Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,552,176	T→C	S184P (TCC→CCC)	rtcR →	DNA‑binding transcriptional regulator RtcR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,552,176	0	T	C	100.0%	82.1 / NA	24	S184P (TCC→CCC)	rtcR	DNA‑binding transcriptional regulator RtcR
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (5/19);  total (5/19)

ACGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGTCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTC  >  NZ_CP009273/3552089‑3552260                                                                                        |                                                                                     aCGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGccc                                                                                    <  1:464852/90‑1 (MQ=255) aCGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGccc                                                                                    <  2:46009/90‑1 (MQ=255) aCGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGccc                                                                                    <  2:361863/90‑1 (MQ=255)  cGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGCCCg                                                                                   >  2:289489/1‑90 (MQ=255)   gATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGCCCgg                                                                                  <  2:376195/90‑1 (MQ=255)      tATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGCCCGGCAt                                                                               <  1:186842/90‑1 (MQ=255)          gATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGCCCGGCATTGcc                                                                           <  1:270486/90‑1 (MQ=255)                  tttAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGCCCGGCATTGCCACGCGTaa                                                                   <  1:139819/90‑1 (MQ=255)                           ttATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGCCCGGCATTGCCACGCGTAACCCCCACtt                                                          >  1:246478/1‑90 (MQ=255)                             ataACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGCCCGGCATTGCCACGCGTAACCCCCACTTCa                                                        <  2:334656/90‑1 (MQ=255)                             ataACGCCACCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGCCCGGCATTGCCACGCGTAACCCCCACTTCa                                                        <  1:291465/90‑1 (MQ=255)                               aaCGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGCCCGGCATTGCCACGCGTAACCCCCACTTCAAc                                                      <  2:344323/90‑1 (MQ=255)                                  gCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGCCCGGCATTGCCACGCGTAACCCCCACTTCAACCGc                                                   <  2:268810/90‑1 (MQ=255)                                  gCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGCCCGGCATTGCCACGCGTAACCCCCACTTCAACCGc                                                   <  1:327710/90‑1 (MQ=255)                                    cATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGCCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCAt                                                 <  2:296152/90‑1 (MQ=255)                                    cATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGCCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCAt                                                 <  1:157610/90‑1 (MQ=255)                                    cATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGCCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCAt                                                 <  1:168019/90‑1 (MQ=255)                                     aTCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGccc                                                                                    >  1:37024/1‑54 (MQ=255)                                     aTCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGccc                                                                                    <  2:37024/54‑1 (MQ=255)                                     aTCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGCCCGGCATTGCCACGCGTAACCCCCACTTCa                                                        >  1:281477/1‑82 (MQ=255)                                     aTCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGCCCGGCATTGCCACGCGTAACCCCCACTTCa                                                        <  2:281477/82‑1 (MQ=255)                                     aTCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGCCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATg                                                >  1:360665/1‑90 (MQ=255)                                            gCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGCCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGATTGAGc                                         <  1:278142/90‑1 (MQ=255)                                                            aCGCCAGCAAACGCTTGATTTTCTTAAGCCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGc                         <  1:432775/90‑1 (MQ=255)                                                            aCGCCAGCAAACGCTTGATTTTCTTAAGCCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGc                         <  2:23645/90‑1 (MQ=255)                                                                   cAAACGCTTGATTTTCTTAAGCCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCaaa                  <  2:208260/90‑1 (MQ=255)                                                                    aaaCGCTTGATTTTCTTAAGCCCGGCATTGCCACGCGTAAccccc                                                              >  1:123166/1‑45 (MQ=255)                                                                    aaaCGCTTGATTTTCTTAAGCCCGGCATTGCCACGCGTAAccccc                                                              <  2:123166/45‑1 (MQ=255)                                                                                   ttAAGCCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTc  <  2:454403/90‑1 (MQ=255)                                                                                        |                                                                                     ACGATTATCGATCTCGATTTAAGCCGTTATAACGCCATCGCCAGCCGCTTTGCCGAGGAACGCCAGCAAACGCTTGATTTTCTTAAGTCCGGCATTGCCACGCGTAACCCCCACTTCAACCGCATGATTGAGCAGATCGAAAAAGTGGCGATCAAATCCCGCGCGCCGATTC  >  NZ_CP009273/3552089‑3552260

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑