Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP025268	2,997,537	(A)8→7	intergenic (‑140/+83)	CXP41_RS15625 ← / ← CXP41_RS24400	response regulator transcription factor/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP025268	2,997,530	0	A	.	100.0%	99.8 / NA	22	intergenic (‑133/+90)	CXP41_RS15625/CXP41_RS24400	response regulator transcription factor/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (11/11);  total (11/11)

GAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCA  >  NZ_CP025268/2997409‑2997657                                                                                                                          |                                                                                                                                gAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTCTTATAAGCAAAATCCAAAGAATACATTGATGAAATAGTAATGAAATATAATTAAAAATAAAATGTTTGCAT‑AAAAAAATACGACAGGAAt                                                                                                              >  2:1313225/1‑140 (MQ=255)               tAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATgag                                                                                                <  1:4032261/140‑1 (MQ=255)                     attcattTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTaaa                                                                                                          <  1:2683712/124‑1 (MQ=255)                     attcattTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTaaa                                                                                                          >  2:2683712/1‑124 (MQ=255)                       tcattTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTaa                                                                                        >  2:819460/1‑140 (MQ=255)                            tataATAATCTCTACCATTATTATTAAAAGCACAAACCAAAGCATACTTTTATGAAATAATAATGAAATATATTAAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAAGTATCAGATGATTAAAatat                                                                                   <  2:1821938/140‑1 (MQ=255)                                        ttCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGAtt                                                                       >  2:751999/1‑140 (MQ=255)                                         tCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGGTGATTAAAATATTACAATTAGATta                                                                      >  2:2133552/1‑140 (MQ=255)                                         tCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATta                                                                      >  2:3322481/1‑140 (MQ=255)                                         tCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATta                                                                      >  2:3322377/1‑140 (MQ=255)                                                                   aaGAATACATTGCTGAATTCATTATAAAAAATCCTTAACAATAACATTTTTGCGT‑AAAACAATACCACCGCCATTAAAAAATCATGAGTAGATTAACGTATTACAATTAGATTATAGTCAAAGCATTAAACTTGAGCCAg                                            <  2:4632789/140‑1 (MQ=255)                                                                     gAATACATTGATGAAATAATAATTAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAggg                                          <  1:986701/140‑1 (MQ=255)                                                                     gAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAggg                                          <  2:4124268/140‑1 (MQ=255)                                                                      aaTACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGTTTAAAATATTACAATTAGATCATATTCAAATCATTAAACTTGAGCCAGGGa                                         <  1:3062489/140‑1 (MQ=255)                                                                      aaTACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGa                                         <  1:1697112/140‑1 (MQ=255)                                                                          cATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATAGTCAAATCATTAAACTTGAGCCAGGGAGCta                                     >  2:3032183/1‑140 (MQ=255)                                                                                       ataatGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAggg                        <  2:3793877/140‑1 (MQ=255)                                                                                            aaaaTATAATTAAAAATAAAATTTTTGCGT‑AAATAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGc                   <  2:2819429/139‑1 (MQ=255)                                                                                             aaaTATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGcc                  >  2:3237172/1‑140 (MQ=255)                                                                                                     ttAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGa          >  2:3203328/1‑140 (MQ=255)                                                                                                     ttAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGa          >  2:3203083/1‑140 (MQ=255)                                                                                                             aaaatTTTTGCGT‑AAAAAAATACCACAGGCAGTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCa  <  2:3471600/140‑1 (MQ=255)                                                                                                                          |                                                                                                                                GAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCA  >  NZ_CP025268/2997409‑2997657

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑