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%	115.3 / NA	25	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 . (15/10);  total (15/10)

TCCCATATATTCATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATT  >  NZ_CP025268/2997392‑2997655                                                                                                                                           |                                                                                                                              tCCCATATATTCATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTaa                                                                                                                              >  1:4334283/1‑140 (MQ=255)               ccTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTCAAAATAAAATTTTTGCGT‑AAAAAAATACCACAgg                                                                                                               >  2:5349896/1‑140 (MQ=255)                       tAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTaaaa                                                                                                       >  1:4134169/1‑140 (MQ=255)                               ttAACGCATTCATTTATAATCATCCCTTCCATTATTATTATGAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAGATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGTCATTAAAAAATCATga                                                                                               >  1:2952460/1‑140 (MQ=255)                               ttAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATga                                                                                               >  1:1369173/1‑140 (MQ=255)                                       ttcattTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTa                                                                                       >  2:4605562/1‑140 (MQ=255)                                       ttcattTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTa                                                                                       >  2:4605406/1‑140 (MQ=255)                                             tataATCATCCCTTCCATTATTATTATAAGCAAACTCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAatat                                                                                 <  1:2366589/140‑1 (MQ=255)                                             tataATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAatat                                                                                 <  1:2367674/140‑1 (MQ=255)                                                    atcCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAAtt                                                                          <  2:903252/140‑1 (MQ=255)                                                    atcCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAAtt                                                                          >  2:5259427/1‑140 (MQ=255)                                                      cccTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAg                                                                        >  1:1421130/1‑140 (MQ=255)                                                                attattatAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCa                                                              <  1:4592192/140‑1 (MQ=255)                                                                 ttattatAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCaa                                                             <  1:1284744/140‑1 (MQ=255)                                                                         aGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTaa                                                     >  2:1199289/1‑140 (MQ=255)                                                                         aGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTaa                                                     >  2:4477432/1‑140 (MQ=255)                                                                           cAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAAc                                                   >  1:4624222/1‑140 (MQ=255)                                                                           cAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAAc                                                   >  1:2104040/1‑140 (MQ=255)                                                                                    aaGAATACCTAGATGAAATAACAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AGAAAAATACCGCAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATAATATTCAAATCATTAAACTTGAGCCAg                                          <  2:3911116/140‑1 (MQ=255)                                                                                         tACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAgc                                     <  1:5259427/140‑2 (MQ=255)                                                                                              tgatgaAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATaa                                <  2:5337392/140‑1 (MQ=255)                                                                                              taataaaaTAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATaa                                <  2:5337393/135‑1 (MQ=255)                                                                                                     ataataatGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCa                         >  1:964175/1‑140 (MQ=255)                                                                                                                           aataaaatTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAattat   >  2:1020585/1‑140 (MQ=255)                                                                                                                           aataaaatTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAattat   >  2:3691005/1‑140 (MQ=255)                                                                                                                            ataaaaaTTTTGCGT‑AAATAAACACCACAGTCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATTATTAAACTAGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAGACAGAattatt  <  2:4205148/140‑1 (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 < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑