Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,799,314	A→G	intergenic (+64/‑108)	espL1 → / → BW25113_RS09005	type III secretion system effector EspL1/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,799,314	0	A	G	100.0%	24.2 / NA	8	intergenic (+64/‑108)	espL1/BW25113_RS09005	type III secretion system effector EspL1/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (3/5);  total (3/5)

ATTTATAACCAGCTATTTACGATATATATCGATACATAATTTTATTTTTTTCATAAAACGCAGAAACAGTGACCATGTGCACAACGCCACCCGACGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACAC  >  NZ_CP009273/1799243‑1799384                                                                        |                                                                       aTTTATAACCAGCTATTTACGATATATATCGATACATAATTTTATTTTTTTCATAAAACGCAGAAACAGTGGCCATGTGCACAACGCCAc                                                      >  2:346834/1‑90 (MQ=255)            gCTATTTACGATATATATCGATACATAATTTTATTTTTTTCATAAAACGCAGAAACAGTGGCCATGTGCACAACGCCACCCGACGGCTGt                                           >  1:350585/1‑90 (MQ=255)                         tatatCGATACATAATTTTATTTTTTTCATAAAACGCAGAAACAGTGGCCATGTGCACAACGCCACCCGACGGCTGTAATAACAAAAAAt                              <  1:69257/90‑1 (MQ=255)                                           tattttTTTCATAAAACGCAGAAACAGTGGCCATGTGCACAACGCCACCCGACGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCt            <  1:346834/90‑1 (MQ=255)                                               tttttCATAAAACGCAGAAACAGTGGCCATGTGCACAACGCCACCCGACGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTg        <  2:370368/90‑1 (MQ=255)                                                 tttCATAAAACGCAGAAACAGTGGCCATGTGCACAACGcc                                                        >  1:125002/1‑40 (MQ=255)                                                 tttCATAAAACGCAGAAACAGTGGCCATGTGCACAACGcc                                                        <  2:125002/40‑1 (MQ=255)                                                     aTAAAACGCAGAAACAGTGGCCATGTGCACATCGCCACCCGACGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTacac  <  1:36375/90‑1 (MQ=255)                                                                        |                                                                       ATTTATAACCAGCTATTTACGATATATATCGATACATAATTTTATTTTTTTCATAAAACGCAGAAACAGTGACCATGTGCACAACGCCACCCGACGGCTGTAATAACAAAAAATCCCTTGATGCCTGTCCCTTTTGTTACAC  >  NZ_CP009273/1799243‑1799384

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑