Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	707,910	A→G	100%	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%	61.9 / NA	19	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 (9/10);  total (9/10)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTT  >  USA300TCH1516_ALE/707782‑708035                                                                                                                                 |                                                                                                                              gAAAATTTACCAGCTCCATTTGGGGCCATGATACCAATTATTTTGCCGCGTATTGGTATCGATAAGGAAATTTATTTAACTACATGCTGATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATAcctc                                                                                                                   <  1:108757/141‑1 (MQ=255)     aTTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTGTCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACACGCGTTTATTCCTCCTac                                                                                                               >  1:33804/1‑140 (MQ=255)         aCCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTaa                                                                                                           >  1:122800/1‑141 (MQ=255)          ccAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTaaa                                                                                                          >  1:103167/1‑141 (MQ=255)                        gCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAAcc                                                                                            <  1:398956/141‑1 (MQ=255)                           cATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCtaa                                                                                         <  1:353988/141‑1 (MQ=255)                                   cAATTATTTCGCCGCGTAATAGTATCAACAAGGAAATGTTTTTAAGTACATGCTTTTTACCTAAAAACAGATTTAAATCTTTTTTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGt                                                                                 <  1:7496/141‑1 (MQ=255)                                    aaTTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGta                                                                                <  1:180308/141‑1 (MQ=255)                                      ttattTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGtata                                                                              <  1:407642/141‑1 (MQ=255)                                           tCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATaaa                                                                         >  1:175685/1‑141 (MQ=255)                                             gccgcGTACTGGTATCGATAAGGAAATGTTTTTAAGTCAAGGCATATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACt                                                                       >  1:458926/1‑141 (MQ=255)                                                 cgTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTgaga                                                                   >  1:226918/1‑141 (MQ=255)                                                          aTCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATc                                                          <  1:365281/141‑1 (MQ=255)                                                                              aaGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTGTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATTTCAAGTAAATTCGTGat                                      >  1:46102/1‑141 (MQ=255)                                                                               aGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGata                                     <  1:136496/141‑1 (MQ=255)                                                                                  aCATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGatataa                                  <  1:295820/141‑1 (MQ=255)                                                                                        ttattaCCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGa                            >  1:445203/1‑141 (MQ=255)                                                                                                       aGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGt             <  1:245842/141‑1 (MQ=255)                                                                                                                  ttttGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTCTCCTGACGTATAGATCCGTGATATAGTATAGACAGTAAATGTGACGTGCAAGTATGtt  >  1:454322/1‑141 (MQ=255)                                                                                                                                 |                                                                                                                              GAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTT  >  USA300TCH1516_ALE/707782‑708035

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: ‑