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%	42.7 / NA	14	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 (4/10);  total (4/10)

CGAATTTCCCGCAAGTGTGATGCCAGTTTGCGGTCAAGCGCACAAATCATATGAAAAATGAATGCTTATACTGAAGACCGCGCTTCGGTAAAAAGATAATTCTGAATAATTGTAACCTTTAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGGAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGAAG  >  NC_000913/4439335‑4439721                                                                                                                                                                                                                                                    |                                                                                                                                                cGAAGTTCCCGCAAGTGTGATGCCAGTTGGCGGTCAAGCGCACAAATCATATGAAAAATGAATGCTTATACTGAAGACCTCGCTTCGGTAAAAAGATAATTCTGAATAATTGTAACCTTTAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATaa                                                                                                                                           <  1:41037/250‑1 (MQ=255)          cGCAAGTGTGATGCCAGTTTGCGGTCAAGCGCACAAATCATATGAAAAATGAATGCTTATACTGAAGGCCGCGCTTCGGGAAAAAGATAATTCTGAATAATTGGAACCTTTAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCCCTAAGCATTAAAATCTGCTCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAAt                                                                                                                                 <  1:23450/251‑1 (MQ=255)                   gATGCCAGTTTGCGGTCAAGCGCACAAATCATATGAAAAATGAATGCTTATACTGAAGACCGCGCTTCGGTAAAAAGATAATTCTGAATAATTGTAACCTTTAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAAc                                                                                                                         <  1:193794/250‑1 (MQ=255)                               cGGTCAACCGCACAAATCATATGAAAAATGAATGCTTATACTGAAGACCGCGCTTCGGTAAAAAGATAATTCTGTATAATTGTAACCTTTAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTACGCATTAAAATTTGCGCCTCATAATAGATGGGCCGATTGTGCCACCGCATAGGCGTAATACTCAGCTGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACt                                                                                                            >  1:109438/1‑251 (MQ=255)                                 gTCAAGCGCACAAATCATATGAAAAATGAATGCTTATACTGAAGACCGCGCTTCGGTAAAAAGATAAGTCTGAATAATTGTATCCTTTAGGTAAAAAAAGGTAGACGCGGAGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATCCTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTc                                                                                                          <  1:133396/251‑1 (MQ=255)                                      gcgcACAAATCATATGAAAAATGAATGCTTATACTGAAGACCGCGCTTCGGTAAAAAGATAATTCTGAATAATTGTAACCTTTAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTg                                                                                                     <  2:78964/251‑1 (MQ=255)                                             aaTCATATGAAAAATGAATGCTTATACTGAAGACCGCGCTTCGGTAAAAAGATAATGCTGAATAATTGTAACCTTTAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGt                                                                                              <  1:145083/251‑1 (MQ=255)                                                                      accgAAGACCGCGCTTCGGTAAAAAGATAATTCTGAATAATTGTAACCTTTAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAAGTTGCGCCGCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGGAATACTCAGCAGAAGATAACAATTAAAATTTTCCAACGGTACAACCCACTGCAGGTGGCGAAGGACGTAAAGATCCTGTGGCGTGGAc                                                                      <  2:159701/247‑1 (MQ=255)                                                                                  gcTTCGGTAAAAAGATAATTCTGAATAATTGTAACCTTTAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCaa                                                         <  1:94254/251‑1 (MQ=255)                                                                                     tCGGTAAAAAGATAATTCTGAATAATTGTAACCTTTAGGTAAAAAAAGTTATACGCAGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAgg                                                       <  1:211052/250‑1 (MQ=255)                                                                                                         aataatTGTAACCTTTAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGACTTCg                                  >  2:28824/1‑251 (MQ=255)                                                                                                                gTAACCTTTAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCACCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCgctacggg                           >  2:236334/1‑244 (MQ=255)                                                                                                                  aaCCTATAGGTAAAAAAAGTTATACGCGGTGGAACCATTGCACGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGt                          >  2:182053/1‑250 (MQ=255)                                                                                                                                         aCGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGAAg  <  1:245117/251‑1 (MQ=255)                                                                                                                                                                                                                                                    |                                                                                                                                                CGAATTTCCCGCAAGTGTGATGCCAGTTTGCGGTCAAGCGCACAAATCATATGAAAAATGAATGCTTATACTGAAGACCGCGCTTCGGTAAAAAGATAATTCTGAATAATTGTAACCTTTAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGGAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGAAG  >  NC_000913/4439335‑4439721

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑