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%	138.9 / NA	30	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 . (12/18);  total (12/18)

ATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCA  >  NZ_CP025268/2997404‑2997657                                                                                                                               |                                                                                                                                aTCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTCTTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACcaca                                                                                                                   >  1:8015111/1‑140 (MQ=255) aTCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACcaca                                                                                                                   >  1:7892582/1‑140 (MQ=255)      gAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCAt                                                                                                              >  1:7777998/1‑140 (MQ=255)      gAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCAt                                                                                                              >  2:6269088/1‑140 (MQ=255)       aGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCAtt                                                                                                             >  1:6748013/1‑140 (MQ=255)         tgtAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTaa                                                                                                           >  1:8884172/1‑140 (MQ=255)         tgtAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTaa                                                                                                           >  1:8884275/1‑140 (MQ=255)                   ttAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATga                                                                                                 >  2:2368548/1‑140 (MQ=255)                    tAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATgag                                                                                                <  2:3527381/140‑1 (MQ=255)                    tAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATgag                                                                                                <  1:9698883/140‑1 (MQ=255)                                 tataATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAatat                                                                                   <  2:2941366/140‑1 (MQ=255)                                     atcatcCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACa                                                                               <  2:6748013/140‑1 (MQ=255)                                      tcatcCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACaa                                                                              <  2:1956253/140‑1 (MQ=255)                                           ccTACCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGa                                                                         <  1:9662119/140‑1 (MQ=255)                                                    attattatAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCa                                                                <  2:676815/140‑1 (MQ=255)                                                     ttattatAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCaa                                                               <  1:1101338/140‑1 (MQ=255)                                                     ttattatAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCaa                                                               <  2:9979620/140‑1 (MQ=255)                                                                  aaTCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTg                                                  >  1:6783393/1‑140 (MQ=255)                                                                         aGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAgg                                           >  2:3906957/1‑140 (MQ=255)                                                                          gAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAggg                                          <  1:3906957/140‑1 (MQ=255)                                                                          gAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAggg                                          <  2:5289453/140‑1 (MQ=255)                                                                          gAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAggg                                          <  2:5208066/140‑1 (MQ=255)                                                                          gAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAggg                                          <  2:5208164/140‑1 (MQ=255)                                                                                 ttGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCtata                                   <  1:1205487/140‑1 (MQ=255)                                                                                 ttGATGAAATAATAATGAAATATAATGAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCtata                                   <  2:5162858/140‑1 (MQ=255)                                                                                              aatGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATAATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCt                      >  2:587486/1‑140 (MQ=255)                                                                                                     tataATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCaaa               >  1:9829320/1‑140 (MQ=255)                                                                                                      ataATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCaaaa              <  1:8521867/140‑1 (MQ=255)                                                                                                      ataATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCaaaa              <  1:5064801/140‑1 (MQ=255)                                                                                                                  aaaatTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCa  <  1:1954235/140‑1 (MQ=255)                                                                                                                               |                                                                                                                                ATCCTGAGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCA  >  NZ_CP025268/2997404‑2997657

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑