Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,074,174	A→G	intergenic (‑163/‑68)	rutA ← / → rutR	pyrimidine oxygenase/DNA‑binding transcriptional dual regulator RutR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,074,174	0	A	G	100.0%	92.3 / NA	27	intergenic (‑163/‑68)	rutA/rutR	pyrimidine oxygenase/DNA‑binding transcriptional dual regulator RutR
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (17/10);  total (17/10)

TTTGCAAAGCGGATGCCAGTTTTTAAAAAGTTAATGTTATTAATCTGTTAACATTACGTTATCTAAAATATCTGGTAAAAAGTGGACTAAACGGTCAAAACAGTTGCACATAAAACATGCATCTGTGCGCGATGAGAGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGCCAATCTACAAGAGGGGAGAGCGCATGACGCAAGGCGCAGTGAAAACAACGGGTAAACGTTCGCGCGCAGTAAGCGCGAAGAAAAA  >  NC_000913/1074038‑1074303                                                                                                                                         |                                                                                                                                  tttGCAAAGCGGATGCCAGTTTTTAAAAAGTTAATGTTATTAATCTGTTAACATTACGTTATCTAAAATATCTGGTAAAAAGTGGACTAAACGGTCAAAACAGTTGCACATAAAACATGCATCTGTGCGCGATGAGGGTg                                                                                                                                >  1:624498/1‑140 (MQ=255)    gCAAAGCGGATGCCAGTTTTTAAAAAGTTAATGTTATTAATCTGTTAACATTACGTTATCTAAAATATCTGGTAAAAAGTGGACTAAACGGTCAAAACAGTTGCACATAAAACATGCATCTGTGCGCGATGAGGGTGCAg                                                                                                                             <  2:624498/140‑1 (MQ=255)                         aaaaaGTTAATGTTATTAATCTGTTAACATTACGTTATCTAAAATATCTGGTAAAAAGTGGACTAAACGGTCAAAACAGTTGCACATAAAACATGCATCTGTGCGCGATGAGGGTGCAGAAGGTCGAGGCCGGGCggggg                                                                                                        <  2:354279/140‑1 (MQ=255)                                tAATGTTATTAATCTGTTAACATTACGTTATCTAAAATATCTGGTAAAAAGTGGACTAAACGGTCAAAACAGTTGCACATAAAACATGCATCTGTGCGCGATGATGGTCCAGAAGGTAGAGGAGGGGCGGGGGTTTTGCt                                                                                                 >  2:300703/1‑140 (MQ=255)                                          aaTCTGTTAACATTACGTTATCTAAAATATCTGGTAAAAAGTGGACTAAACGGTCAAAACAGTTGCACATAAAACATGCATCTGTGCGCGATGAGGGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGc                                                                                       <  2:32345/140‑1 (MQ=255)                                            tCTGTTAACATTACGTTATCTAAAATATCTGGTAAAAAGTGGACTAAACGGTCAAAACAGTTGCACATAAAACATGCATCTGTGCGCGATGAGGGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGCCa                                                                                     <  1:463070/140‑1 (MQ=255)                                               gTTAACATTACGTTATCTAAAATATCTGGTAAAAAGTGGACTAAACGGTCAAAACAGTTGCACATAAAACATGCATCTGTGCGCGATGAGGGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGCCAATc                                                                                  <  1:102049/140‑1 (MQ=255)                                                ttAACATTACGTTATCTAAAATATCTGGTAAAAAGTGGACTAAACGGTCAAAACAGTTGCACATAAAACATGCATCTGTGCGCGATGAGGGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGc                                                                                       <  2:636820/134‑1 (MQ=255)                                                ttAACATTACGTTATCTAAAATATCTGGTAAAAAGTGGACTAAACGGTCAAAACAGTTGCACATAAAACATGCATCTGTGCGCGATGAGGGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGc                                                                                       >  1:636820/1‑134 (MQ=255)                                                ttAACATTACGTTATCTAAAATATCTGGTAAAAAGTGGACTAAACGGTCAAAACAGTTGCACATAAAACATGCATCTGTGCGCGATGAGGGTGCAGAAGGTCGAGGCCGGACGGGGGTTTTGCTATCCTGTTGCCAATCt                                                                                 >  1:322186/1‑140 (MQ=255)                                                       tACGTTATCTAAAATATCTGGTAAAAAGTGGACTAAACGGTCAAAACAGTTGCACATAAAACATGCATCTGTGCGCGATGAGGGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGCCAATCTACAagag                                                                          >  2:366230/1‑140 (MQ=255)                                                        aCGTTATCTAAAATATCTGGTAAAAAGTGGACTAAACGGTCAAAACAGTTGCACATAAAACATGCATCTGTGCGCGATGAGGGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGCCAATCTACAAGAgg                                                                         >  2:47993/1‑140 (MQ=255)                                                              tCTAAAATATCTGGTAAAAAGTGGACTAAACGGTCAAAACAGTTGCACATAAAACATGCATCTGTGCGCGATGAGGGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGCCAATCTa                                                                                <  1:69892/127‑1 (MQ=255)                                                              tCTAAAATATCTGGTAAAAAGTGGACTAAACGGTCAAAACAGTTGCACATAAAACATGCATCTGTGCGCGATGAGGGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGCCAATCTa                                                                                >  2:69892/1‑127 (MQ=255)                                                                        cTGGTAAAAAGTGGACTAAACGGTCAAAACAGTTGCACATAAAACATGCATCTGTGCGCGATGAGGGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGCCAATCTACAAGAGGGGAGAGCGCATGACGc                                                         >  1:514683/1‑140 (MQ=255)                                                                        cTGGTAAAAAGTGGACTAAACGGTCAAAACAGTTGCACATAAAACATGCATCTGTGCGCGATGAGGGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGCCAATCTACAAGAGGGGAGAGCGCATGACGc                                                         >  1:4909/1‑140 (MQ=255)                                                                        cTGGTAAAAAGTGGACTAAACGGTCAAAACAGTTGCACATAAAACATGCATCTGTGCGCGATGAGGGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGCCAATCTACAAGAGGGGAGAGCGCATGACGc                                                         >  1:452107/1‑140 (MQ=255)                                                                          ggTAAAAAGTGGACTAAACGGTCAAAACAGTTGCACATAAAACATGCATCTGTGCGCGATGAGGGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGCCAATCTACAAGAGGGGAGAGCGCATGACGCaa                                                       >  2:471291/1‑140 (MQ=255)                                                                               aaaGTGGACTAAACGGTCAAAACAGTTGCACATAAAACATGCATCCGTGCGCGATGAGGGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGCCAATCTACAAGAGGGGAGAGCGCATGACGCAAGgcgc                                                  <  2:452107/140‑1 (MQ=255)                                                                                     gACTAAACGGTCAAAACAGTTGCACATAAAACATGCATCTGTGCGCGATGAGGGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGCCAATCTACAAGAGGGGAGAGCGCATGACGCAAGGCGCAGTGaa                                            <  1:47993/140‑1 (MQ=255)                                                                                     gACTAAACGGTCAAAACAGTTGCACATAAAACATGCATCTGTGCGCGATGAGGGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGCCAATCTACAAGAGGGGAGAGCGCATGACGCAAGGCGCAGTGaa                                            >  2:550867/1‑140 (MQ=255)                                                                                                          gCACATAAAACATGCATCTGTGCGCGATGAGGGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGCCAATCTACAAGAGGGGAGAGCGCATGACGCAAGGCGCAGTGAAAACAACGGGTAAACGTTcgcg                       <  1:366230/140‑1 (MQ=255)                                                                                                           cacaTAAAACATGCATCTGTGCGCGATGAGGGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGCCAATCTACAAGAGGGGAGAGCGCATGACGCAAGGCGCAGTGAAAACAACGGGTAAACGTTcgcgc                      >  2:31314/1‑140 (MQ=255)                                                                                                             caTAAAACATGCATCTGTGCGCGATGAGGGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGCCAATCTACAAGAGGGGAGAGCGCATGACGCAAGGCGCAGTGAAAACAACGGGTAAACGTTCgcgcgc                    >  2:606260/1‑140 (MQ=255)                                                                                                                     aTGCATCTGTGCGCGATGAGGGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGCCAATCTACAAGAGGGGAGAGCGCATGACGCAAGGCGCAGTGAAAACAACGGGTAAACGTTCGCGCGCAGTAAgcg            >  1:24873/1‑140 (MQ=255)                                                                                                                            tgtgCGCGATGAGGGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGCCAATCTACAAGAGGGGAGAGCGCATGACGCAAGGCGCAGTGAAAACAACGGGTAAACGTTCGCGCGCAGTAAGCGCgaagaa     >  1:442118/1‑140 (MQ=255)                                                                                                                               gcgcGATGAGGGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGCCAATCTACAAGAGGGGAGAGCGCATGACGCAAGGCGCAGTGAAAACAACGGGTAACCGTTCGGGCGCAGGAAGCGCGAAGaaaaa  >  1:267553/1‑140 (MQ=255)                                                                                                                                         |                                                                                                                                  TTTGCAAAGCGGATGCCAGTTTTTAAAAAGTTAATGTTATTAATCTGTTAACATTACGTTATCTAAAATATCTGGTAAAAAGTGGACTAAACGGTCAAAACAGTTGCACATAAAACATGCATCTGTGCGCGATGAGAGTGCAGAAGGTCGAGGCCGGGCGGGGGTTTTGCTATCCTGTTGCCAATCTACAAGAGGGGAGAGCGCATGACGCAAGGCGCAGTGAAAACAACGGGTAAACGTTCGCGCGCAGTAAGCGCGAAGAAAAA  >  NC_000913/1074038‑1074303

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑