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%	52.3 / NA	18	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 (10/8);  total (10/8)

GATGCCAGTTTGCGGTCAAGCGCACAAATCATATGAAAAATGAATGCTTATACTGAAGACCGCGCTTCGGTAAAAAGATAATTCTGAATAATTGTAACCTTTAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGGAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGAAGGATAAGCTGCATTTGTCAGTGATGTCCGAAGTTAACCGTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCT  >  NC_000913/4439353‑4439820                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                                   gATGCCAGTTTGCGGTCAAGCGCACAAATCATATGAAAAAGGAATGCTTATACTGAAGACCGCGCTTCGGTAAAAAGATAATTCTGAATAATTGTAACCTTTAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACTATTAAAATTTTCCAACg                                                                                                                                                                                                                           <  1:302703/251‑1 (MQ=255)                               atatGAAAAATGAATGCTTATACTGAAGACCGCGCTTCGGTAAAAAGATAATTCTGAATAATTGTAACCTTTAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGt                                                                                                                                                                                             >  1:196060/1‑251 (MQ=255)                                                                         aaaaGATAATTCTGAATAATTGTAACCTTTAGGAAAAAAAATTTATACGCGGTTGAAACATTACCCGGATAGTCTATAGTCACTAAACATTAAAATTTGCGCCTCATAATAGTTGGGCCGAGTGTGGCACCGCACAAGCGTAATACTCAGCAGAATATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCAAAGTACGACAAGATCCTGATCTGATGAGGATTATACATCAAGGACGTTgg                                                                                                                                                   >  2:130323/1‑251 (MQ=255)                                                                                       aataatTTTAATCTTTAAGTAAAAAAAGTTATACGCGGTGTAAACATTGCCCGGATAGTTTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAACGACGTTGGCGCTTTTGAATTCg                                                                                                                                     <  2:59416/251‑1 (MQ=255)                                                                                         aaatttgaaCCTTTATGTAAAAAAAGGTATACGCGGTGGAAACAGTGCCCGGATATTCTATAGTCACTAAGCAGTAAAAGTTGGTCCGCATAATAGTTGGGCCGATTGGGGCACCGCACATGCGTAATACTCAGCAGAAGAGAACAATGAAAATTTTCCAACGGTGCTACCGACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTTGCGCGTTTGAAGTCGAt                                                                                                                                   <  2:348998/244‑1 (MQ=255)                                                                                                             aaacaGTTATACGAGGTGGAAACATTGCCCGGATAGACTATAGTCACTAAGCATTAAACTTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTACTACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACACACTTCAGGTGGCGAAGTACGGAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCACTTTTGGATTCGATAAGGGGAAGATTCTTATccc                                                                                                               >  1:238073/5‑251 (MQ=255)                                                                                                              aaaaGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATccc                                                                                                               >  1:10962/1‑250 (MQ=255)                                                                                                                 aGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCACaaa                                                                                                            >  1:56509/1‑250 (MQ=255)                                                                                                                         gcgGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGAAGGa                                                                                                   <  1:122717/251‑1 (MQ=255)                                                                                                                                       gCCCTGATAGGCTATAGTAAATAAGCATTAAAATTTGCGCCTCATAATATTTGGGCCTCTTGTGGCACCGCACAGGCGTAATACTCAGCATAAGATAACAAAGAATATTTTCCAACTGGACAACCAACTTCATGTGGCTAAGTACGTAAAGATCCTGTTCCTTGGACGGGTATACATCAAGGACGTTGTCGCTTTTGAATTCTATAAGGGTTAGATTCTTATCCCAAAAGTGAAGGATAAGCTGCATTTg                                                                                      <  2:230520/250‑1 (MQ=255)                                                                                                                                             aTAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGAAGGATAAGCTGCATTTGTCAGTg                                                                                >  1:119816/1‑250 (MQ=255)                                                                                                                                                          aCTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACCATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCACAAAAGTGAAGGATAAGCTGCATTTGTCAGTGATGTCCGCAGTTa                                                                   >  1:293523/1‑250 (MQ=255)                                                                                                                                                                                    aataGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAAAGAAAATTTTCCAACGGTACAACCCACCTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGAAGGATAAGCTGCATTTGTCAGTGATGTCCGAAGTTAACCGTCAGGTTATGCGTCTGCAAACag                                        <  2:313205/251‑1 (MQ=255)                                                                                                                                                                                        gTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGAAGGATAAGCTGCATTTGTCAGTGATGTCCGAAGTTAACCGTCAGGTTATGCGTCTGCAAACag                                        >  1:348227/1‑247 (MQ=255)                                                                                                                                                                                                gATTGTGGCACCGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGAAGGATAAGCTGCATTTGTCAGTGATGTCCGAAGTTAACCGTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAAc                            >  1:78844/1‑251 (MQ=255)                                                                                                                                                                                                 aTTGTGGCACCGCACAGGCTTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAATGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGAAGGATAAGCTGCATTTGTCAGTGATGTCCGAAGTTAACCGTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAAcc                           <  1:29865/251‑1 (MQ=255)                                                                                                                                                                                                    gtgGCACAGCACAGGCGTAATACTCAGCAGAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGAAGGATAGGCTGCATTTGTACGTGATGTCCGAAGTTAACCGTACGGTTATGCGTCTGCAAACAGAGATGGCTTAACCac                         >  2:143531/1‑249 (MQ=255)                                                                                                                                                                                                                            cagcagAAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGAAGGATAAGCTGCATTTGTCAGTGATGTCCGAAGTTAACCGTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCaaagtgctatgcagtaaaaagtgct  <  1:31919/249‑1 (MQ=255)                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                                   GATGCCAGTTTGCGGTCAAGCGCACAAATCATATGAAAAATGAATGCTTATACTGAAGACCGCGCTTCGGTAAAAAGATAATTCTGAATAATTGTAACCTTTAGGTAAAAAAAGTTATACGCGGTGGAAACATTGCCCGGATAGTCTATAGTCACTAAGCATTAAAATTTGCGCCTCATAATAGTTGGGCCGATTGTGGCACCGCACAGGCGTAATACTCAGCAGGAGATAACAATGAAAATTTTCCAACGGTACAACCCACTTCAGGTGGCGAAGTACGTAAAGATCCTGTTCCGTGGACGGTTATACATCAAGGACGTTGGCGCTTTTGAATTCGATAAGGGTAAGATTCTTATCCCAAAAGTGAAGGATAAGCTGCATTTGTCAGTGATGTCCGAAGTTAACCGTCAGGTTATGCGTCTGCAAACAGAGATGGCTTAACCAAAGTGCTATGCAGTAAAAAGTGCT  >  NC_000913/4439353‑4439820

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑