Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,000,873	C→T	R51H (CGC→CAC)	fliZ ←	RpoS antagonist, putative regulator of FliA activity

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,000,873	0	C	T	100.0%	57.0 / NA	18	R51H (CGC→CAC)	fliZ	RpoS antagonist, putative regulator of FliA activity
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (6/12);  total (6/12)

AAGAAATTGCTTAAAGCCGATAATATCGAAAAAATCACTCTGCGTTTTGCAATGTAAATCACCGCAAAATCGGCACAATGCCGCCCATGATTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCAATGGGTCTGGCTGTGTTTAAAGTCTTTAAGATAGCGGCTTAATGGCCGT  >  NC_000913/2000737‑2001001                                                                                                                                         |                                                                                                                                 aaGAAATTGCTTAAAGCCGATAATATCGAAAAAATCACTCTGCGTTTTGCAATGTAAATCACCGCAAAATCGGCACAATGCCGCCCATGATTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGTgg                                                                                                                                <  2:70866/139‑1 (MQ=255)                                  aTCACTCTGCGTTTTGCAATGTAAATCACCGCAAAATCGGCACAATGCCGCCCATGATTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGTGGGAAATCTCGATTTTATTCACTATTTTGCCGTcg                                                                                               <  2:557558/139‑1 (MQ=255)                                      ctctGCGTTTTGCAATGTAAATCACCGCAAAATCGGCACAATGCCGCCCATGATTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGTGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGaa                                                                                           <  2:227322/139‑1 (MQ=255)                                                         aaTCACCGCAAAATCGGCACAATGCCGCCCATGATTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGTGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAg                                                                        <  1:625009/139‑1 (MQ=255)                                                          aTCACCGCAAAATCGGCACAATGCCGCCCATGATTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGTGGGAAATCTCGATTTTAtt                                                                                                               <  1:389096/99‑1 (MQ=255)                                                          aTCACCGCAAAATCGGCACAATGCCGCCCATGATTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGTGGGAAATCTCGATTTTAtt                                                                                                               >  2:389096/1‑99 (MQ=255)                                                                              aTGCCGCCCATGATTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGTGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCa                                                   <  1:283010/139‑1 (MQ=255)                                                                              aTGCCGCCCATGATTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGTGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCa                                                   <  2:389271/139‑1 (MQ=255)                                                                                gccgccCATGATTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGTGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCGAt                                                 >  2:498695/1‑139 (MQ=255)                                                                                gccgccCATGATTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGTGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCAAt                                                 <  1:85507/139‑1 (MQ=255)                                                                                     ccATGATTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGTGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCAATGGGTc                                            <  1:48700/139‑1 (MQ=255)                                                                                                   ccGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGTGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCAATGGGTCTGGCTGTGTTTaaa                              <  1:139616/139‑1 (MQ=255)                                                                                                              ccaTTTTCATCAAGCAGCGTGTCCAGGTGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCAATGGGTCTGGCTGTGTTTAAAGTCTTTAAGAt                   >  1:62557/1‑139 (MQ=255)                                                                                                                          agcagcGTGTCCAGGTGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCa                                                   <  1:530106/95‑1 (MQ=255)                                                                                                                          agcagcGTGTCCAGGTGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCa                                                   >  2:530106/1‑95 (MQ=255)                                                                                                                           gcagcGTGTCCAGGTGGGAAATCTCGATTTTATTCACTATTTTGCCGTcg                                                                                               <  2:422495/50‑1 (MQ=255)                                                                                                                           gcagcGTGTCCAGGTGGGAAATCTCGATTTTATTCACTATTTTGCCGTcg                                                                                               >  1:422495/1‑50 (MQ=255)                                                                                                                               cGTGTCCAGGTGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCAATGGGTCTGGCTGTGTTTAAAGTCTTTAAGATAGCGGCTTAATGGCCGt  >  1:596006/1‑139 (MQ=255)                                                                                                                                         |                                                                                                                                 AAGAAATTGCTTAAAGCCGATAATATCGAAAAAATCACTCTGCGTTTTGCAATGTAAATCACCGCAAAATCGGCACAATGCCGCCCATGATTTTTGTTCCGTTTGCCAGCCATTTTCATCAAGCAGCGTGTCCAGGCGGGAAATCTCGATTTTATTCACTATTTTGCCGTCGCGAACTAAGGTAATGCGATCGAGTAATTTACGGCAATGCGCGCAATGGGTCTGGCTGTGTTTAAAGTCTTTAAGATAGCGGCTTAATGGCCGT  >  NC_000913/2000737‑2001001

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑