Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,492,074	(T)5→4	intergenic (‑300/‑76)	alaC ← / → ypdA	alanine transaminase/two‑component system sensor histidine kinase YpdA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,492,070	0	T	.	100.0%	34.7 / NA	9	intergenic (‑296/‑80)	alaC/ypdA	alanine transaminase/two‑component system sensor histidine kinase YpdA
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (4/5);  total (4/5)

TGCATTATCAAGAGATGCATTGCTAATACACCATTTATCTATCAATCCCCTTTTAAAATTGTGGTTTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCTTCAGGTTACCTATCATAGAGGTTTAATCCTTATTCAGAGTCACCCGTG  >  NZ_CP009273/2492006‑2492152                                                                 |                                                                                   tGCATTATCAAGAGATGCATTGCTAATACACCATTTATCTATCAATCCCCTTTTAAAATTGTGG‑TTTTCATCAAAAACGGCCTGCTGGtc                                                          <  2:283288/90‑1 (MQ=255)      tATCAAGAGATGCATTGCTAATACACCATTTATCTATCAATCCCCTTTTAAAATTGTGG‑TTTTCCTCAAAAACGGCCTGCTGGTCATCAg                                                     >  2:138085/1‑90 (MQ=255)          aaGAGATGCATTGCTAATACACCATTTATCTATCAATCCCCTTTTAAAATTGTGG‑TTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCtt                                                 >  1:232342/1‑90 (MQ=255)               aTGCATTGCTAATACACCATTTATCTATCAATCCCCTTTTAAAATTGTGG‑TTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCTTCAGGt                                            <  2:184429/90‑1 (MQ=255)                   aTTGCTAATACACCATTTATCTATCAATCCCCTTTTAAAATTGTGG‑TTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCTTCAGGTTAcc                                        <  2:232342/90‑1 (MQ=255)                                         atcAATCCCCTTTTAAAATTGTGG‑TTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCTTCAGGTTACCTATCATAGAGGTTTAATCCTTa                  >  1:48390/1‑90 (MQ=255)                                                   ttttAAAATTGTGG‑TTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCTTCAGGTTACCTATCATAGAGGTTTAAt                       >  1:200951/1‑75 (MQ=255)                                                   ttttAAAATTGTGG‑TTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCTTCAGGTTACCTATCATAGAGGTTTAAt                       <  2:200951/75‑1 (MQ=255)                                                         aaTTGTGG‑TTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCTTCAGGTTACCTATCATAGAGGTTTAATCCTTATTCAGAGTCACCCGTg  <  1:210088/90‑1 (MQ=255)                                                                 |                                                                                   TGCATTATCAAGAGATGCATTGCTAATACACCATTTATCTATCAATCCCCTTTTAAAATTGTGGTTTTTCCTCAAAAACGGCCTGCTGGTCATCAGCCTTCAGGTTACCTATCATAGAGGTTTAATCCTTATTCAGAGTCACCCGTG  >  NZ_CP009273/2492006‑2492152

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑