Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,599,483	A→C	D59A (GAT→GCT)	lsrB →	autoinducer 2 ABC transporter substrate‑binding protein LsrB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,599,483	0	A	C	100.0%	114.3 / NA	32	D59A (GAT→GCT)	lsrB	autoinducer 2 ABC transporter substrate‑binding protein LsrB
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (15/17);  total (15/17)

GCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGCCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGATGTGACCTACGACGGGCCGACAGAACCCAGTGTTTCTGGTCAGGTACAGTTGATTAATAACTTCGTCAATCAAGGTTATAACGCCATTAT  >  NZ_CP009273/1599347‑1599573                                                                                                                                         |                                                                                           gcTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGCCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCtg                                                                                          <  2:763796/139‑1 (MQ=255)      tGGCATTGCCGCAATCTCTATGAATGTGCAGGCCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGAcc                                                                                     >  2:825210/1‑139 (MQ=255)       ggCATTGCCGCAATCTCTATGAATGTGCAGGCCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGAc                                                                                      <  2:17549/137‑1 (MQ=255)                   aTCTCTATGAATGTGCAGGCCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGa                                                                        >  2:243993/1‑139 (MQ=255)                             aTGTGCAGGCCGCAGAGCGTATTGCATTGATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGTCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCAg                                                              <  1:707442/139‑1 (MQ=255)                              tgtgCAGGCCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCAgt                                                             >  2:540289/1‑139 (MQ=255)                                tgCAGGCCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGGCAACTGCACACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGCCGGGCCGACAGAACACAgtgt                                                           >  2:395258/1‑139 (MQ=255)                                tgCAGGCCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCAgtgt                                                           >  1:139248/1‑139 (MQ=255)                                  cAGGCCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTacga                                                                                <  1:189960/116‑1 (MQ=255)                                  cAGGCCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTacga                                                                                >  2:189960/1‑116 (MQ=255)                                   aGGCCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCAGTGTTTc                                                        <  1:243993/139‑1 (MQ=255)                                      ccGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCAGTGTTTCTgg                                                     <  1:540289/139‑1 (MQ=255)                                        gCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCAGTGCTTCTGGTc                                                   <  1:737107/139‑1 (MQ=255)                                                 aTTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCAGTGTTTCTGGTCAGGTACAGt                                          >  1:684899/1‑139 (MQ=255)                                                  ttGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCAGTGTTTCTGGTCAGGTACAGtt                                         <  2:130038/139‑1 (MQ=255)                                                   tGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCAGTGTTTc                                                        <  2:6643/123‑1 (MQ=255)                                                   tGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCAGTGTTTc                                                        >  1:6643/1‑123 (MQ=255)                                                        ttATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCa                                                               >  1:677277/1‑111 (MQ=255)                                                        ttATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCa                                                               <  2:677277/111‑1 (MQ=255)                                                        ttATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCAGTGTTTCTGGTCAGGTACAGTTGATtaa                                   >  2:165999/1‑139 (MQ=255)                                                                aaaCTGGTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCAGTGTTTCTGGTCAGGTACAGTTGATTAATAACTTCg                           <  1:379845/139‑1 (MQ=255)                                                                     ggTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCAGTGTTTCTGGTCAGGTACAGTTg                                        >  1:318891/1‑121 (MQ=255)                                                                     ggTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCAGTGTTTCTGGTCAGGTACAGTTg                                        <  2:318891/121‑1 (MQ=255)                                                                      gTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCAGTGTTTCTgg                                                     >  2:196880/1‑107 (MQ=255)                                                                      gTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCAGTGTTTCTgg                                                     <  1:196880/107‑1 (MQ=255)                                                                      gTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCAGTGTTTCTGGTCAGGTACAGTTGATTAATAACTTCGtcaat                      >  2:485387/1‑138 (MQ=255)                                                                      gTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCAGTGTTTCTGGTCAGGTACAGTTGATTAATAACTTCGtcaat                      >  1:321893/1‑138 (MQ=255)                                                                               ggATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCAGTGTTTCTGGTCAGGTACAGTTGATTAATAACTTCGTCAATCAAGGTtat             <  1:165999/138‑1 (MQ=255)                                                                                         ccAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCAGTGTTTCTGGTCAGGTACAGTTGATTAATAACTTCGTCAATCAAGGTTATAACGCCATTAt  <  1:454927/139‑1 (MQ=255)                                                                                         ccAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCAGTGTTTCTGGTCAGGTACAGTTGATTAATAACTTCGTCAATCAAGGTTATAACGCCATTAt  <  2:321893/139‑1 (MQ=255)                                                                                                                        tAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCAGTGTTTCTgg                                                     <  2:118022/57‑1 (MQ=255)                                                                                                                        tAAAGAGCTGGGCGTTGCTGTGACCTACGACGGGCCGACAGAACCCAGTGTTTCTgg                                                     >  1:118022/1‑57 (MQ=255)                                                                                                                                         |                                                                                           GCTCTTGGCATTGCCGCAATCTCTATGAATGTGCAGGCCGCAGAGCGTATTGCATTTATTCCCAAACTGGTTGGCGTGGGATTTTTTACCAGCGGTGGCAACGGCGCACAACAAGCGGGTAAAGAGCTGGGCGTTGATGTGACCTACGACGGGCCGACAGAACCCAGTGTTTCTGGTCAGGTACAGTTGATTAATAACTTCGTCAATCAAGGTTATAACGCCATTAT  >  NZ_CP009273/1599347‑1599573

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑