Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,787,398	(T)5→6	intergenic (‑286/‑47)	ppsA ← / → ppsR	phosphoenolpyruvate synthetase/posphoenolpyruvate synthetase regulatory protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,787,393	1	.	T	100.0%	34.7 / NA	11	intergenic (‑281/‑52)	ppsA/ppsR	phosphoenolpyruvate synthetase/posphoenolpyruvate synthetase regulatory protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base T (9/2);  total (9/2)

AAATGCTGTTTTCATAAAAAATAAAATTGAAGGTTCATTTTATAAACCAGACATAACGTTCTACGCTTCTGTGCG‑TTTTTAATTTATGCTTTCATAGAATTATGTCTGCATCACGGGAAGAACAAAATGGATAATGCTGTTGATCGCCAC  >  NC_000913/1787319‑1787468                                                                            |                                                                            aaatgCTGTTTTCATAAAAAATAAAATTGAAGGTTCATTTTATAAACCAGACATAACGTTCTACGCTTCTGTGCG‑tttttt                                                                       <  1:329226/81‑2 (MQ=255)                aaaaaaTAAAATTGAAGGTTCATTTTATAAACCAGACATAACGTTCTACGCTTCTGTGCGTTTTTTAATTTATGCTTTCa                                                          >  1:329237/1‑80 (MQ=255)                aaaaaaTAAAATTGAAGGTTCATTTTATAAACCAGACATAACGTTCTACGCTTCTGTGCGTTTTTTAATTTATGCTTTCa                                                          >  2:329239/1‑80 (MQ=255)                            tGAAGGTTCATTTTATAAACCAGACATAACGTTCTACGCTTCTGTGCGTTTTTTAATTTATGCTTTCATAGAATTATGTCt                                             >  2:329245/1‑81 (MQ=255)                              aaGGTTCATTTTATAAACCAGACATAACGTTCTACGCTTCTGTGCGTTTTTTAATTTATGCTTTCATAGAATTATGTCTg                                            >  2:329242/1‑80 (MQ=255)                                 gTTCATTTTATAAACCAGACATAACGTTCTACGCTTCTGTGCGTTTTTTAATTTATGCTTTCATAGAATTATGTCTGCATc                                        <  2:329227/81‑1 (MQ=255)                                       tttATAAACCAGACATAACGTTCTACGCTTCTGTGCGTTTTTTAATTTATGCTTTCATAGAATTATGTCTGCATCACggg                                   >  1:329240/1‑80 (MQ=255)                                           taAACCAGACATAACGTTCTACGCTTCTGTGCGTTTTTTAATTTATGCTTTCATAGAATTATGTCTGCATCACGGgaagaa                              >  2:329238/1‑81 (MQ=255)                                             aaCCAGACATAACGTTCTACGCTTCTGTGCGTTTTTTAATTTATGCTTTCATAGAATTATGTCTGCATCACGGGAAGAAc                             >  2:329243/1‑80 (MQ=255)                                                   aCATAACGTTCTACGCTTCTGTGCGTTTTTTAATTTATGCTTTCATAGAATTATGTCTGCATCACGGGAAGAACAAAATgg                      <  2:329228/81‑1 (MQ=255)                                                          gTTCTACGCTTCTGTGCGTTTTTTAATTTATGCTTTCATAGAATTATGTCTGCATCACGGGAAGAACAAAATGGATAATGc               >  1:329241/1‑81 (MQ=255)                                                                       gtgCGTTTTTTAATTTATGCTTTCATAGAATTATGTCTGCATCACGGGAAGAACAAAATGGATAATGCTGTTGATCGCCAc  >  1:329233/1‑81 (MQ=255)                                                                            |                                                                            AAATGCTGTTTTCATAAAAAATAAAATTGAAGGTTCATTTTATAAACCAGACATAACGTTCTACGCTTCTGTGCG‑TTTTTAATTTATGCTTTCATAGAATTATGTCTGCATCACGGGAAGAACAAAATGGATAATGCTGTTGATCGCCAC  >  NC_000913/1787319‑1787468

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑