Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP025268	3,652,831	A→G	intergenic (+107/+38)	CXP41_RS19090 → / ← CXP41_RS19095	hypothetical protein/IS5‑like element IS5 family transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP025268	3,652,831	0	A	G	100.0%	89.1 / NA	33	intergenic (+107/+38)	CXP41_RS19090/CXP41_RS19095	hypothetical protein/IS5‑like element IS5 family transposase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (27/6);  total (27/6)

TAATATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAAACCGTTTCTTCGCCATTTAA  >  NZ_CP025268/3652694‑3652851                                                                                                                                          |                     tAATATAAATTTCACTGACGCAAATGTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGAc                    >  2:1650029/1‑140 (MQ=255)  aaTATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTAGTTAGAcc                   >  2:3079581/1‑140 (MQ=255)    tataAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGt                 >  2:680410/1‑140 (MQ=255)    tataAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGt                 >  2:3493011/1‑140 (MQ=255)    tataAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGt                 >  2:1262013/1‑140 (MQ=255)    tataAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGt                 >  1:5442468/1‑140 (MQ=255)    tataAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGt                 >  1:5337583/1‑140 (MQ=255)    tataAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGt                 >  2:3943502/1‑140 (MQ=255)    tataAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGt                 >  1:4333819/1‑140 (MQ=255)    tataAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGt                 <  1:2325560/140‑1 (MQ=255)       aaaTTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTttc              >  1:3977643/1‑140 (MQ=255)       aaaTTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATATTTAAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTttc              >  1:3977382/1‑140 (MQ=255)         aTTTCAGTGAAGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGGTGAGGCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTGCCGTAGAAGCCTGGAATGAGCCTATGTAGACCGTgtctt            >  2:3712671/1‑140 (MQ=11)         aTTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGAGTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTttctt            >  2:3363208/1‑140 (MQ=255)         aTTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTttctt            >  1:3003183/1‑140 (MQ=255)         aTTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTttctt            >  2:4918646/1‑140 (MQ=255)         aTTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTttctt            >  2:3520269/1‑140 (MQ=255)          tttCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTCGAATCAGCCTATTTAGACCGTttcttc           <  2:4111476/140‑1 (MQ=255)            tCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGc         <  1:3988086/140‑1 (MQ=37)              aCTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCGTTGAATCAGCCTATTTAGACCGTTTTTTCGCCa       >  2:3768329/1‑140 (MQ=255)              aCTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCa       >  2:5146343/1‑140 (MQ=25)              aCTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCa       >  1:153638/1‑140 (MQ=25)              aCTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCa       >  2:2298507/1‑140 (MQ=25)              aCTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCa       >  1:2446862/1‑140 (MQ=25)              aCTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCa       >  1:1464531/1‑140 (MQ=25)              aCTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTCAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGccc       >  1:3115274/1‑139 (MQ=255)              aCTGACGCAAATTGAGGGAATGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTGATTTCTTCATGTTTGAGTCGATTTTTTCTCCCGTAAATGCCTTGTATCCTCCTATTTAGACCGTTTCTTCGCCa       >  2:5226339/1‑140 (MQ=11)                  aCGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTa   <  1:77977/140‑1 (MQ=17)                  aCGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTa   <  1:1798671/140‑1 (MQ=17)                  aCGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAAGGCCTTGAATCAGCCTATTTAGACCGTTTCTTCGCCATTTa   >  1:5138455/1‑140 (MQ=12)                  aCGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCGGGCTCAGTCATTGCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACGGTTTCTTCGCCCTTTa   >  2:563555/1‑140 (MQ=11)                  aCGCAAATTTAGGGAAGGTGAGAATAAGCAGAGAAATTCTTCTCGGCTGACTCAGAACTTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAGACCCTTTCTTCGCCATTTa   <  2:2090632/140‑1 (MQ=11)                   cGCAAATTTAGGGAAGGTGCGACTAAGCGGGGCAGTTCTTCTCGGCTGACTCAGTCATGTCATTTCTTCATGTTTGAGCCGGTTTGTTCTCCCGTAAATGGCTTGGATGAGCCTAGTTAGCCCGTTTCTTCGCCCTTTaa  >  2:1273270/1‑140 (MQ=11)                                                                                                                                          |                     TAATATAAATTTCACTGACGCAAATTTAGGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAATGCCTTGAATCAGCCTATTTAAACCGTTTCTTCGCCATTTAA  >  NZ_CP025268/3652694‑3652851

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: ‑