Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,566,195	A→T	25.0%	intergenic (‑312/‑168)	PP_1374 ← / → pcaR	hypothetical protein/pca regulon transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,566,195	0	A	T	25.0%	27.0 / 5.9	16	intergenic (‑312/‑168)	PP_1374/pcaR	hypothetical protein/pca regulon transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base A (5/7);  new base T (2/2);  total (7/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.59e-01

TACGCAACCCTGACATCATCTGGCGTAAGTAGCAGATTGTGCCCGCGAACAGTTGGGACCTTTCGTACAAAGTTTGAAAGGAATGGCGGATAGAAGTTCGTTGCAATGTCAGGGCGGGCCGTAATGAAAAACGGCCTCGCCGAAAGGCGAGGCCGTTGCCTGGGGACTTCTACGGTGGGTACCTGACCAGTCTCTCCAAAGAAGCCACAAGTGGCATGGGAAAGGTATAAGCAAAAGTGTCGGCGGTCAATTGCGATTATCGGCCGTTTGTTCGATAATCGCAC  >  NC_002947/1566052‑1566335                                                                                                                                                |                                                                                                                                             tACGCAACCCTGACATCATCTGGCGTAAGTAGCAGATTGTGCCCGCGAACAGTTGGGACCTTTCGTACAAAGTTTGAAAGGAATGGCGGATAGAAGTTCGTTGCAATGTCAGGGCGGGCCGTAATGAAAAACGGCCTCGCCGAAAGGCGa                                                                                                                                        <  2:556487/150‑1 (MQ=255)     cAACCCTGAAATCATCTGGCGTAAGTAGCAGATTGTGCCCGCGAACAGTTGGGACCTTTCGTACAAAGTTTGAAAGGAATGGCGGATAGAAGTTCGTTGCAATGTCAGGGCGGGCCGTAATGAAAAACGGCCTCGCCGAAAGGCGAGGcc                                                                                                                                    <  1:95461/150‑1 (MQ=255)           tGACATCATCTGGCGTAAGTAGCAGATTGTGCCCGCGAACAGTTGGGACCTTTCGTACAAAGTTAGACAGGCCTCGGGGATAGAAGTTCGCGGGAGGGTCAGGGCGGGCCGTAATGAAAAACGGCCTCGCCTTTCGGCGAGGCCGttttt                                                                                                                              <  1:75575/150‑4 (MQ=255)                                gCAGATTGTGCCCGCGAACAGTTGGGACCTTTCGTACAAAGTTTGAAAGGAATGGCGGATAGAAGTTCGTTGCAATGTCAGGGCGGGCCGTAATGAAAAACGGCCTCGCCGAAAGGCGAGGCCGTTGCCTGGGGACTTCTACGGTGGGTa                                                                                                         >  2:83878/1‑150 (MQ=255)                                                 aCAGTTGGGACCTTTCGTACAAAGTTTGAAAGGAATGGCGGATAGAAGTTCGTTGCAATGTCAGGGCGGGCCGTAATGAAAAACGGCCTCGCCGAAAGGCGAGGCCGTTGCCTGGGGACTATGATGAGGGGTACCTGACCAGTCTCTCCa                                                                                        >  1:157019/1‑150 (MQ=255)                                                   aGTTGGGACCTTTCGTACAAAGTTTGAAAGGAATGGCGGATAGAAGTTCGTTGCAATGTCAGGGCGGGCCGTAATGAAAAACGGCCTCGCCGAAAGGCGAGGCCGTTGCCTGGGGACTTCTACGGTGGGTACCTGACCAGTCTCTCCaaa                                                                                      <  2:475373/150‑1 (MQ=255)                                                                   aCAACGTTTGAAAGGAATGGCGGATAGAAGTTCGTTGCAATGTCAGGGCGGGCCGTAATGAAAAACGGCCTCGCCGAAAGGCGAGGCCGTTGCCTGGGGACTTCTACGGTGGGTACCTGACCAGTCTCTCCAAAGAAGCCACaa                                                                            >  2:313150/1‑144 (MQ=255)                                                                   aCAAAGTTTGAAAGGAATGGCGGATAGAAGTTCGTTGCAATGTCAGGGCGGGCCGTAATGAAAAACGGCCTCGCCGAAAGGCGAGGCCGTTGCCTGGGGACTTCTACGGTGGGTACCTGACCAGTCTCTCCAAAGAAGCCACaa                                                                            <  1:313150/144‑1 (MQ=255)                                                                               aGGAATGGCGGATAGAAGTTCGTTGCAATGTCAGGGCGGGCCGTAATGAAAAACGGCCTCGCCGAAAGGCGAGGCCGTTGCCTGGGGACTTCTACGGTGGGTACCTGACCAGTCTCTCCAAAGAAGTCACAAGTGGCATGGGAAAGGtat                                                          <  1:83878/150‑1 (MQ=255)                                                                                                     ttGCAATGTCAGGGCGGGCCGTAATGAAAAACGGCCTCGCCTTTCGGCGAGGCCGttt                                                                                                                                <  1:461917/58‑2 (MQ=17)                                                                                                     ttGCAATGTCAGGGCGGGCCGTAATGAAAAACGGCCTCGCCTTTCGGCGAGGCCGttt                                                                                                                                >  2:461917/1‑57 (MQ=17)                                                                                                                           aaTGAAAAACGGCCTCGCCGAAAGGCGAGGCCGTTGCCTGGGGACTTCTACGGTGGGTACCTGACCAGTCTCTCCAAAGAAGCCACAAGTGGCATGGGAAAGGTATAAGCAAAAGTGTCGGCGGTCAATTGCGATTATCGGCCGTTTGtt              <  2:525683/150‑1 (MQ=255)                                                                                                                                    cGGCCTCGCCTTTCGGCGAGGCCGTTGCCTGGGGACTTCTACGGTGGGTACCTGACCAGTCTCTCCAAAGAAGCCACAAGTGGCATGGGAAAGGTATAAGCAAAAGTGTCGGCGGTCAATTGCGATTATCGGCCGTTTGTTCGATAATCg     >  1:277757/1‑150 (MQ=255)                                                                                                                                     ggCCTCGCCGAAAGGCGAGGCCGTTGCCTGGGGACTTCTACGGTGGGTACCTGACCAGTCTCTCCAAAGAAGCCACAAGTGGCATGGGAAAGGt                                                            >  1:164480/1‑94 (MQ=255)                                                                                                                                     ggCCTCGCCGAAAGGCGAGGCCGTTGCCTGGGGACTTCTACGGTGGGTACCTGACCAGTCTCTCCAAAGAAGCCACAAGTGGCATGGGAAAGGt                                                            <  2:164480/94‑1 (MQ=255)                                                                                                                                       ccTCGCCGAAAGGCGAGGCCGTTGCCTGGGGACTTCTACGGTGGGTACCTGACCAGTCTCTCCAAAGAAGCCACAAGTGGCATGGGAAAGGTATAAGCAAAAGTGTCGGCGGTCAATTGCGATTATCGGCCGTTTGTTCGATAATCGCAc  >  1:251331/1‑150 (MQ=255)                                                                                                                                                |                                                                                                                                             TACGCAACCCTGACATCATCTGGCGTAAGTAGCAGATTGTGCCCGCGAACAGTTGGGACCTTTCGTACAAAGTTTGAAAGGAATGGCGGATAGAAGTTCGTTGCAATGTCAGGGCGGGCCGTAATGAAAAACGGCCTCGCCGAAAGGCGAGGCCGTTGCCTGGGGACTTCTACGGTGGGTACCTGACCAGTCTCTCCAAAGAAGCCACAAGTGGCATGGGAAAGGTATAAGCAAAAGTGTCGGCGGTCAATTGCGATTATCGGCCGTTTGTTCGATAATCGCAC  >  NC_002947/1566052‑1566335

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑