Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	707,910	A→G	intergenic (‑1/‑121)	znuC_1 ← / → ideR	High‑affinity zinc uptake system ATP‑binding protein ZnuC/Iron‑dependent repressor IdeR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	707,910	0	A	G	100.0%	95.9 / NA	29	intergenic (‑1/‑121)	znuC_1/ideR	High‑affinity zinc uptake system ATP‑binding protein ZnuC/Iron‑dependent repressor IdeR
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (18/11);  total (18/11)

AAGACTTGATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTGAAGAAAAAGAGG  >  USA300TCH1516_ALE/707768‑708052                                                                                                                                               |                                                                                                                                               aaGACTTGATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGttt                                                                                                                                           >  1:137393/1‑148 (MQ=255) aaGACTTGATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGttt                                                                                                                                           >  1:76031/1‑148 (MQ=255) aaGACTTGATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGttt                                                                                                                                           >  1:442135/1‑148 (MQ=255)    aCTTGATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTtata                                                                                                                                        >  1:296920/1‑148 (MQ=255)           aaGGCAAGATTTACCAGCACCATTCGGGCCCATGATTCCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTa                                                                                                                                 <  1:154876/148‑1 (MQ=255)             gggAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTACATCTTTTGTTTCTAACAAGAGTTTATACCTCCTAAt                                                                                                                               >  1:35641/1‑148 (MQ=255)             gggAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAAt                                                                                                                               >  1:270814/1‑148 (MQ=255)                aaGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTCATTaa                                                                                                                            >  1:259678/1‑148 (MQ=255)                                              tACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTataa                                                                                              <  1:458794/148‑1 (MQ=255)                                                          cgccgcGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAat                                                                                  >  1:635702/1‑148 (MQ=255)                                                                 tACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATc                                                                           <  1:92541/148‑1 (MQ=255)                                                                         tCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAg                                                                   <  1:627892/148‑1 (MQ=255)                                                                                ggAAATGTTTTTAAGTACATGCTTATTAACTAAAAACAGATTTAAATCTTTTTTTTCTAATAAGCGGTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAAGAAACTGAGAATATTTATCGTGTCAAGTAAATTc                                                            >  1:385953/1‑148 (MQ=255)                                                                                 taaaTGTTTTTAAGTACATGTTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCg                                                           <  1:540252/147‑1 (MQ=255)                                                                                 gAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCg                                                           <  1:469135/148‑1 (MQ=255)                                                                                   aaTGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTg                                                         >  1:162011/1‑148 (MQ=255)                                                                                   aaTGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTg                                                         <  1:45601/148‑1 (MQ=255)                                                                                    aTGTTTTGAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTACTTGGATAATAATCTGAGAATATTTATCATGTCAAGTAAATTCGTGa                                                        <  1:564070/148‑1 (MQ=255)                                                                                            aattACATGCTAATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGatataatat                                                <  1:327035/145‑1 (MQ=255)                                                                                               tACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGa                                             >  1:548446/1‑148 (MQ=255)                                                                                                      ttattaCCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAatgta                                      <  1:247465/148‑1 (MQ=255)                                                                                                          taCCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTAtgtg                                  <  1:417309/148‑1 (MQ=255)                                                                                                                  aaCAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAAGGTATGTGAGGTGaag                          >  1:23214/1‑147 (MQ=255)                                                                                                                             aTCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATACTAAACTGAGAATATTTATCATTTCAAGTAATTTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTACCt               >  1:39362/1‑148 (MQ=255)                                                                                                                             aTCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACt               >  1:508448/1‑148 (MQ=255)                                                                                                                              tCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAAGTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTg              >  1:494125/1‑148 (MQ=255)                                                                                                                                  ttGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTgaaga          >  1:186663/1‑148 (MQ=255)                                                                                                                                   tttttCTAACAAGCGTTTATACCTCCTAATTAACGGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTgaagaa         >  1:184681/3‑148 (MQ=255)                                                                                                                                          aaCAAGCGTTTATACCTCCTAATTAAAAGTTTATGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTGAAGAAAAAGAgg  >  1:448989/1‑148 (MQ=255)                                                                                                                                               |                                                                                                                                               AAGACTTGATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTGAAGAAAAAGAGG  >  USA300TCH1516_ALE/707768‑708052

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑