Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,660,392	Δ1 bp	coding (549/1401 nt)	gadA ←	glutamate decarboxylase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,660,389	0	G	.	100.0%	29.9 / NA	16	coding (552/1401 nt)	gadA	glutamate decarboxylase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (5/11);  total (5/11)

AATTTATCCAGCGCATCGTGCAGCGGTTGTGGGAACTCATAGTTACCGGTGTAGGTCACGCCGAAAGTCGGCACCACGCCGATGGTGTTTTCGTCACAGGCTTCAATCATGCGTTTCGGGTCCATAAACAACTGACCGGGGCGCATAGGGATCTCACGCAGCTCCACATCCCAGTAGC  >  NZ_CP009273/3660252‑3660429                                                                                                                                          |                                         aaTTTATCCAGCGCATCGTGCAGCGGTTGTGGGAACTCATAGTTACCGGTGTAGGTCACGCCGAAAGTCGGCACCACGCCGATGGTGTTTTCGTCACAGGCTTCAATCATGCGTTTCGGGTCCATAAACAACTGACCgg                                         <  2:565887/139‑1 (MQ=32)  aTTTATCCAGCGCATCGTGCAGCGGTTGTGGGAACTCATAGTTACCGGTGTAGGTCACGCCGAAAGTCGGCACCACGCCGATGGTGTTTTCGTCACAGGCTTCAATCATGCGTTTCGGGTCCATAAACAACTGACCggg                                        <  2:346976/139‑1 (MQ=32)   tttATCCAGCGCATCGTGCAGCGGTTGTGGGAACTCATAGTTACCGGTGTAGGTCACGCCGAAAGTCGGCACCACGCCGATGGTGTTTTCGTCACAGGCTTCAATCATGCGTTTCGGGTCCATAAACAACTGACCgggc                                       <  1:336219/139‑2 (MQ=17)              cATCGTGCAGCGGTTGTGGGAACTCATAGTTACCGGTGTAGGTCACGCCGAAAGTCGGCACCACGCCGATGGTGTTTTCGTCACAGGCTTCAATCATGCGTTTCGGGTCCATAAACAACTGACC‑GGGCGCATAGGGAtc                           <  2:3651/139‑1 (MQ=17)                   tGCAGCGGTTGTGGGAACTCATAGTTACCGGTGTAGGTCACGCCGAAAGTCGGCACCACGCCGATGGTGTTTTCGTCACAGGCTTCAATCATGCGTTTCGGGTCCATAAACAACTGACC‑GGGCGCATAGGGATCTCACg                      <  2:487621/139‑1 (MQ=17)                      aGCGGTTGTGGGAACTCATAGTTACCGGTGTAGGTCACGCCGAAAGTCGGCACCACGCCGATGGTGTTTTCGTCACAGGCTTCAATCATGCGTTTCGGGTCCATAAACAACTGACC‑GGGCGCATAGGGATCTCACGCAg                   <  2:647171/139‑1 (MQ=17)                      aGCGGTTGTGGAAACTCATAGTTACCGGTGTAGGTCACGCCGAAAGTCGGCACCACGCCGATGGTGTTTTCGTCACAGGCTTCAATCATGCGTTTCGGGTCCATAAACAACTGACC‑GGGCGCATAGGGATCTCACGCAg                   <  2:537360/139‑1 (MQ=12)                         ggTTGTGGGAACTCATAGTTACCGGTGTAGGTCACGCCGAAAGTCGGCACCACGCCGATGGTGTTTTCGTCACAGGCTTCAATCATGCGTTTCGGGTCCATAAACAACTGACC‑GGGCGCATAGGGATCTCACGCAGCTc                <  2:230382/139‑1 (MQ=17)                           ttGTGGGAACTCATAGTTACCGGTGTAGGTCACGCCGAAAGTCGGCACCACGCCGATGGTGTTTTCGTCACAGGCTTCAATCATGCGTTTCGGGTCCATAAACAACTGACC‑GGGCGCATAGGGATCTCACGCAGCTCca              <  2:675932/139‑1 (MQ=17)                           ttGTGGGAACTCATAGTTACCGGTGTAGGTCACGCCGAAAGTCGGCACCACGCCGATGGTGTTTTCGTCACAGGCTTCAATCATGCGTTTCGGGTCCATAAACAACTGACC‑GGGCGCATAGGGATCTCACGCAGCTCca              <  2:486267/139‑1 (MQ=17)                           ttGTGGGAACTCATAGTTACCGGTGTAGGTCACGCCGAAAGTCGGCACCACGCCGATGGTGTTTTCGTCACAGGCTTCAATCATGCGTTTCGGGTCCATAAACAACTGACC‑GGGCGCATAGGGATCTCACGCAGCTCca              <  2:351759/139‑1 (MQ=17)                           ttGTGGGAACTCATAGTTACCGGTGTAGGTCACGCCGAAAGTCGGCACCACGCCGATGGTGTTTTCGTCACAGGCTTCAATCATGCGTTTCGGGTCCATAAACAACTGACC‑GGGCGCATAGGGATCTCACGCAGCTCca              <  1:662737/139‑1 (MQ=17)                           ttGTGGGAACGCATAGTTACCGGTGTAGGTCACGCCGAAAGTCGGCACCACGCCGATGGTGTTTTCGTCACAGGCTTCAATCATGCGTTTCGGGTCCATAAACAACTGACC‑GGGCGCATAGGGATCTCACGCAGCTCca              <  2:47771/139‑1 (MQ=12)                             gtgGGAACTCATAGTTACCGGTGTAGGTCACGCCGAAAGTCGGCACCACGCCGATGGTGTTTTCGTCACAGGCTTCAATCATGCGTTTCGGGTCCATAAACAACTGACC‑GGGCGCATAGGGATCTCACg                      <  2:55426/129‑1 (MQ=17)                             gtgGGAACTCATAGTTACCGGTGTAGGTCACGCCGAAAGTCGGCACCACGCCGATGGTGTTTTCGTCACAGGCTTCAATCATGCGTTTCGGGTCCATAAACAACTGACC‑GGGCGCATAGGGATCTCACg                      >  1:55426/1‑129 (MQ=17)                             gtgGGAACTCATAGTTACCGGTGTAGGTCACGCCGAAAGTCGGCACCACGCCGATGGTGTTTTCGTCACAGGCTTCAATCATGCGTTTCGGGTCCATAAACAACTGACC‑GGGCGCATAGGGATCTCACGCAGCTCcaca            >  2:673281/1‑139 (MQ=17)                                     tCATAGTTACCGGTGTAGGTCACGCCGAAAGTCGGCACCACGCCGATGGTGTTTTCGTCACAGGCTTCAATCATGCGTTTCGGGTCCATAAACAACTGACC‑GGGCGCATAGGGATCTCACGCAGCTCCACATCCCAg      >  1:734319/1‑137 (MQ=17)                                     tCATAGTTACCGGTGTAGGTCACGCCGAAAGTCGGCACCACGCCGATGGTGTTTTCGTCACAGGCTTCAATCATGCGTTTCGGGTCCATAAACAACTGACC‑GGGCGCATAGGGATCTCACGCAGCTCCACATCCCAg      >  1:705069/1‑137 (MQ=17)                                       aTAGTTACCGGTGTAGGTCACGCCGAAAGTCGGCACCACGCCGATGGTGTTTTCGTCACAGGCTTCAATCATGCGTTTCGGGTCCATAAACAACTGACC‑GGGCGCATAGGGATCTCACGCAGCTCCACATCCCAGTAGc  >  1:650969/1‑139 (MQ=17)                                                                                                                                          |                                         AATTTATCCAGCGCATCGTGCAGCGGTTGTGGGAACTCATAGTTACCGGTGTAGGTCACGCCGAAAGTCGGCACCACGCCGATGGTGTTTTCGTCACAGGCTTCAATCATGCGTTTCGGGTCCATAAACAACTGACCGGGGCGCATAGGGATCTCACGCAGCTCCACATCCCAGTAGC  >  NZ_CP009273/3660252‑3660429

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑