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	96.2%	81.8 / ‑4.6	26	F16S (TTC→TCC)	pspD	phage shock protein PspD
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (13/12);  total (13/13)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCACGTTACGTAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAGTT  >  NZ_CP009273/1363610‑1363778                                                                                       |                                                                                   tCACGTTACGTAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCaa                                                                                 <  2:1202456/90‑1 (MQ=255)        aCGTAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCa                                                                          >  2:349155/1‑90 (MQ=255)           tcgCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGc                                                                       <  1:568704/88‑1 (MQ=255)            aGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCa                                                                      >  1:938429/1‑90 (MQ=255)                  ttCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTgg                                                                >  2:439405/1‑90 (MQ=255)                     cGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAACGCCTGGTTCCAAATTAGCAGGCAAGCTGGTAc                                                             <  1:654740/90‑1 (MQ=255)                     cGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTAc                                                             <  2:41544/90‑1 (MQ=255)                     cGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTAc                                                             <  2:235390/90‑1 (MQ=255)                       tCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTActt                                                           <  1:349155/90‑1 (MQ=255)                       tCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTActt                                                           <  1:402681/90‑1 (MQ=255)                             gtgAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTAcc                                                     >  1:1123626/1‑90 (MQ=255)                               gAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGc                                                                       <  1:1211681/70‑1 (MQ=255)                               gAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGc                                                                       >  2:1211681/1‑70 (MQ=255)                                 ggAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCAc                                                 <  1:404878/90‑1 (MQ=255)                                 ggAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCAc                                                 <  1:1225445/90‑1 (MQ=255)                                    aaGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTgc                                              >  2:324899/1‑90 (MQ=255)                                       ttATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCt                                           >  2:560084/1‑90 (MQ=255)                                       ttATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCt                                           >  1:981304/1‑90 (MQ=255)                                        tATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTa                                          <  1:2368/90‑1 (MQ=255)                                           gAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATgg                                       >  2:461980/1‑90 (MQ=255)                                                cTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCcgg                                  >  1:745290/1‑90 (MQ=255)                                                cTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCcgg                                  >  1:483217/1‑90 (MQ=255)                                                   gCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCcggcgg                               >  1:1115501/1‑90 (MQ=255)                                                    cTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCggg                              <  1:174328/90‑1 (MQ=255)                                                     tGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCgggg                             >  1:369714/1‑89 (MQ=255)                                                                                ccTGGTTCCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAGtt  <  1:1053806/90‑1 (MQ=255)                                                                                       |                                                                                   TCACGTTACGTAGCCGTTTCCGTCAACTGTGAGGAAAGTTATGAATACTCGCTGGCAACAGGCCGGGCAAAAGGTAAAGCCTGGTTTCAAATTAGCAGGCAAGCTGGTACTTCTTACCGCACTGCGCTATGGCCCGGCGGGTGTGGCGGGCTGGGCGATAAAATCAGTT  >  NZ_CP009273/1363610‑1363778

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑