Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,629,389	(T)8→7	intergenic (+42/+18)	creD → / ← arcA	cell envelope integrity protein CreD/two‑component system response regulator ArcA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,629,382	0	T	.	100.0%	101.6 / NA	24	intergenic (+35/+25)	creD/arcA	cell envelope integrity protein CreD/two‑component system response regulator ArcA
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (12/12);  total (12/12)

AGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTC  >  NZ_CP009273/4629303‑4629466                                                                                |                                                                                     aGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGtttttttgacg                                                                            <  2:115715/90‑5 (MQ=255) aGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGtttttttgacg                                                                            <  1:613097/90‑5 (MQ=255)  gTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACgg                                                                          >  1:162104/1‑90 (MQ=255)         agTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTaaa                                                                   >  2:235412/1‑90 (MQ=255)                 cGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTa                                                           <  1:41277/90‑1 (MQ=255)                   gACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAAt                                                         <  1:221597/90‑1 (MQ=255)                     cGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCt                                                       <  2:221788/90‑1 (MQ=255)                        tGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTcc                                                    <  1:127011/90‑1 (MQ=255)                             tACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATc                                               >  2:175742/1‑90 (MQ=255)                                   tCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCa                                         >  1:48548/1‑90 (MQ=255)                                    cTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAg                                        <  2:392441/90‑1 (MQ=255)                                     tGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGa                                       >  1:91079/1‑90 (MQ=255)                                     tGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGa                                       <  1:96764/90‑1 (MQ=255)                                      ggAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGaa                                      <  1:128737/90‑1 (MQ=255)                                      ggAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGaa                                      <  2:361740/90‑1 (MQ=255)                                           tAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGAt                                 >  1:112249/1‑90 (MQ=255)                                            aaGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATa                                <  1:366399/90‑1 (MQ=255)                                            aaGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATa                                <  1:103744/90‑1 (MQ=255)                                             aGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATaa                               >  1:272006/1‑90 (MQ=255)                                             aGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATaa                               >  2:450241/1‑90 (MQ=255)                                                 tGAAAAATAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCtt                           >  1:368094/1‑90 (MQ=255)                                                   aaaaaTAAAAACGGCGCTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCa                         <  2:39335/90‑1 (MQ=255)                                                                gcgcTAAAAAGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAAtggtgg            >  2:293894/1‑90 (MQ=255)                                                                     aaaaaGCGCCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCgatg       <  1:175742/90‑1 (MQ=255)                                                                          gcgcCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTtc  >  2:162285/1‑90 (MQ=255)                                                                          gcgcCG‑TTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTtc  >  1:188646/1‑90 (MQ=255)                                                                                |                                                                                     AGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGATAACCTTCACCGTGAATGGTGGCGATGATTTC  >  NZ_CP009273/4629303‑4629466

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑