Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	248,221	T→C	intergenic (+87/+137)	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	248,221	0	T	C	100.0%	15.4 / NA	10	intergenic (+87/+137)	rayT/lfhA	REP‑associated tyrosine transposase/flagellar system protein, promoterless fragment
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (7/3);  total (7/3)

GGGACGTAACGGATTTTAGTGCCGGGGAGCGTATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCGGATCGGTAGGCCGGATAAGGCGTTTATGCCGCATCCGGCAGTTATGCGCAGA  >  NC_000913/248091‑248246                                                                                                                                   |                          gggACGTAACGGATTTTAGTGCCGGGGAGCGTATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATcc                  >  2:710286/1‑140 (MQ=18)    aCGTAACGGATTTTAGTGCCGGGGAGCGTATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGc               >  1:895130/1‑140 (MQ=18)       tAACGGATTTTAGTGCCGGGGAGCGTATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGt            >  2:430347/1‑140 (MQ=17)         aCGGATTTTAGTGCCGGGGAGCGTATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGTGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGttg          <  1:106148/140‑2 (MQ=17)           ggATTTTAGTGCCGGGGAGCGTATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTtgtg        >  1:503740/1‑140 (MQ=17)           ggATTTTAGTGCCGGGGAGCGTATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTtgtg        >  1:757000/1‑140 (MQ=17)             aTTTTAGTGCCGGGGAGCGTATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTgca      >  2:451216/1‑139 (MQ=14)              ttttAGTGCCGGGGAGCGTATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTgcac     <  2:479382/140‑3 (MQ=14)               tttAGTGCCGGGGAGCGTATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTgcacc    >  1:282354/1‑137 (MQ=14)                 tAGTGCCGGGGAGCGTATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCTGAACGGTAGGACGGATAAGGCGTTCACGCCGCATCCGGCAGTTGTgcaccaa  <  1:112571/140‑6 (MQ=11)                                                                                                                                   |                          GGGACGTAACGGATTTTAGTGCCGGGGAGCGTATCATTTCATAATTGTGCGCAGATGCCTGATGCGACGCTAGCGCGTCTTATCATGCCTACAAACTTGTGCCGGATCGGTAGGCCGGATAAGGCGTTTATGCCGCATCCGGCAGTTATGCGCAGA  >  NC_000913/248091‑248246

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑