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%	29.6 / NA	11	F16S (TTC→TCC)	pspD	phage shock protein PspD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (4/7);  total (4/7)

TAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGG  >  NZ_CP009273/1363620‑1363746                                                                             |                                                   tAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGc                                       <  1:94242/90‑1 (MQ=255)    ccGTTTCCGTCAACTGTGAGGAAAGTTATGAATTCTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAg                                    <  2:273547/90‑1 (MQ=255)      gTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCt                                  >  1:186992/1‑90 (MQ=255)      gTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCt                                  <  1:452268/90‑1 (MQ=255)        ttCCGTCAACTGTGAGGAAAGTTATGAATACTCGCAGGCAACAGGCCGGGCAAAAGGTAACGCCTGGTTCCAAATTCGCAGGCGACCTgg                                >  2:397843/1‑90 (MQ=255)           cGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTAc                             <  2:228795/90‑1 (MQ=255)                       ggAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCAc                 <  2:398242/90‑1 (MQ=255)                         aaaGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTg               <  1:154873/90‑1 (MQ=255)                                      cTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTAc                             <  1:195149/63‑1 (MQ=255)                                      cTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTAc                             >  2:195149/1‑63 (MQ=255)                                      cTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCcgg  >  2:178643/1‑90 (MQ=255)                                                                             |                                                   TAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGG  >  NZ_CP009273/1363620‑1363746

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑