Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,076,727	(T)5→4	intergenic (+458/‑85)	putP → / → BW25113_RS05295	sodium/proline symporter PutP/FTR1 family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,076,723	0	T	.	100.0%	50.3 / NA	13	intergenic (+454/‑89)	putP/BW25113_RS05295	sodium/proline symporter PutP/FTR1 family protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (10/3);  total (10/3)

CTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAA  >  NZ_CP009273/1076643‑1076793                                                                                 |                                                                       cTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGc                                                              >  1:295220/1‑90 (MQ=255) cTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGc                                                              >  2:301390/1‑90 (MQ=255)        aatCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATg                                                       >  2:191214/1‑90 (MQ=255)            gTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATaa                                                   <  2:572186/90‑1 (MQ=255)                       ttGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACt                                        >  2:192859/1‑90 (MQ=255)                       ttGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACt                                        >  2:338306/1‑90 (MQ=255)                              tACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGAttt                                 >  1:252697/1‑90 (MQ=255)                                          tttACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATaa                                                   >  1:497681/1‑60 (MQ=255)                                          tttACATTCCAACATCATTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATaa                                                   <  2:497681/60‑1 (MQ=255)                                                        tcatTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAg       >  1:18700/1‑90 (MQ=255)                                                        tcatTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAg       >  2:399874/1‑90 (MQ=255)                                                          atTTTATAAACATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGaa     >  1:390437/1‑90 (MQ=255)                                                             ttATAAGCATTCCGCTTGTG‑TTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGaaaaa  <  1:74757/90‑1 (MQ=255)                                                                                 |                                                                       CTGGAATAATCGTTTATATCCCTTGGCATTACCTCTCTTTGTTTACATTCCAACATCATTTTATAAACATTCCGCTTGTGTTTTTCTTTGCCGTAATGATAATCGCTATCACTGCGATTTACTTTTCTTTGCATAGATTGACTCAGAAAAA  >  NZ_CP009273/1076643‑1076793

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑