Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	296,721	C→T	E126K (GAA→AAA)	intF ←	putative phage integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	296,721	0	C	T	100.0%	12.5 / NA	6	E126K (GAA→AAA)	intF	putative phage integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (3/3);  total (3/3)

GGCAGGTTGAGCAAACTAGCCAATGGTCCAGCCGAAGTCGGGCCTTGGCCTCTTTTTTTACTTTCGCCTCCACGACTGGACAAGTTAATGTGATCGGCAATGTATCGAGTAGAATATGGGCGTTTAGTTTTTGCACTGATACCGGTTCTCAATTCTTGAAGATAGTCTTCCCAGGCGACGGAGAAAGTCACTTTTGTTTTACGTGATTCTGCCTGCAGGGATTCTGCTTCTGCGATTTTTACAGCCTTAGCAATTCGTGGATCTATCCCTGTATCGATCAATGTTTGTAACCGTCTTGCCTCGGCTCTCGCATCATCAATCTTCCAGTCGTTAATGTTGCCAATAGTCATGCGAAGGGTTTTCCCCGCATATACGCTTTGGAATACAAAGGCTTTTGCTCCGCTAGTTGCTCGGCATGCCAGGGTTGTTACATCTGCATCCCAAAGAAAAG  >  NC_000913/296498‑296948                                                                                                                                                                                                                                |                                                                                                                                                                                                                                    ggCAGGTTGAGCAAACTAGCCAATGGTCCAGCCGAAGTCGGGCCTTGGCCTCTTTTTTTACTTTCGCCTCCACGACTGGACAAGTTAATGTGATCGGCAATGTATCGAGTAGAAGATGGGTGTTTAGTTTTTGCACTGATACCGGTTCTCAATTCTTGAAGATAGTCTTCCCAGGCGACGGAGAAAGTCACTTTTGTTTTACGTGATTCTGCCTGCAGGGATTTTGCTTCTGCGATTTTTACAGCCTTAGc                                                                                                                                                                                                          <  1:46081/251‑1 (MQ=255)               aCTAGCCAATGGTCCAGCCGAAGTCGGGCCTTGGCCTCTTTTTTTACTTTCGCCTCCACGACTGGACAAGTTAATGTGATCGGCAATGTATCGAGTAGAATATGGGTGTTTAGTTTTTGCACTGATACCGGTTCTCAATTCTTGAATATATTCTGCCCAGGCGACTGAGAAAGTCACTTTTTTTTTACGTGATTCTGCCTGCAGGGATTTTGCTTCTGCGATTTTTACAGCCTTATCAATTCGTGGATCTa                                                                                                                                                                                            <  1:136230/251‑1 (MQ=255)                                           ccTTGGCCTCTTTTTTTACTTTCGCCTCCACGACTGGACAAGTTAATGAGATCGGCAATGTATCGAGTAGAATATGGGGGTTTAGTTTTTGAACTGATACCGGTTCTCAATTCTTGAAGATAGTCTTCCCAGGCGACGGAGAAAGACACTTTTGTTTTACGTGATTCTGCCTGCAGGGATTTTGCTTCTGCGATTTTTACAGCCTTAGCAATTCGTGGATCTATCCCTGTATCGATCAATGTTTGTAACCg                                                                                                                                                                >  1:96654/1‑251 (MQ=255)                                                                                                                                                                     gTCTTCCCAGGCGACGGAGAAAGTCANTTTTGTNNTANGTGATTCTGCCTGCAGGGANTTNNNTNNNGNGCTTTNTANNGCCTTAGCANTTCGTGGATCTATCCCTGTATCGATCAATGTTTGTAACCGTCTTGCCTCGGCTNTCGCATCATNNATCTTCCAGTCGTTAATGTTGNCAANNGNNANGCGNAgn                                                                                                >  2:60644/1‑192 (MQ=255)                                                                                                                                                                     gTCTTCCCAGGCGACGGAGAAAGTCACTTTTGTTTTACGTGATTCTGCCTGCAGGGATTTTGCTTCTGCGATTTTTACAGCCTTAGCAATTCGTGGATCTATCCCTGTATCGATCAATGTTTGTAACCGTCTTGCCTCGGCTCTCGCATCATCAATCTTCCAGTCGTTAATGGTGCCAATAGTCATGCGAAGGGTTTTccc                                                                                        <  1:60644/201‑1 (MQ=255)                                                                                                                                                                                                          cGTGATTATGCCTGCAGGGATTTTGCTTCTGCGATTTTTACAGCCTTAGCAATTCGTGGATCTATCCCTGTATCGATCAATGTTTGTCACCGTCTTGCCTCGGCTCTGGCACCATCAATCTTCCAGTCGTTAATGTTGCCAAAAGTCATGCGAAGGGTTTTCCCCGCATATACGCGTTGGCATACAAAGGCTTTTGCTCCGCTAGTTGATCGGCATGCCAGGGTTGTTACATCTGCCTCCCAACGaaaaa  >  1:175427/1‑249 (MQ=255)                                                                                                                                                                                                                                |                                                                                                                                                                                                                                    GGCAGGTTGAGCAAACTAGCCAATGGTCCAGCCGAAGTCGGGCCTTGGCCTCTTTTTTTACTTTCGCCTCCACGACTGGACAAGTTAATGTGATCGGCAATGTATCGAGTAGAATATGGGCGTTTAGTTTTTGCACTGATACCGGTTCTCAATTCTTGAAGATAGTCTTCCCAGGCGACGGAGAAAGTCACTTTTGTTTTACGTGATTCTGCCTGCAGGGATTCTGCTTCTGCGATTTTTACAGCCTTAGCAATTCGTGGATCTATCCCTGTATCGATCAATGTTTGTAACCGTCTTGCCTCGGCTCTCGCATCATCAATCTTCCAGTCGTTAATGTTGCCAATAGTCATGCGAAGGGTTTTCCCCGCATATACGCTTTGGAATACAAAGGCTTTTGCTCCGCTAGTTGCTCGGCATGCCAGGGTTGTTACATCTGCATCCCAAAGAAAAG  >  NC_000913/296498‑296948

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑