Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,439,578	G→A	intergenic (‑316/‑9)	ytfJ ← / → ytfK	PF09695 family protein YtfJ/stringent response modulator YtfK

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,439,578	0	G	A	100.0%	61.1 / NA	20	intergenic (‑316/‑9)	ytfJ/ytfK	PF09695 family protein YtfJ/stringent response modulator YtfK
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (9/11);  total (9/11)

TTCCCGCAAGTGTGATGCCAGTTTGCGGTCAAGCGCACAAATCATATGAAAAATGAATGCTTATACTGAAGACCGCGCTTCGGTAAAAAGATAATTCTGAATAATTGTAACCTTTAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGGAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGAAGGATAAGCTGCATTTGTCAGTGATGTCCGAAGTTAACCGTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATG  >  NC_000913/4439340‑4439823                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                      ttCCCGCAAGTGTGATGCCAGTTTGCGGTCAAGCGCACAAATCATATGAAAAATGAATGCTTATACTGAAGACCGCGCTTCGGTAAAAAGATAATTCTGAATAATTGTAACCTTTAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCCCAGGCGTAATACTCAGCAGAAGATAACAATg                                                                                                                                                                                                                                            >  1:437787/1‑250 (MQ=255)                   cAGTTTGCGGTCAAGCGCACAAATCATATGAAAAATGAATGCTTATACTGAAGACCGCGCTTCGGTAAAAAGATAATTCTGAATAATTGTAACCTTTAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACa                                                                                                                                                                                                                         <  2:226858/251‑1 (MQ=255)                                                gAAAAATGAATGCTTGTACTGAAGACCGCGCTTCGGTAAAAAGATAATTCTGAATAATTGTAACCTTTAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAg                                                                                                                                                                                            <  1:223638/251‑1 (MQ=255)                                                gAAAAATGAATGCTTATACTGAAGACCGCGCTTCGGTAAAAAGATAATTCTGAATAATTGTAACCTTTAGGTAAAAAAAGTTATACGCGGAGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGAGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAATCCACTTCAGGTGGAGAAGTACGTaa                                                                                                                                                                                              >  1:197866/1‑249 (MQ=255)                                                            cTTATACTGAAGACCGAGCTTCGGTAAAAAGATAATTCTGAATAATTGTAACCTTTAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGGACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCgg                                                                                                                                                                                >  1:405595/1‑250 (MQ=255)                                                                                        aaGATAATTCTGAATAATTGTAACCTTGAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGgcg                                                                                                                                                    <  1:229946/251‑1 (MQ=255)                                                                                                      taatTGTAACCTTTAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCCGAAGATAACAATGAAAATTTTCCAACGGAACACACCACTTCAGGTGGCGAAGAACGTAAAGATCCTGTTCCTTGGACGGATATACATCAAGGACGTTGGCGCTTTTGATTTCGa                                                                                                                                       >  2:100256/1‑250 (MQ=255)                                                                                                                  ttAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGa                                                                                                                            <  1:381745/249‑1 (MQ=255)                                                                                                                               ggtataCGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAg                                                                                                             <  1:83052/249‑1 (MQ=255)                                                                                                                                ttATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGAAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACCTCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGt                                                                                                            >  1:10888/1‑251 (MQ=255)                                                                                                                                    aCGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAGATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGaa                                                                                                         <  1:176589/250‑1 (MQ=255)                                                                                                                                     cgcgGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGAAgg                                                                                                       >  1:448023/1‑251 (MQ=255)                                                                                                                                                          aTAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGAAGGATAAGCTGCATTTGTCAGTg                                                                                   >  2:213038/1‑250 (MQ=255)                                                                                                                                                                   aGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGAAGGATAAGCTGc                                                                                              >  2:47096/1‑230 (MQ=255)                                                                                                                                                                   aGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGAAGGATAAGCTGc                                                                                              <  1:47096/230‑1 (MQ=255)                                                                                                                                                                                                        gggCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGAAGGATAAGCTGCATTTGTCAGTGATGTCCGAAGTTAACCGTCAGGTTATGCGTCTGCAAACAGAGATgg                                     <  1:213038/250‑1 (MQ=255)                                                                                                                                                                                                          gctgATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGAAGGATAAGCTGCATTTGTCAGTGATGTCCGAAGTTAACCGTCAGGTTATGCGTCTGCAAACAGAGATGGCtt                                  <  1:81484/248‑1 (MQ=255)                                                                                                                                                                                                                      aCCGCACAGGCGTAATACTCAGCAGAAGATAACAAGGAAAATTTTCCAACGGTTCAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTAGACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGAAGGATAAGCTGCATTTGTCAGTGATGTCCGAAGTTAACCGTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCaaagtgct                      <  2:405595/251‑1 (MQ=255)                                                                                                                                                                                                                                cGTAATACTCAGCAGAAGAGAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGAAGGATAAGCTGCATTTGTCAGTGATGTCCGAAGTTAACCGTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCaaagtgctatgcagtaaa            <  2:437787/251‑1 (MQ=255)                                                                                                                                                                                                                                          agcagAAGATAACAATGAAAATTATCCAACGGTACAACCCCCTTCAGGAGGCAAAGTACGTAAAGATCCTGTTCCGTGGACGGTTCTACATCAAGGACGTTGGCGATTTTGAATTCGATAAGGGTAAGATTATTATCCCAAAAGGGAAGGATAAGCTGCATTAGTCAGTGATGTCAGAAGTTAAACGTCAGGTTATGCGTCTGAAAACAGAGATGGCTAAACCaaagagctatgtagtaaaaagtgctatg  >  2:281904/1‑251 (MQ=255)                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                      TTCCCGCAAGTGTGATGCCAGTTTGCGGTCAAGCGCACAAATCATATGAAAAATGAATGCTTATACTGAAGACCGCGCTTCGGTAAAAAGATAATTCTGAATAATTGTAACCTTTAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGGAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGAAGGATAAGCTGCATTTGTCAGTGATGTCCGAAGTTAACCGTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCTATG  >  NC_000913/4439340‑4439823

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: ‑