Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	6,148,724	G→T	19.1%	M100I (ATG→ATT)	cusF →	copper efflux protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	6,148,724	0	G	T	19.1%	47.5 / 4.7	21	M100I (ATG→ATT)	cusF	copper efflux protein
Reads supporting (aligned to +/- strand):  ref base G (11/6);  new base T (2/2);  total (13/8)
Fisher's exact test for biased strand distribution p-value = 6.18e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.46e-01

ATGCATGGACCGGTTGCTGCGTTGAAATGGCCGGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGATATTCGCAAACAGTAATTCGCCTAATTATCCTGTCTGCCAACGCTTGATTCGCCCATGACCTCCTGACGCCTCCTAGCAACTGGAAAAGCTT  >  NC_002947/6148608‑6148842                                                                                                                     |                                                                                                                       aTGCATGGACCGGTTGCTGCGTTGAAATGGCCGGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGa                                                                                                     >  2:369686/1‑136 (MQ=255)    cATGGACCGGTTGCTGCGTTGAAATGGCCGGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGAttt                                                                                                  >  1:252302/1‑135 (MQ=255)         aCCGGTTGCTGCGTTGAAATGGCCGGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGat                                                                                             >  1:181/1‑136 (MQ=255)            ggTTGCTGCGTTGAAATGGCCGGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGATAtt                                                                                          >  1:267560/1‑136 (MQ=255)                gctgcGTTGAAATGGCCGGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATTGATGGCAGCACGGCAACGATTGTTGATATTCGCa                                                                                      >  1:164861/1‑136 (MQ=255)                gctgcGTTGAAATGGCCGGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATTGATGGCAGCACGGCAACGATTGTTGATATTCGCa                                                                                      >  1:409948/1‑136 (MQ=255)                gctgcGTTGAAATGGCCGGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAGCGATTGCTGATATTCGCa                                                                                      >  1:147394/1‑136 (MQ=255)                      ttGAAATGGCCGGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGATATTCGCAAACAGt                                                                                >  2:348545/1‑136 (MQ=255)                                                  tCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGATATTCGCAAACAGTAATTCGCCTAATTATCCTGTCTGCCAAc                                                    <  1:63408/136‑1 (MQ=255)                                                      aGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGATATTCGCAAACAGTAATTCGCCTAATTATCCTGTCTGCCAACGCtt                                                <  1:78251/136‑1 (MQ=255)                                                      aGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGATATTCGCAAACAGTAATTCGCCTAATTATCCTGTCTGCCAACGCtt                                                <  2:267560/136‑1 (MQ=255)                                                              cgcAACAGCTCGATGGATTTAAGGTGGGAGACAACGTAGAGTTTGATTTACGGATGGATGGCAGCACGGCAACGATTGTTGATATTCGCAAACAGTAATTAGCCTAATTATACTGTCTGCCAACGCTTGAATAGcc                                        >  2:206336/1‑136 (MQ=255)                                                               gcAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATTGATGGCAGCACGGCAACGATTGTTGATATTCGCAAACAGTAATTCGCCTAATTATCCTGTCTGCCAACGCTTGATTCGccc                                       <  2:164861/136‑1 (MQ=255)                                                               gcAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATTGATGGCAGCACGGCAACGATTGTTGATATTCGCAAACAGTAATTCGCCTAATTATCCTGTCTGCCAACGCTTGATTCGccc                                       <  2:409948/136‑1 (MQ=255)                                                                        cGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGATATTCGCAAACAGTAATTCGCCTAATTATCCTGTCTGCCAACGCTTGATTCGCCCATGAcctcc                              <  1:348545/136‑1 (MQ=255)                                                                                 gAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGATATTCGCAAACAGTAATTCGCCTAATTATCCTGTCTGCCAACGCtt                                                <  2:250164/109‑1 (MQ=255)                                                                                 gAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGATATTCGCAAACAGTAATTCGCCTAATTATCCTGTCTGCCAACGCtt                                                >  1:250164/1‑109 (MQ=255)                                                                                       gggAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGATATTCGCAAACAGTAATTCGCCTAATTATCCTGTCTGCCAACGCTTGATTCGCCCATGACCTCCTGACGCCTCCTAGCa               >  2:141357/1‑136 (MQ=255)                                                                                           gaCAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGATATTCGCAAACAGTAATTCGCCTAATTATCCTGTCTGCCAACGCTTGATTCGCCCATGACCTCCTGACGCCTCCTAGCAACTg           >  1:97356/1‑136 (MQ=255)                                                                                             cAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGATATTCGCAAACAGTAATTCGCCTAATTATCCTGTCTGCCAACGCTTGATTCGCCCATGACCTCCTGACGCCTCCTAGCAACTGGa         >  2:319240/1‑136 (MQ=255)                                                                                                    gagTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGATATTCGCAAACTGTAATTCGCCTAATTATCCTGTCTGCCAACGCTTGATTCGCCCATGACCTCCTGACGCCTCCTAGCAACTGGAAAAGCtt  <  1:101538/136‑1 (MQ=255)                                                                                                                     |                                                                                                                       ATGCATGGACCGGTTGCTGCGTTGAAATGGCCGGCCATGACCATGGCCTTCAAAGCCTCTGCGCAACAGCTCGATGGATTGAAGGTGGGAGACAACGTAGAGTTTGATTTCCGGATGGATGGCAGCACGGCAACGATTGTTGATATTCGCAAACAGTAATTCGCCTAATTATCCTGTCTGCCAACGCTTGATTCGCCCATGACCTCCTGACGCCTCCTAGCAACTGGAAAAGCTT  >  NC_002947/6148608‑6148842

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑