Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	559,691	C→T	intergenic (+25/‑6)	sfmC → / → sfmD	putative periplasmic pilus chaperone/putative outer membrane export usher protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	559,691	0	C	T	100.0%	64.3 / NA	18	intergenic (+25/‑6)	sfmC/sfmD	putative periplasmic pilus chaperone/putative outer membrane export usher protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (9/9);  total (9/9)

GGCTGCACCCAGAGTTAATTCACAAATTCCCTTACCCTCAGGAGTGCAGGGAAAGCTGAAATTTCAGACCGTTAATGATTATGGTTCAGTAACTCCGGTCAGAGAAGTGAACTTAAACTAACCGAATCATCTGACAATATCAGAGCTAATTATGAAAATACCCACTACTACGGATATTCCGCAGAGGTATACCTGGTGTCTGGCCGGAATTTGTTATTCATCTCTTGCCATTTTACCCTCCTTTTTAAGCTATGCGGAAAGTTATTTCAACCCGGCATTTTTATTAG  >  NC_000913/559546‑559832                                                                                                                                                  |                                                                                                                                              ggCTGCACCCAGAGTTAATTCACAAATTCCCTTACCCTCAGGAGTGCAGGGAAAGCTGAAATTTCAGACCGTTAATGATTATGGTTCAGTAACTCCGGTCAGAGAAGTGAACTTAAACTAACCGAATCATCTGACAATATCAGAGTTAAtt                                                                                                                                          >  1:156877/1‑151 (MQ=255)     gCACCCAGAGTTAATTCACAAATTCCCTTACCCTCAGGAGTGCAGGGAAAGCTGAAATTTCAGACCGTTAATGATTATGGTTCAGTAACTCCGGTCAGAGAAGTGAACTTAAACTAACCGAATCATCTGACAATATCAGAGTTAATTATGa                                                                                                                                      >  2:267319/1‑151 (MQ=255)                             cccTTACCCTCAGGAGTGCAGGGAAAGCTGAAATTTCAGACCGTTAATGATTATGGTTCAGTAACTCCGGTCAGAGAAGTGAACTTAAACTAACCGAATCATCTGACAATATCAGAGTTAATTATGAAAATACCCACTACTACGGATAtt                                                                                                               >  2:187808/1‑150 (MQ=255)                                  aCCCTCAGGAGTGCAGGGAAAGCTGAAATTTCAGACCGTTAATGATTATGGTTCAGTAACTCCGGTCAGAGAAGTGAACTTAAACTAACCGAATCATCTGACAATATCAGAGTTAATTATGAAAATACCCACTACTACGGATATTCCGCag                                                                                                         >  1:39722/1‑151 (MQ=255)                                  aCCCTCAGGAGTGCAGGGAAAGCTGAAATTTCAGACCGTTAATGATTATGGTTCAGTAACTCCGGTCAGAGAAGTGAACTTAAACTAACCGAATCATCTGACAATATCAGAGTTAATTATGAAAATACCCACTACTACGGATATTCCGCag                                                                                                         >  2:126000/1‑151 (MQ=255)                                   cccTCAGGAGTGCAGGGAAAGCTGAAATTTCAGACCGTTAATGATTATGGTTCAGTAACTCCGGTCAGAGAAGTGAACTTAAACTAACCGAATCATCTGACAATATCAGAGTTAATTATGAAAATACCCACTACTACGGATATTCCGCaga                                                                                                        >  2:133542/1‑151 (MQ=255)                                             tGCAGGGAAAGCTGAAATTTCAGACCGTTAATGATTATGGTTCAGTAACTCCGGTCAGAGAAGTGAACTTAAACTAACCGAATCATCTGACAATATCAGAGTTAATTATGAAAATACCCACTACTACGGATATTCCGCAGAGGTATAcc                                                                                                <  1:268899/149‑1 (MQ=255)                                             tGCAGGGAAAGCTGAAATTTCAGACCGTTAATGATTATGGTTCAGTAACTCCGGTCAGAGAAGTGAACTTAAACTAACCGAATCATCTGACAATATCAGAGTTAATTATGAAAATACCCACTACTACGGATATTCCGCAGAGGTATAcc                                                                                                <  1:97636/149‑1 (MQ=255)                                             tGCAGGGAAAGCTGAAATTTCAGACCGTTAATGATTATGGTTCAGTAACTCCGGTCAGAGAAGTGAACTTAAACTAACCGAATCATCTGACAATATCAGAGTTAATTATGAAAATACCCACTACTACGGATATTCCGCAGAGGTATACCt                                                                                               <  2:46236/150‑1 (MQ=255)                                             tGCAGGGAAAGCTGAAATTTCAGACCGTTAATGATTATGGTTCAGTAACTCCGGTCAGAGAAGTGAACTTAAACTAACCGAATCATCTGACAATATCAGAGTTAATTATGAAAATACCCACTACTACGGATATTCCGCAGAGGTATACCt                                                                                               <  2:187403/150‑1 (MQ=255)                                                                             gATTATGGTTCAGTAACTCCGGTCAGAGAAGTGAACTTAAACTAACCGAATCATCTGACAATATCAGAGTTAATTATGAAAATACCCACTACTACGGATATTCCGCAGAGGTATACCTGGTGTCTGGCCGGAATTTGTTATTCATCTCTTg                                                              >  1:216813/1‑151 (MQ=255)                                                                                                   tCAGAGAAGTGAACTTAAACTAACCGAATCATCTGACAATATCAGAGTTAATTATGAAAATACCCACTACTACGGATATTCCGCAGAGGTATACCTGGTGTCTGGCCGGAATTTGTTATTCATCTCTTGCCATTTTACCCTCCTTTTTAAg                                        <  2:60023/151‑1 (MQ=255)                                                                                                       agaAGTGAACTTAAACTAACCGAATCATCTGACAATATCAGAGTTAATTATGAAAATACCCACTACTACGGATATTCCGCAGAGGTATACCTGGTGTCTGGCCGGAATTTGTTATTCATCTCTTGCCATTTTACCCTCCTTTTTAAGc                                       <  1:238278/148‑1 (MQ=255)                                                                                                       agaAGTGAACTTAAACTAACCGAATCATCTGACAATATCAGAGTTAATTATGAAAATACCCACTACTACGGATATTCCGCAGAGGTATACCTGGTGTCTGGCCGGAATTTGTTATTCATCTCTTGCCATTTTACCCTCCTTTTTAAGc                                       <  1:70267/148‑1 (MQ=255)                                                                                                       agaAGTGAACTTAAACTAACCGAATCATCTGACAATATCAGAGTTAATTATGAAAATACCCACTACTACGGATATTCCGCAGAGGTATACCTGGTGTCTGGCCGGAATTTGTTATTCATCTCTTGCCATTTTACCCTCCTTTTTAAGc                                       <  2:153666/148‑1 (MQ=255)                                                                                                                                      aCAATATCAGAGTTAATTATGAAAATACCCACTACTACGGATATTCCGCAGAGGTATACCTGGCGTCTGGCCGGAATTTGTTATTCATCTCTTGCCATTTTACCCTCCTTTTTAAGCTATGCGGAAAGTTATTTCAACCCGGCATTTttat     >  1:103254/1‑151 (MQ=255)                                                                                                                                         atatCAGAGTTAATTATGAAAATACCCACTACTACGGATATTCCGCAGAGGTATACCTGGTGTCTGGCCGGAATTTGTTATTCATCTCTTGCCATTTTACCCTCCTTTTTAAGCTATGCGGAAAGTTATTTCAACCCGGCATTTTTATTag  >  2:110854/1‑151 (MQ=255)                                                                                                                                         atatCAGAGTTAATTATGAAAATACCCACTACTACGGATATTCCGCAGAGGTATACCTGGTGTCTGGCCGGAATTTGTTATTCATCTCTTGCCATTTTACCCTCCTTTTTAAGCTATGCGGAAAGTTATTTCAACCCGGCATTTTTATTag  <  1:206974/151‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                              GGCTGCACCCAGAGTTAATTCACAAATTCCCTTACCCTCAGGAGTGCAGGGAAAGCTGAAATTTCAGACCGTTAATGATTATGGTTCAGTAACTCCGGTCAGAGAAGTGAACTTAAACTAACCGAATCATCTGACAATATCAGAGCTAATTATGAAAATACCCACTACTACGGATATTCCGCAGAGGTATACCTGGTGTCTGGCCGGAATTTGTTATTCATCTCTTGCCATTTTACCCTCCTTTTTAAGCTATGCGGAAAGTTATTTCAACCCGGCATTTTTATTAG  >  NC_000913/559546‑559832

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑