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%	94.1 / NA	27	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 (19/8);  total (19/8)

AAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTGAAGAAA  >  USA300TCH1516_ALE/707783‑708046                                                                                                                                |                                                                                                                                         aaGATTTACCAGCACCAGTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATAcctcc                                                                                                                             <  1:89756/141‑1 (MQ=255)        aCCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATCaa                                                                                                                      >  1:284905/1‑141 (MQ=255)                          cATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCtaa                                                                                                    >  1:27547/1‑141 (MQ=255)                           aTGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCtaat                                                                                                   <  1:250714/141‑1 (MQ=255)                             gATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCtaatta                                                                                                 >  1:464581/1‑141 (MQ=255)                                    attattTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTCATTAAAAGGTTTGGCTAACCTCATTAATTGtat                                                                                          >  1:392314/1‑141 (MQ=255)                                    attattTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGtat                                                                                          >  1:295269/1‑141 (MQ=255)                                       attTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTataat                                                                                       >  1:149448/1‑141 (MQ=255)                                         ttCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTAtaataa                                                                                     >  1:36893/1‑141 (MQ=255)                                             ccgcGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTg                                                                                 >  1:272876/1‑141 (MQ=255)                                                      ggTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTTTTAGTTGATGGTTTAGGCTAAACTAATGAATTGTATAATAAACTGAGAATAttt                                                                        >  1:235768/1‑141 (MQ=255)                                                                aGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAAACCATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCaa                                                              >  1:96612/1‑141 (MQ=255)                                                                 ggAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGACAAg                                                             <  1:341401/141‑1 (MQ=255)                                                                  gAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGt                                                            <  1:329017/141‑1 (MQ=255)                                                                        tttttAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTc                                                      <  1:495999/141‑1 (MQ=255)                                                                                  cATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGGGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGatataat                                            >  1:483733/1‑141 (MQ=255)                                                                                  cATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGatataat                                            >  1:357676/1‑141 (MQ=255)                                                                                   aTGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGatataata                                           <  1:293362/141‑1 (MQ=255)                                                                                                  aaaCAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTACTAATTAGAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTAtgtg                            >  1:390082/1‑141 (MQ=255)                                                                                                   aaCAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGa                           <  1:457308/141‑1 (MQ=255)                                                                                                     cAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATCCGTGATATAATATAGACAATGTAGTTGAgg                         >  1:212728/1‑141 (MQ=255)                                                                                                       gATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTg                       >  1:487647/1‑141 (MQ=255)                                                                                                           tAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAg                   >  1:374416/1‑141 (MQ=255)                                                                                                           tAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAg                   <  1:308770/141‑1 (MQ=255)                                                                                                                          tAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAGGTATGTTAACTgaaga    >  1:12451/1‑141 (MQ=255)                                                                                                                          tAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTgaaga    >  1:71208/1‑141 (MQ=255)                                                                                                                            aCAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTGATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTGAAGaaa  >  1:501144/1‑141 (MQ=255)                                                                                                                                |                                                                                                                                         AAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTGAAGAAA  >  USA300TCH1516_ALE/707783‑708046

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑