Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,997,421	T→C	T40A (ACG→GCG)	rarD ←	EamA family transporter RarD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,997,421	0	T	C	100.0%	108.3 / NA	30	T40A (ACG→GCG)	rarD	EamA family transporter RarD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (14/16);  total (14/16)

TTTTAAATAGGACCACTGGCGGCAAATGCTCATCAGCACCACCATAAAGAAAAACGACCAGATCACGCGATGCGTCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGT  >  NZ_CP009273/3997347‑3997506                                                                           |                                                                                      ttttAAATAGGACCACTGGCGGCAAATGCTCATCAGCACCACCATAAAGAAAAACGACCAGATCACGCGATGCGCCAGGATTTCATcggc                                                                        <  2:361532/90‑1 (MQ=255)  tttAAATAGGACCACTGGCGGCAAATGCTCATCAGCACCACCATAAAGAAAAACGACCAGATCACGCGATGCGCCAGGATTTCATcggcg                                                                       <  1:478895/90‑1 (MQ=255)       aTAGGACCACTGGCGGCAAATGCTCATCAGCACCACCATAAAGAAAAACGACCAGATCACGCGATGCGCCAGGATTTCATCGGCGGGCAc                                                                  <  1:191389/90‑1 (MQ=255)       aTAGGACCACTGGCGGCAAATGCTCATCAGCACCACCATAAAGAAAAACGACCAGATCACGCGATGCGCCAGGATTTCATCGGCGGGCAc                                                                  <  1:238213/90‑1 (MQ=255)       aTAGGACCACTGGCGGCAAATGCTCATCAGCACCACCATAAAGAAAAACGACCAGATCACGCGATGCGCCAGGATTTCATCGGCGGGCAc                                                                  <  2:67518/90‑1 (MQ=255)       aTAGGACCACTGGCGGCAAATGCTCATCAGCACCACCATAAAGAAAAACGACCAGATCACGCGATGCGCCAGGATTTCATCGGCGGGCAc                                                                  <  1:63747/90‑1 (MQ=255)          ggACCACTGGCGGCAAATGCTCATCAGCACCACCATAAAGAAAAACGACCAGATCACGCGATGCGCCAGGATTTCATCGGCGGGGACgga                                                               >  1:176687/1‑88 (MQ=255)          ggACCACTGGCGGCAAATGCTCATCAGCACCACCATAAAGAAAAACGACCAGATCACGCGATGCGCCAGGATTTCATCGGCGGGGACgca                                                               >  2:73132/1‑88 (MQ=255)          ggACCACTGGCGGCAAATGCTCATCAGCACCACCATAAAGAAAAACGACCAGATCACGCGATGCGCCAGGATTTCATCGGCGGGCACgta                                                               >  1:222644/1‑90 (MQ=255)          ggACCACTGGCGGCAAATGCTCATCAGCACCACCATAAAGAAAAACGACCAGATCACGCGATGCGCCAGGATTTCATCGGCGGGCACgta                                                               <  1:80466/90‑1 (MQ=255)                  ggcggcAAATGCTCATCAGCACCACCATAAAGAAAAACGACCAGATCACGCGATGCGCCAGGATTTCATCGGCGGGCACGTAGTAAATCa                                                       <  1:470961/90‑1 (MQ=255)                                       ccaccaTAAAGAAAAACGACCAGATCACGCGATGCGCCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCta                                  <  2:342883/90‑1 (MQ=255)                                       ccaccaTAAAGAAAAACGACCAGATCACGCGATGCGCCAGGATTTCATCGGCGGGCACGGAGTAAAAAAAACTGAAGAAAGCCGGCGCta                                  >  2:128559/1‑90 (MQ=255)                                         accaTAAAGAAAAACGACCAGATCACGCGATGCGCCAGGATTTCATCGGCGGGGACGGAGTAAAAAAAATTTAAGAAAGCTGGCGCtata                                >  2:121319/1‑90 (MQ=255)                                         accaTAAAGAAAAACGACCAGATCACGCGATGCGCCAGGATTTCATCGGCGGGGACGGAGTAAAAAAAAATGAAGTAAGCTGGCGCtata                                >  2:240300/1‑90 (MQ=255)                                         accaTAAAGAAAAACGACCAGATCACGCGATGCGCCAGGATTTCATCGGCGGGCACGGAGGAAAACAAATTTAAGGACGCCGGGGCtata                                >  1:297395/1‑90 (MQ=255)                                            aTAAAGAAAAACGACCAGATCACGCGATGCGCCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATAccc                             <  2:78059/90‑1 (MQ=255)                                                 gAAAAACGACCAGATCACGCGATGCGCCAGGATTTCATcggcg                                                                       <  2:228789/43‑1 (MQ=255)                                                 gAAAAACGACCAGATCACGCGATGCGCCAGGATTTCATcggcg                                                                       >  1:228789/1‑43 (MQ=255)                                                 gAAAAACGACCAGATCACGCGATGCGCCAGGATTTCATCGGCGGGGACGGAGTAAAAAAAATTGAAAAAAGCTGGGGGTATACCCCcaaa                        >  2:272449/1‑89 (MQ=255)                                                 gAAAAACGACCAGATCACGCGATGCGCCAGGATTTCATCGGCGGGCACGGAGTAAAACAACTTGAAGGACGCTGGCGCCATACCCCcaaa                        >  2:6300/1‑89 (MQ=255)                                                 gAAAAACGACCAGATCACGCGATGCGCCAGGATTTCATCGGCGGGCACGGAGGAAAACAAATTTAAGAAAGCCGGGGCCATACCCCcaaa                        >  2:110135/1‑89 (MQ=255)                                                    aaaCGACCAGATCACGCGATGCGCCAGGATTTCATCGGCGGGGAAGGAGTAAAAAAAAATTAAGTAAGGTGGGGCTTTACCCCcaaaaaa                     >  2:400938/1‑90 (MQ=255)                                                        gACCAGATCACGCGATGCGCCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAaataaaataa                 <  1:496448/90‑1 (MQ=255)                                                        gACCAGATCACGCGATGCGCCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAaataaaataa                 <  1:466470/90‑1 (MQ=255)                                                         aCCAGATCACGCGATGCGCCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAg                <  2:285458/90‑1 (MQ=255)                                                               tCACGCGATGCGCCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCaa          <  2:297395/90‑1 (MQ=255)                                                                 aCGCGATGCGCCAGGATTTCATCGGCGGGCACGTAGGAAAACAACTTTAAGGAAGCTGGCGCTATACCCCCAAAAAAAAAAACGGCAaga        >  1:269136/1‑90 (MQ=255)                                                                    cgATGCGCCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCg     <  2:181496/90‑1 (MQ=255)                                                                       tGCGCCAGGATTTCATCGGCGGGCACGTAGGAAATCAACTTTAAGTAAGCTGGCGCTATACCCCAAAAAAAAAAAACGGCAAAAGCGAgg  >  1:320509/1‑89 (MQ=255)                                                                           |                                                                                      TTTTAAATAGGACCACTGGCGGCAAATGCTCATCAGCACCACCATAAAGAAAAACGACCAGATCACGCGATGCGTCAGGATTTCATCGGCGGGCACGTAGTAAATCAACTTGAAGTACGCTGGCGCTATACCCCAAATAAAATAAGCGGCAAGAGCGAGT  >  NZ_CP009273/3997347‑3997506

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑