTTAAAGTACAAATAAGCCTATAAGGAAAAGAGAGAATGGCt                                                                                                                                                                                                                 >  2:57776/1‑250 (MQ=255)                                    gAAATGGTTTATCGAGGTGTTTGCGCCACGAGACAGTTGGCGAAGCGGCAGATAACCTGGCTGCGTGGTTGGGAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTGCGCAATTGTTTCAGAATCGAAAGGTTTAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAg                                                                                                                                                                                                              <  2:43505/250‑1 (MQ=255)                                                 gAGGTGTTTGCGCCACGAGACAGTTGGCGAAGCGGCAGATAACCTGGCTGCGTGGTTGGGAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTTAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACa                                                                                                                                                                                                <  1:63648/251‑1 (MQ=255)                                                        gtGCGCCTCGAGACAGTTGGCGAAGCGGCAGATAACCTGGCTGCGTGGTTGGGAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTTAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATcc                                                                                                                                                                                          <  2:168068/249‑1 (MQ=255)                                                                               aGCGGCAGATAACCTGGCTGCGTGGTTGGGAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTTAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCggg                                                                                                                                                                   >  1:315681/1‑250 (MQ=255)                                                                                 cGGCAGATAACCTGGCTGCGTGGTTGGGAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGCATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTTAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAAc                                                                                                                                                                >  1:244201/1‑251 (MQ=255)                                                                                       aTAACCTGGCTGCGTGGTTGGGAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTTAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTc                                                                                                                                                          <  1:56987/251‑1 (MQ=255)                                                                                                   cGTGGTTGGGAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTTAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCtattt                                                                                                                                              <  1:57776/251‑1 (MQ=255)                                                                                                           ggAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTTAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTg                                                                                                                                      <  1:177015/251‑1 (MQ=255)                                                                                                                              gACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTCTCGCAGGCCGAATGTGTGCAATTGAGACTGATCGTGCGCAATGTTGTCAGATTCGAAAGGTTTAAAGTACAAATAAGCATATAAGGCAAAGAGAGAATGGCTAAGGGGCAATCTTTTCAAGTTTCGTTCCTGAGCGCTCTGCGTAGTGAACGTGTTCCAGTTGCTATTTATGTGGTGAATGGTATTTAGCTGCAAg                                                                                                                   <  2:138096/251‑1 (MQ=255)                                                                                                                                  gTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTAGTTGCTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGAGCGCAATTTTTTCCAAATCGAAAGGTTTACAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGAACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGATATTAAGCTGCAAGGGc                                                                                                                >  1:314691/1‑250 (MQ=255)                                                                                                                                    gAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTTAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCaa                                                                                                              >  1:17218/1‑250 (MQ=255)                                                                                                                                                                      aGGTTGATGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTTAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGATCCTGTTGa                                                                            >  1:249833/1‑250 (MQ=255)                                                                                                                                                                                    aTCGCAGGCTGAATGTGTACAATTGAGAAGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTTAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGc                                                              <  2:27255/250‑1 (MQ=255)                                                                                                                                                                                       gCAGGCTGAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTTAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGa                                                          <  1:4341/251‑1 (MQ=255)                                                                                                                                                                                              gAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTTAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGttt                                                    >  1:225966/1‑250 (MQ=255)                                                                                                                                                                                              gAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTAAGAATCGAAAGGTTTAAAGTACAAATAAGCATATAAGGAAAAGAGAGACTGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGttt                                                    >  1:27924/1‑250 (MQ=255)                                                                                                                                                                                                  gtgtACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTTAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGt                                                                                                                                >  1:206759/1‑170 (MQ=255)                                                                                                                                                                                                  gtgtACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTTAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTGTCTATTTATTTGGTGAATGGt                                                                                                                                <  2:206759/170‑1 (MQ=255)                                                                                                                                                                                                               aCGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTTAAAGTACAAATAAGCATATAAGGAAAAgagaga                                                                                                                                                                                                                       >  2:70229/1‑70 (MQ=255)                                                                                                                                                                                                               aCGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTTAAAGTACAAATAAGCATATAAGGAAAAgagaga                                                                                                                                                                                                                       <  1:70229/70‑1 (MQ=255)                                                                                                                                                                                                                  tATCGTGCGCAATTTTTTCAGAATCGAAAGATTTAAAGTAACAATATGAATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACtg                               >  1:294653/1‑251 (MQ=255)                                                                                                                                                                                                                             aTTTTTTCAGAATCGAAAGGTTTAAAGTACCACTAAGCCTATCAGGAAAAGAGACAATGGCTAAGGGGCAATCTTTACGAGATCCGTTCCTGACCGCACTGCGTCGGGACCGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTCAGCTGCAAGAGCAAATCGCGTCTTTTGATCAGTTCGTGATCCTGTTGAAAAACACGGCCAGCCCGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGtct                    >  1:259034/1‑251 (MQ=255)                                                                                                                                                                                                                                       aaTCGAAAGGTTTAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGTGAACGTGTTCCATTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCTGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTTTCCCGTCTCGCCCGGttt          <  2:102763/251‑1 (MQ=255)                                                                                                                                                                                                                                       aaTCGAAAGGTTTAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTa                                                                                                                               >  2:142102/1‑134 (MQ=255)                                                                                                                                                                                                                                       aaTCGAAAGGTTTAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTa                                                                                                                               <  1:142102/134‑1 (MQ=255)                                                                                                                                                                                                                                               ggTTTAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCCCTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAGATCGAGTCTTTTGATCAGATCGTGATCCTGTTGAAAAACACGGTCCGCCAGATGGTTTACAAGCACGCGAATTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATcac  >  1:218472/1‑251 (MQ=255)                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                       TGTGGTCTTACCTTGAAGGCGAAATCTCATACGATGAAATGGTTTATCGAGGTGTTTGCGCCACGAGACAGTTGGCGAAGCGGCAGATAACCTGGCTGCGTGGTTGGGAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCAC  >  NC_000913/4400012‑4400500

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑