Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,581,070	G→A	A39A (GCG→GCA)	acrD →	multidrug efflux RND transporter permease AcrD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,581,070	0	G	A	100.0%	71.9 / NA	20	A39A (GCG→GCA)	acrD	multidrug efflux RND transporter permease AcrD
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (7/13);  total (7/13)

CTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCGCCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGT  >  NZ_CP009273/2580946‑2581188                                                                                                                             |                                                                                                                       ctctTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGc                                                                                                           >  2:85607/1‑138 (MQ=255)      ttAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGt                                                                                                       <  2:261752/137‑1 (MQ=255)            gCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCt                                                                                                <  2:287676/138‑1 (MQ=255)                            aTCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCt                                                                                                >  2:407103/1‑122 (MQ=255)                            aTCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCt                                                                                                <  1:407103/122‑1 (MQ=255)                                               ggTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCa                                                                                 <  1:279834/118‑1 (MQ=255)                                               ggTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCa                                                                                 >  2:279834/1‑118 (MQ=255)                                                 tGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAacac                                                          <  1:139214/139‑1 (MQ=255)                                                         aTCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGaaaa                                                             <  2:126813/128‑1 (MQ=255)                                                         aTCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGaaaa                                                             >  1:126813/1‑128 (MQ=255)                                                                            gTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACg                                                                     >  2:100726/1‑101 (MQ=255)                                                                            gTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACg                                                                     <  1:100726/101‑1 (MQ=255)                                                                              aCCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACg                                                                     >  2:134463/1‑99 (MQ=255)                                                                              aCCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACg                                                                     <  1:134463/99‑1 (MQ=255)                                                                               cccTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGAc                            <  1:570005/139‑1 (MQ=255)                                                                                    gCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCt                                                                                                <  2:202943/66‑1 (MQ=255)                                                                                    gCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCt                                                                                                >  1:202943/1‑66 (MQ=255)                                                                                           tttCATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATa                 <  2:495034/138‑1 (MQ=255)                                                                                              cATTGCCCGTTGAACAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAAtc              <  1:85607/138‑1 (MQ=255)                                                                                                          aaCAATACCCCGATCTCGCACCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGt  <  2:186220/138‑1 (MQ=255)                                                                                                                             |                                                                                                                       CTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCGCCACCGAATGTGCGAGTGACCGCTAACTATCCCGGCGCATCGGCCCAGACGCTGGAAAACACCGTGACCCAGGTTATCGAGCAAAATATGACCGGCCTCGATAATCTCATGTATATGT  >  NZ_CP009273/2580946‑2581188

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑