Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	248,263	G→A	intergenic (+129/+95)	rayT → / ← lfhA	REP‑associated tyrosine transposase/flagellar system protein, promoterless fragment

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	248,263	0	G	A	100.0%	44.4 / NA	14	intergenic (+129/+95)	rayT/lfhA	REP‑associated tyrosine transposase/flagellar system protein, promoterless fragment
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (9/5);  total (9/5)

GTTATGCGCAGATGCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCG  >  NC_000913/248235‑248398                             |                                                                                                                                        attgtGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCa                          <  1:710286/136‑1 (MQ=255)   tgtGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATa                        <  2:588027/138‑1 (MQ=255)     tGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAAt                      >  1:570074/1‑140 (MQ=255)     tGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACAACAACGCCCCCATAAt                      >  1:582690/1‑140 (MQ=255)       cgcAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCt                    >  1:622015/1‑140 (MQ=255)       cgcAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCt                    >  2:289747/1‑140 (MQ=255)       cgcAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCt                    >  2:591242/1‑140 (MQ=255)        gcAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCtt                   <  2:282354/140‑1 (MQ=255)        gcAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCtt                   <  2:370727/140‑1 (MQ=255)            aTGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAAc               >  2:379772/1‑140 (MQ=255)            aTGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAAc               >  2:614058/1‑140 (MQ=255)               ccTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTcc            >  2:368774/1‑140 (MQ=255)                cTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCa           <  1:240277/140‑1 (MQ=255)                         cGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCg  >  1:338713/1‑140 (MQ=255)                             |                                                                                                                                        GTTATGCGCAGATGCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTGCACCAATGCTGGATACTTACATCAACGCCCCCATAATCTTCAACTCCAGCTCATCCG  >  NC_000913/248235‑248398

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: ‑