Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,363,696	T→C	F16S (TTC→TCC)	pspD →	phage shock protein PspD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,363,696	0	T	C	100.0%	34.7 / NA	11	F16S (TTC→TCC)	pspD	phage shock protein PspD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (3/8);  total (3/8)

TAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAGTT  >  NZ_CP009273/1363620‑1363778                                                                             |                                                                                   tAGCCGTTTCCGTCAACTGTGAGGAAAGTTTTGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCGAAATTCGCAGGc                                                                       <  1:528935/90‑1 (MQ=255) tAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGTCTGGTTCCAAATTAGCAGGc                                                                       <  2:223899/90‑1 (MQ=255)        ttCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTgg                                                                >  1:116369/1‑90 (MQ=255)         tCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGt                                                               <  1:249653/90‑1 (MQ=255)             tCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTActt                                                           <  2:710401/90‑1 (MQ=255)                  tgtgAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTAc                                                      <  2:755261/90‑1 (MQ=255)                   gtgAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTAcc                                                     >  2:172623/1‑90 (MQ=255)                        gAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACt                                                <  1:356084/90‑1 (MQ=255)                                                        ggCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGc                                                                       >  1:655400/1‑35 (MQ=255)                                                        ggCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGc                                                                       <  2:655400/35‑1 (MQ=255)                                                                      ccTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAGtt  <  1:354237/90‑1 (MQ=255)                                                                             |                                                                                   TAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAGTT  >  NZ_CP009273/1363620‑1363778

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑