Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,423,602	T→C	R99R (CGT→CGC)	stfR →	prophage tail fiber N‑terminal domain‑containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,423,602	0	T	C	100.0%	110.9 / NA	34	R99R (CGT→CGC)	stfR	prophage tail fiber N‑terminal domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (15/19);  total (15/19)

CCGGGACCATTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGTCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGCGGTGGCACAGA  >  NZ_CP009273/1423520‑1423672                                                                                   |                                                                       ccGGGACCATTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAgg                                                                 <  1:1009029/90‑1 (MQ=255)         aTTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTgcgc                                                         <  1:1053925/90‑1 (MQ=255)         aTTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTgcgc                                                         >  2:444637/1‑90 (MQ=255)         aTTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTgcgc                                                         <  1:1153894/90‑1 (MQ=255)         aTTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTgcgc                                                         <  1:1231349/90‑1 (MQ=255)               gtgtATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGtttt                                                   >  2:252924/1‑90 (MQ=255)               gtgtATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGtttt                                                   >  2:129474/1‑90 (MQ=255)               gtgtATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGtttt                                                   >  2:464806/1‑90 (MQ=255)               gtgtATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATCACGGAGGTTGATGCCCCCCCGGAGGCACTGCGCCGtttt                                                   >  1:1180980/1‑90 (MQ=255)                 gtATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGa                                                 >  2:1183175/1‑90 (MQ=255)                   aTGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAAc                                               >  1:904769/1‑90 (MQ=255)                       aGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGAt                                           <  1:1066013/90‑1 (MQ=255)                         aTTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGAtgg                                         >  2:1183805/1‑90 (MQ=255)                           tctcAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGAtggtg                                       >  1:784100/1‑90 (MQ=255)                                aCCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAaga                                  <  2:1214382/90‑1 (MQ=255)                                     gTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTgg                             >  2:1012631/1‑90 (MQ=255)                                          cTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGt                        >  2:318062/1‑90 (MQ=255)                                           tGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTa                       <  2:259718/90‑1 (MQ=255)                                             aaTGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAAc                     <  1:14638/90‑1 (MQ=255)                                                   tttCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTcc               <  2:392710/90‑1 (MQ=255)                                                   tttCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTcc               <  1:624492/90‑1 (MQ=255)                                                   tttCTCGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTcc               <  1:205379/90‑1 (MQ=255)                                                      ctcGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGATGGCGGAAGAGGTGGCGCGTAACGCGTCcgcg            >  2:1137313/1‑90 (MQ=255)                                                      ctcGGTGCCAGGACGAAGGGTGATACCCGCCCGGAGGCACTGCGCCGTTTTGAACGGATGGTGGAAGAGGCGGCGCGTAACGCGTCcgcg            >  1:1147734/1‑90 (MQ=255)                                                        cGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGCGGt          <  2:1103896/90‑1 (MQ=255)                                                        cGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGCGGt          <  2:1130186/90‑1 (MQ=255)                                                        cGGTGCCATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGATGGCGGAAGAGGTGGCGCGTAACGCGTCCGCGGt          <  1:1137313/90‑1 (MQ=255)                                                             ccATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGCGGTGGcac     <  1:795522/90‑1 (MQ=255)                                                             ccATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGCGGTGGcac     <  1:696572/90‑1 (MQ=255)                                                             ccATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGCGGTGGcac     <  2:52896/90‑1 (MQ=255)                                                             ccATGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGCGGTGGcac     <  2:904769/90‑1 (MQ=255)                                                                tGACGGAGGATGATGCCCGCCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGGGGCGCGTAACGCGTCCGCGGTGGCACAGa  >  2:34861/1‑90 (MQ=255)                                                                            atgCCCGCCCGGAGGCACTGCGCCGTTTTGAACTg                                             >  2:272752/1‑35 (MQ=38)                                                                            atgCCCGCCCGGAGGCACTGCGCCGTTTTGAACTg                                             <  1:272752/35‑1 (MQ=38)                                                                                   |                                                                       CCGGGACCATTACCGTGTATGAAGATTCTCAACCCGGTACGCTGAATGATTTTCTCGGTGCCATGACGGAGGATGATGCCCGTCCGGAGGCACTGCGCCGTTTTGAACTGATGGTGGAAGAGGTGGCGCGTAACGCGTCCGCGGTGGCACAGA  >  NZ_CP009273/1423520‑1423672

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑