Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	296,399	G→A	A233V (GCT→GTT)	intF ←	putative phage integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	296,399	0	G	A	100.0%	71.7 / NA	22	A233V (GCT→GTT)	intF	putative phage integrase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (6/16);  total (6/16)

CGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAGCAAAAGTACTTGGAGATAGGCCGATGCAATAGGATTATTGAGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGCCAGGAATGATCCCTTGATATTTTTTCTGATAATTACTCCATTTGATGAAAGCACGTAGTAGGCGATAAGCGTGAGCAGTGACGGTAGGTCTATTTTGCCTTTCTGTACTCAGCCACGCTGCTATGTAATCTGGGGTTAGCTCCGATAACGGCAGGTTGAGCAAACTAGCCAATGGTCCAGCCGAAGTCGGGCCTTGGCCTCTTTTTTTACTTTCGCCTCCACGACTGGACAAGTTAATGTGATCGGCAATGTATCGAGTAGAATATGGGCGTTTAGTTTTTGCACTGATACCGGTT  >  NC_000913/296156‑296644                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                      cgaagcgaCGCAATTTCTTCACGCCGAGCACCAGTGAGCAAAAGTACTTGGAGATAGGCCGATGCAATAGGATTAATGAGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGCCAGGAATGATCCCTTGATATTTTTTCTGATAATTACTCCATTTGATGAAAACACgtag                                                                                                                                                                                                                                                <  1:129578/251‑1 (MQ=255)                                  gTGAGCAAAAGTACTTGGAGATAGGCCGATGCAATAGGATTATTGAGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGCCAGGAATGATCCCTTGATATTTTTTCTGATAATTACTCCATTTGATGAAAACACGTAGTAGGCGATAAGCGTGAGCAGTGACGGTAGGTCt                                                                                                                                                                                                               >  2:64486/1‑251 (MQ=255)                                     aGCAAAAGTACTTGGAGATAGGCCGAGGCAATAGGATTATTGAGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCATGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGCCAGGAATGATCCCTTGATATTTTTTCTGATAATTTCTCCATTTGATGAAAACACGGAGTAGGCTATCAGCGTGAGCAGTGACGGTAGGTCTAtt                                                                                                                                                                                                            <  2:160780/251‑1 (MQ=255)                                                      aTAGGCCGATGCAATAGGATTATTGAGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGCCAGGAATGATCCCTTGATATTTTTTCTGATAATTACTCCATTTGATGAAAACACGTAGTAGGCGATAAGCGTGAGCAGTGACGGTAGGTCTATTTTGCCTTTCTGTACTCa                                                                                                                                                                                           <  1:137358/251‑1 (MQ=255)                                                                                ggCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGCCAGGAATGATCCCTTGATATTTGTTCTGATAATTACTCCATTTGATGAAAACACGTAGTAGGCGATAAGCGTGAGCAGTTACGGTAGGTCTATTTTGCCTTTCTGTACTCAGCCACGCTGCTATGTAATCTGGGGtt                                                                                                                                                                 <  1:166853/251‑1 (MQ=255)                                                                                                aaaCCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGCCAGGAATGATCCCTTGATATTTTTTCTGATAATTACTCCATTTGATGAAAACACGTAGTAGGCGATAAGCGTGAGCAGTGACGGTAGGTCTATTTTGCCTTTCTGTACTCAGCCACGCTGCTATGTAATCTGGGGTTAGCTCCGATAACGGCa                                                                                                                                                 <  1:111972/251‑1 (MQ=255)                                                                                                     aGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGCCAGGAATGATCCCTTGATATTTTTTCTGATAATTACTCCATTTGATGAAAACACGTAGTAGGCGATAAGCGTGAGCAGTGACGGTAGGTCTATTTTGCCTTTCTGTACTCAGCCACGCTGCTATGTAATCTGGGGTTAGCTCCGATAACGGCAGGTTg                                                                                                                                            <  2:132698/251‑1 (MQ=255)                                                                                                                           cAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGCCAGGAATGATCCCTTGATATTTTTTCTGATAATTACTCCATTTGATGAAAACATGTAGTAGGCGATAAGCGTGAGCAGTGACGGTAGGTCTATTTTGCCTTTCTGTACTCAGCCACGCTGCTATGTAATCTGGTGTTAGCTCCGATAACGGCAGGGTGaaccaacttacccatggtcc                                                                                                                        >  2:174055/1‑230 (MQ=255)                                                                                                                            aGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGCCAGGAATGATCCCTTGATATTTTTTCTGATAATTACTCCATTTGATGAAAACACGTAGTAGGCGATAAGCGTGAGCAGTGACGGTAGGTCTATTTTGCCTTTCTGTACTCAGCCACGCTGCTATGTAATCTGGGGTTAGCTCCGATAACGGCAGGTTGAGCAAACTAACCAAAGGTCCAGc                                                                                                                     >  2:49823/1‑251 (MQ=255)                                                                                                                             ggCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGCCAGGAATGATCCCTTGATATTTTTTCTGATAATTACTCCATTTGATGAAAACACGTAGTAGGCGATAAGCGTGAGCAGTGACGGTAGGTCTATTTTGCCTTTCTGTACTCAGCCACGCTGCTATGTAATCTGGGGTTAGCTCCGATAACGGCAGGTTGAGCAAACTAGCCAATGGTCCAGcc                                                                                                                    <  1:91081/251‑1 (MQ=255)                                                                                                                                  tcatcaGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGCCAGGAATGATCCCTTGATATTTTTTCTGATAATTACTCCATTTGATGAAAACACGTCGTAGGCGATAAGAGTGAGCAGTGACGGTAGGTCTAATCTGCCTTTCTGGACTCAGCCACGCTGCTATGGAATCTGGGGTTAGCTCCGATAACGGCAGGGTTAGCAAAcatggcaacggtacaggcgcagt                                                                                                               >  1:137041/1‑229 (MQ=255)                                                                                                                                             aCTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGCCAGGAATGATCCCTTGATATTTTTTCTGATAATTACTCCATTTGATGAAAACACGTAGTAGGCGATAAGCGTGAGCAGTGACGGTAGGTCTATTTTGCCTTTCTGTACTCAGCCACGCTGCTATGTAATCTGGGGTTAGCTCCGATAACGGCAGGTTGAGCAAACTAGCCAATGGTCCAGCCGAAGTCGGGCCTTgg                                                                                                     <  2:83223/250‑1 (MQ=255)                                                                                                                                                                     tCTTACGTTGTAATCTTGTGCCAGATCGCCAGGAATGATCCCTTGATATTTTTTCTGATAATTACTCCATTTGATGAAAACACGTAGTAGGCGATAAGCGTGAGCAGTGACGGTAGGTCTATTTTGCCTTTCTGTACTCAGCCACGCTGCTATGTAATCTGGGGTTAGCTCCGATAACGGCAGGTTGAGCAAACTAGCCAATGGTCCAGCCGAAGTCGGGCCTTGGCCTCTTTTTTTACTTTCGCCTCCa                                                                             <  1:238961/250‑1 (MQ=255)                                                                                                                                                                                           aGATCGCCAGGAATGATCCCTTGATATTTTTTCTGATAATTACTCCATTTGATGAAAACACGTAGTAGGCGATAAGCGTGAGCAGTGACGGTAGGTCTATTTTGCCTTTCTGTACTCAGCCACGCTGCTATGTAATCTGGGGTTAGCTCCGATAACGGCAGGTTGAGCAAACTAGCCAATGGTCCAGCCGAAGGCGGGCCTTGGCCTCTTTTTTTACTTTCGCCTCCACGACTGGACAAGTTAATGTGATc                                                      >  1:129882/1‑251 (MQ=255)                                                                                                                                                                                                             ccTTGATATTTTTTCTGATAATTACTCCATTTGATGAAAACACGTAGTAGGCGATAAGCGTGAGCAGTGACGGTAGGTCTATTTTGCCTTTCTGTACTCAGCCACGCTGCTATGTAATCTGGGGTTAGCTCCGATAACGGCAGGTTGAGCAAACTAGCCAATGGTCCAGCCGAAGTCGGGCCTTGGCCTCTTTTTTTACTTTCGCCTCCACGACTGGACAAGTTAATGTGATCGGCAATGTATCGAGTAGa                                    <  1:104017/251‑1 (MQ=255)                                                                                                                                                                                                                tGATATTTTTTCTGATAATTACTCCATTTGATGAAAACACGTAGTAGGCGATAAGCGTGAGCAGTGACGGTAGGTCTATTTTGCCTTTCTGTACTCAGCCACGCTGCTATGTAATCTGGGGTTAGCTCCGATAACGGCAGGTTGAGCAAACTAGCCAATGGTCCAGCCGAAGTCGGGCCTTGGCCTCTTTTTTTACTTTCGCCTCCACGACTGGACAAGTTAATGTGATCGGCAATGTATCGAGTAGaa                                   <  2:105669/249‑1 (MQ=255)                                                                                                                                                                                                                tGATATTTTTTCTGATAATTACTCCATTTGATGAAAACACGTAGTAGGCGATAAGCGTGAGCAGTGACGGTAGGTCTATTTTGCCTTTCTGTACTCAGCCACGCTGCTATGTAATCTGGGGTTAGCTCCGATAACGGCAGGTTGAGCAAACTAGCCAATGGTCCAGCCGAAGTCGGGCCTTGGCCTCTTTTTTTACTTTCGCCTCCACGACTGGACAAGTTAATGTGATCGGCAATGTATCGAGTAGaa                                   <  2:204301/249‑1 (MQ=255)                                                                                                                                                                                                                           cTGATAATTACTCCATTTGATGAAAACACGTAGTAGGCGATAAGCGTGAGCAGTGACGGTAGGTCTATTTTGCCTTTCTGTACTCAGCCACGCTGCTATGTAATCTGGGGTTAGCTCCGATAACGGCAGGTTGAGCAAACTCGCCAATGGTCCAGCCGAAGTCGGGCCTTGGCCTCTTTTTTTACTTTCGCCTCCACGACTGGACAAGTTAATGTGATCGGCAATGTATCGCGTAGAATATGGGCGttt                        >  1:116284/1‑249 (MQ=255)                                                                                                                                                                                                                             gATAATAACTCCATTTGATGAAAACACGTAGTAGGCGATAAGCGTGAGCAGTGACGGTAGGTCTATTTTGCCTTTCTGTACTCAGCCACGCTGCTATGTAATCTGGGGTTAGCTCCGATAACGGCAGGTTGAGCAAACTAGCCAATGGTCCAGCCGAAGTCGGGCCTTGGCCTCTTTTTTTACTTTCGCCTCCACGACTGGACAAGTTAATGTGATCGGCAATGTATCGAGTAGAATATGGGCGTTTa                       <  2:105103/248‑1 (MQ=255)                                                                                                                                                                                                                                        cATTTGATGAAAACACGTAGTAGGCGATAAGCGTGAGCAGTGACGGTAGGTCTATTTTGCCTTTCTGTACTCAGCCACGCTGCTATGTAATCTGGGGTTAGCTCCGATAACGGCAGGTTGAGCAAACTAGCCAATGGTCCAGCCGAAGTCGGGCCTTGGCCTCTTTTTTTACTTTCGCCTCCACGACTGGACAAGTTAATGTGATCGGCAATGTATCGAGTAGAATATGGGCGTTTAGTTTTTGCACTGAt         <  1:64486/251‑1 (MQ=255)                                                                                                                                                                                                                                        cATTTGATGAAAACACGTAGTAGGCGATAAGCGTGAGCAGTGACGGTAGGTCTATTTTGCCTTTCTGTACTCAGCCACGCTGCTATGTAATCTGGGGTTAGCTCCGATAACGGCAGGTTGAGCAAACTAGCCAATGGTCCAGCCGAAGTCGGGCCTTGGCCTCTTTTTTTACTTTCGCCTCCACGACTGGACAAGTTAATGTGATCGGCAATGTATCGAGTAGAATATGGGCGTTTAGTTTTTGCACTGAt         <  1:154024/251‑1 (MQ=255)                                                                                                                                                                                                                                               ggaAAACACGTAGTAGGCGATAAGCGTGAGCAGTGACGGTAGGTCTATTTTGCCTTTCTGTACTCAGCCACGCTGCTATGTAATCGGGGGTTAGCTCCGATAACGGCAGGTTGAGCAAACTAGCCAGTGGTCCAGCCGAAGTCGGGCCTTGGCCTCTTTTTTTACTTTCGCCTCCACGACTGGACAAGTTAATGTGATCGGCAATGTATCGAGTAGAATATGGGCGTTTAGTTTTTGCACTGATACCGGtt  <  2:172371/250‑1 (MQ=255)                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                      CGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAGCAAAAGTACTTGGAGATAGGCCGATGCAATAGGATTATTGAGGCTACGCACGGCACTAAACCAGCTTTTTAGTTGTTCCTTTTGCAGGCAATCATCAGCTTTACTCGCTGACACGGGAACCATTTTTCTTACGTTGTAATCTTGTGCCAGATCGCCAGGAATGATCCCTTGATATTTTTTCTGATAATTACTCCATTTGATGAAAGCACGTAGTAGGCGATAAGCGTGAGCAGTGACGGTAGGTCTATTTTGCCTTTCTGTACTCAGCCACGCTGCTATGTAATCTGGGGTTAGCTCCGATAACGGCAGGTTGAGCAAACTAGCCAATGGTCCAGCCGAAGTCGGGCCTTGGCCTCTTTTTTTACTTTCGCCTCCACGACTGGACAAGTTAATGTGATCGGCAATGTATCGAGTAGAATATGGGCGTTTAGTTTTTGCACTGATACCGGTT  >  NC_000913/296156‑296644

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑