Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,756,920	G→A	E254E (GAG→GAA)	intA →	integrase IntA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,756,920	0	G	A	100.0%	23.8 / NA	10	E254E (GAG→GAA)	intA	integrase IntA
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (7/3);  total (7/3)

CCTTTGTCAGCGTATTAACGAAGTCATGATTTATGCGCAGAACACAGGCCTGATTGATGCTGTTCCTAGTGTAAATATCGGAAAAGCTTTCGAGAAACCGCAAAAGAAAAACATGCCAAGCATCCGGCCGGATCAACTTCCGCAGCTAATGCACACCATGCGTACGGCAAGTATCAGCATGTCCACAAGATGCCTGTTCATGTGGCAACTTCTAACCATCACCCGCCCTGCCGAAGCTGCTGAGGCTCGATGGGATGAGATCGATTTCAATGCTAGCGAATGGAAAATTCCTGCAGCTCGAATGAAGATGAACCGGGACCATACGGTTCCACTATCTGATGGGGCTCTTGCTATTCTGGAAATGATGAAGCCTCTCAGTGGTGGCCGAGAATTTATCTTTCCTAGCCGTATCAAGCCCAACCAACCAATGAATAGCCAAACAGTGAATGCAGCACTCAAGCGTGCTGGCTTAGGAGGTGTACTTGT  >  NC_000913/2756677‑2757162                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                   ccTTTGTCAGCGTATTAACGAAGTCATGATTTATGCGCAGAACACAGGCCTGATTGATGCTGTTCCTAGTGTAAATATCGGAAAAGCTTTCGAGAAACCGCAAAAGAAAAACATGCCAAGCATCCGGCCGGATCAACTTCCGCAGCTAATGCACACCATGCGTACGGCAAGTATCAGCATGTCCACAAGATGCCTGTTCATGTGGCAACTTCTAACCATCACCCGCCCTGCCGAAGCTGCTGAAGCTCGAt                                                                                                                                                                                                                                             >  1:84879/1‑251 (MQ=255)        cAGCGTATTAACGAAGTCATGATTTATGCGCAGAACACAGGCCTGATTGATGCTGTTCCTAGTGTAAATATCGGAAAAGCTTTCGAGAAACCGCAAAAGAAAAACATGCCAAGCATCCGGCCGGATCAACTTCCGCAGCTAATGCACACCATGCGTACGGCAAGTATCAGCATGTCCACAAGATGCCTGTTCATGTGGCAACTTCTAACCATCACCCGCCCTGCCGAAGCTGCTGAAGCTCGATGGGATg                                                                                                                                                                                                                                       <  1:36034/250‑1 (MQ=255)                                                                                              gaAACCGCACAAGAAAAACATGCCAAGCATCCGGCCGGATCAACTTCCGCAGCTAATGCACACCATGCGTACGGCAAGTATCAGCATGTCCACAAGATGCCTGTTCATGTGGCAACTTCTAACCATCACCCGCCCTGCCGAAGCTGCTGAAGCTCGATGGGATGAGATCGATTTCAATGCTAGCGAATGGAAAATTCCTGCAGCTCGAATGAAGATGAACCGGGACCATACGGTTCCACTATCTGATgggg                                                                                                                                                >  1:59767/1‑251 (MQ=255)                                                                                                                   gCCAAGCATCCGGCCGGATCAACTTCCGCAGCTAATGCACACCATGCGTACGGCAAGTATCAGCATGTCCACAAGATGCCTGTTCATGTGGCAACTTCTAACCATCACCCGCCCTGCCGAAGCTGCTGAAGCTCGATGGGATGAGATCGATTTCAATGCTAGCGAATGGAAAATTCCTGCAGCTCGAATGAAGATGAACCGGGACCATACGGTTCCACTATCTGATGGGGCTCTTGCTATTCTGGAAatg                                                                                                                            >  1:95082/1‑250 (MQ=255)                                                                                                                                   gATCAACTTCCGCAGCTAATGCACACCATGCGTACGACAAGTATCAGCATGTCCACAAGATGCCTGTTCATGTGGCAACTTCTAACCATCACCCGCCCTGCCGAAGCTGCTGAAGCTCGATGGGATGAGATCGATTTCAATGCTAGCGAATGGAAAATTCCTGCAGCTCGAATGAAGATGAACCGGGACCATACGGTTCCACTATCTGATGGGGctc                                                                                                                                             <  1:1487/217‑1 (MQ=255)                                                                                                                                                 gCTAATGCACACCATGCGTACGGCAAGTATCAGCATGTCCACAAGATGCCTGTTCATGTGGCAACTTCTAACCATCACCCGCCCTGCCGAAGCTGCTGAAGCTCGATGGGATGAGATCGATTTCAATGCTAGCGAATGGAAAATTCCTGCAGCTCGAATGAAGATGAACCGGGACCATACGGTTCCACTATCTGATGGGGCTCTTGCTATTCTGGAAATGATGAAGCCTCTCAGtggtgg                                                                                                        >  1:180264/1‑240 (MQ=255)                                                                                                                                                      tGCACACCATGCGTACGGCAAGTATCAGCATGTCCACAAGATGCCTGTTCATGTGGCAACTTCTAACCATCACCCGCCCTGCCGAAGCTGCTGAAGCTCGATGGGCTGAGATCGATTTCAATGCTAGCGAATGGAAAATTCCTGCCGCTCGAATGAAGATGAACCGGGACCATACGGTTCCACTATCTGATGGGGCTCTTGCTATTCTGGAAATGATGAAGCCTCTCAGTGGTGGCCGAGAATTTa                                                                                             >  1:205231/1‑246 (MQ=255)                                                                                                                                                             cATGCGTACGGCAAGTATCAGCATGTCCACAAGATGCATGTTCATGTGGCAACATCTAACCATCACCCGCCCTGCCGAAGCTGCTGAAGCTCGATGGGATGAGATCGATTTCAATGCTAGCGAATGGAAAATTCATGCAGCTCGAATGAAGATGAACCGGGACCATACGGTTCCACTATCTGATGGGGCTCTTGCTATTCTGCACCTGATGAAGCCTCTCAGTGGTGGCCGAGAATTTATCTTTCCTAGcc                                                                                 >  1:240406/1‑251 (MQ=255)                                                                                                                                                                               cNGCANGNNCNNAAGNTGCCTGTTCATGTGGCAACTTNNAACCAGCACNCGCCCTGCCGAAGCTGCTGAAGCTCGATGGGATGAGATCGATTTCAATGCTAGNGAATGGAAANNTCNTGCAGNTNNNANNNAGNTGAACCGGGACCATACGGTNCCNNTATCTGNTGGGGCTCTTGCTATTCTGGAAatga                                                                                                                           <  2:59767/191‑1 (MQ=255)                                                                                                                                                                                                                                            gctgctGAAGCTCGATGGGATGAGATCGATTTCAATGCTAGCGAATGGAAAATTCCTGCAGCTCGAATGAAGATGAACCGGGACCATACGGTTCCAATATCTGATGGGGCTCTTGCTATTCTGGAAATGATGAAGCCTCTCAGTGGTGGCCGAGAATTTATCTTTCCTAGCCGTATCAAGCCCAACCAACCAATGAATAGCCAAACAGTGAATGCAGCACTCAAGCGTGCTGGCTTAGGAGGTGTACTTGt  >  1:167161/1‑251 (MQ=255)                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                   CCTTTGTCAGCGTATTAACGAAGTCATGATTTATGCGCAGAACACAGGCCTGATTGATGCTGTTCCTAGTGTAAATATCGGAAAAGCTTTCGAGAAACCGCAAAAGAAAAACATGCCAAGCATCCGGCCGGATCAACTTCCGCAGCTAATGCACACCATGCGTACGGCAAGTATCAGCATGTCCACAAGATGCCTGTTCATGTGGCAACTTCTAACCATCACCCGCCCTGCCGAAGCTGCTGAGGCTCGATGGGATGAGATCGATTTCAATGCTAGCGAATGGAAAATTCCTGCAGCTCGAATGAAGATGAACCGGGACCATACGGTTCCACTATCTGATGGGGCTCTTGCTATTCTGGAAATGATGAAGCCTCTCAGTGGTGGCCGAGAATTTATCTTTCCTAGCCGTATCAAGCCCAACCAACCAATGAATAGCCAAACAGTGAATGCAGCACTCAAGCGTGCTGGCTTAGGAGGTGTACTTGT  >  NC_000913/2756677‑2757162

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑