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%	99.5 / 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 . (14/8);  total (14/8)

TCCCATATATTCATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATT  >  NZ_CP025268/2997392‑2997655                                                                                                                                           |                                                                                                                              tCCCATATATTCATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTaa                                                                                                                              <  2:3130773/140‑1 (MQ=255)   ccATATATTCATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTaaaa                                                                                                                            <  1:2110295/140‑1 (MQ=255)             agccTGAGTGTAAATGCTTTAACGCATTCCTTTATAATCATCCCTTCCATTATTATTATAAGCAAATTCCAAATAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACcaca                                                                                                                 >  2:291216/3‑140 (MQ=255)               ccTGAGTGTAAATGCTTTAACGCATTCATTTTTAATCATCCCTTCCAGTATTATTATACGCAAAATCCAAAGTATCCATTGATGAAATAATAATAAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAGAATACCACTgg                                                                                                               >  2:2419379/1‑140 (MQ=255)                   aGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCAtt                                                                                                           >  2:3677825/1‑140 (MQ=255)                   aGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCAtt                                                                                                           >  1:3396314/1‑140 (MQ=255)                      gtAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTaaa                                                                                                        <  1:23835/140‑1 (MQ=255)                             cTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCAt                                                                                                 >  1:3464048/1‑140 (MQ=255)                             cTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCAt                                                                                                 >  1:4011087/1‑140 (MQ=255)                               ttAACGCATTCATTTATAATCATCCCTTCCATGATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATga                                                                                               >  2:2645055/1‑140 (MQ=255)                                       ttcattTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTa                                                                                       >  1:4513141/1‑140 (MQ=255)                                         cattTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTaaa                                                                                     <  1:2425616/140‑1 (MQ=255)                                                    atcCCTTCCATTATTATTATAATCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACATGCATTAAAAAATCATGAGATTATTAAAATATTACAAtt                                                                          <  2:3203344/140‑1 (MQ=255)                                                    atcCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACTACAGGCATTAAAAAATGATGAGATGATTAAAATATTACAAtt                                                                          >  2:2859288/1‑140 (MQ=255)                                                    atcCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAAtt                                                                          >  2:75691/1‑140 (MQ=255)                                                       ccTTACATTATTATTATAATCAAAATACAAAGAATACATTGATAAAAAAATAATGAAATATAATTAAAAAAAAAATTTTTGCAT‑AAAAAAATAACACAGGCATTAAAAAATCATGAAATAAATAACATATTAAAATAAGa                                                                       <  2:507256/140‑1 (MQ=255)                                                                         aGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTaa                                                     >  2:1648019/1‑140 (MQ=255)                                                                              aaTCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTg                                                >  2:4726005/1‑140 (MQ=255)                                                                                    aaGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTGGAGCCAg                                          <  1:2873775/140‑1 (MQ=255)                                                                                        aTACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAg                                      <  1:3207738/140‑1 (MQ=255)                                                                                                 tgaAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAACAATCCCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTTAGCCAGGGAGCTATAAGTc                             >  2:2375671/1‑140 (MQ=255)                                                                                                 tgaAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTc                             >  2:1269297/1‑140 (MQ=255)                                                                                                                  ataACTAAAAACAAAATTGTTGCGT‑AAAACAATACCACAGGCATTAAAAAGTCCTGAGATAATTAAAATATTACAATTAGATTCTATTCAAATCATTAAACTTCAGCAAGGGAGCTATTAGTCCCCAGGGCTTGCCaaat            <  2:2081040/140‑2 (MQ=255)                                                                                                                            ataaaatTTTTGCGT‑AAAAAAATACCACAGGCCTTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAattatt  <  1:1573936/140‑1 (MQ=255)                                                                                                                                           |                                                                                                                              TCCCATATATTCATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATT  >  NZ_CP025268/2997392‑2997655

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑