Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	4,466,422	C→T	17.5%	P275P (CCG→CCA)	treR ←	DNA‑binding transcriptional repressor TreR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,466,422	0	C	T	17.5%	45.6 / 5.4	23	P275P (CCG→CCA)	treR	DNA‑binding transcriptional repressor TreR
Reads supporting (aligned to +/- strand):  ref base C (9/10);  new base T (2/2);  total (11/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.08e-01

ATATATTGCGCGGAAAAATTTAAAAACGGGAACGTTCCCGAAACGCAGCGAAGATCACAATTTATCGTTCAGGAAACGATCAGGACAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCGTTGCTCTTGCAGGTATTTACTTGCGCCAAGTGCCAGCGTGTCGGTTGCGCACAGTAAGGCGGTAGTTTCAGGCGTAATCACTTTTGCAACGTTCTCATAGCCTTGCTTCATAGCAAGCCCTGGCAGGGCGGCAACGGGATGCAGTTTATGCGCTTTGCAGAACGCCAGGTAGGCTTCGTGACGTCGCTTACCGGTTGTCACGT  >  NC_000913/4466220‑4466687                                                                                                                                                                                                           |                                                                                                                                                                                                                                                                          atatagAGCGAGAAAAAATTAAAAAACGGGAACGTTCCCGAAACGCAGCGAAGATCACAATTTATCGGTCAGGAAACGATCAGGACAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGAGCTACGGTTACGATCTCTGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCGTTGCTCTTGc                                                                                                                                                                                                   <  2:189332/275‑1 (MQ=255) aaatatCGCACGAAAAAATTTAAAACCGGGAACGTCCCCGAAACGCAGCGAAGAGCACAATGTAGCGTTCAGGAAACGAACAGGACAGGGTGGCGGGGATGATGGTTTGGTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCGTCGGCGTAACCGGGAGCTACGGTTACGATCTCTGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCGTTGCTCTTGc                                                                                                                                                                                                   <  2:189325/273‑1 (MQ=255)       tGCGCGGAAAAATTTAAAAACGGGAACGTTCCCGAAACGCAGCGAAGATCACAATTTATCGTTCAGGAAACGATCAGGACAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGGGCGATCAACTGGTAAGCCGCCTGGCGTCCCGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGACTTTCa                                                                                                                                                                                                                                                           >  1:377527/1‑213 (MQ=255)          gcgGAAAAATTTAAAAACGGGAACGTTCCCGAAACGCAGCGAAGATCACAATTTATCGTTCAGGAAACGATCAGGACAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCTGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCGTTGctc                                                                                                                                                                                                       >  1:189326/1‑262 (MQ=255)          gcgGAAAAATTTAAAAACGGGAACGTTCCCGAAACGCAGCGAAGATCACAATTTATCGTTCAGGAAACGATCAGGACAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCTGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCGTTGctc                                                                                                                                                                                                       >  1:189333/1‑262 (MQ=255)                aaaTTTAAAAACGGGAACGTTCCCGAAACGCAGCTAAGATCACAATTTATCGTGCAGGGAACGATCAGGACAGGGTGGCGGGGCTGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTaa                                                                                                                                                                                                                                                       <  1:212947/208‑1 (MQ=255)                                                             tttATCGTTCAGGAAACGATCAGGACAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAg                                                                                                                                                                                                                        <  1:54933/194‑1 (MQ=255)                                                                                   ggACAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGCTGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCGTTGCTCTTGCAGGTATTTACTTTCGCAAAGTGCCAGCGTGTCGGTTGCGCACAGTAAGGCGGTAGTTTCCGGCCTAATCACTTTTGCAAc                                                                                                                   >  1:15591/1‑273 (MQ=255)                                                                                              cGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCCAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGCTCTCCGGATGGAGGAATTTCATTAACGGCGTGTTACCGACGCTATCCAGTTGCAAGgt                                                                                                                                                                                                                      >  1:111417/1‑163 (MQ=255)                                                                                              cGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCa                                                                                                                                                                                                                                                           >  2:318750/1‑126 (MQ=255)                                                                                              cGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCGTTGCTCtt                                                                                                                                                                                                     >  1:146019/1‑180 (MQ=255)                                                                                              cGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCGTTGCTCTTGCAGGTATTTACTTGCGCCAAGTGCCAGCGTGTCGGTTGCGCACAGTAAGGCGGTAGTTTCAGGCGTAATCACTTTTGc                                                                                                                      >  1:270343/1‑259 (MQ=255)                                                                                                  gatgatgatTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCGTTGCTCTTGCAg                                                                                                                                                                                                 <  2:146018/180‑1 (MQ=255)                                                                                                  gatgatgatTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGACGGAGGAATTTCATTaa                                                                                                                                                                                                                                                       <  1:318751/126‑1 (MQ=255)                                                                                                                                              tCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGTATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCCTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCGTTGCTCTTGCAGGTATTTACTTGCGCCAAGTGCCAGCGTGTCGGTTGCGCACAGTAAGGCg                                                                                                                                                <  1:32511/185‑1 (MQ=255)                                                                                                                                                aaCTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATCGAGGAATTTCAGTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCGTTGCTCTTGCAGGTATTTACTTGCGcc                                                                                                                                                                                  <  1:206773/149‑1 (MQ=255)                                                                                                                                                                 gcctCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAAGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCGTTGCTCTTGCAGGTATTTACTTGCGCCAAGTGCCAGCGTGTCGGTTGCGCACAGTAAGGCg                                                                                                                                                <  1:332969/163‑1 (MQ=255)                                                                                                                                                                            cGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCGTTGCTCTTGCAGGTATTTACTTGCGCCAAGTGCCAGc                                                                                                                                                                        >  2:268968/1‑131 (MQ=255)                                                                                                                                                                                gTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCGTTGCTCTTGCAGGTATTTACTTGCGCCAAGTGCCAGCgtgt                                                                                                                                                                    <  1:268969/131‑1 (MQ=255)                                                                                                                                                                                             aCGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCGTTGCTCTTGCAGGTATTTACTTGCGCCAAGTGcc                                                                                                                                                                           <  1:217477/111‑1 (MQ=255)                                                                                                                                                                                              cGGTTACGATCTCCGGAGGGAGGAATTTCATGAACGGCGTATAACCGACGCTCGCCAGTTGCAAGGTGTCGATGCGTTGCTCTTGCAGGTATTTACTTGCGCCAAGTGCCAGCGTGTCGGt                                                                                                                                                                >  1:33341/1‑121 (MQ=255)                                                                                                                                                                                                  tACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGCCGCTCCCCAGTTGCAAGGTGTCGATGCGTTTCTCTTGCAGGTATTTACTTGCGCCAAGTGCCAGCGTGTCGGTTccg                                                                                                                                                            <  2:33341/121‑1 (MQ=255)                                                                                                                                                                                                   aCGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCGTTGCTCTTGCAGGTATTTACTTGCGCCAAGTGCCAGCGTGTCGGTTGCGCACAGTAAGGCGGTAGTTTCAGGCGTAATCACTTTTGCAACGTTCTAATAGCCTTGCTTCATAGCAAGCCCTGGCAGGGCGGCAACGGGATGCAGTTTATGCGCTTTGCAGAACGCCAGGTAGGCTTCCTGACGTCCCTTACCGGTTttctcgt  >  1:232886/1‑274 (MQ=255)                                                                                                                                                                                                           cGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCGTTGCTCTTGCAGGTATTTACTTGCGCCAAGTGCCAGCGTGTCGGTTGCGCACAGTAAGGCGGTAGTTTCAGGCGTAATCACTTTTGCAACGTTCTCATCGCCtt                                                                                                     >  1:352443/1‑167 (MQ=255)                                                                                                                                                                                                           |                                                                                                                                                                                                                                                                          ATATATTGCGCGGAAAAATTTAAAAACGGGAACGTTCCCGAAACGCAGCGAAGATCACAATTTATCGTTCAGGAAACGATCAGGACAGGGTGGCGGGGATGATGATTTGTTGCGGTTCGCTGCGCCCGGTTACCTGCGCGATCAACTGGCAAGCCGCCTGGCGTCCAGCTTCGGCGTAACCGGGATCTACGGTTACGATCTCCGGATGGAGGAATTTCATTAACGGCGTATTACCGACGCTCGCCAGTTGCAAGGTGTCGATGCGTTGCTCTTGCAGGTATTTACTTGCGCCAAGTGCCAGCGTGTCGGTTGCGCACAGTAAGGCGGTAGTTTCAGGCGTAATCACTTTTGCAACGTTCTCATAGCCTTGCTTCATAGCAAGCCCTGGCAGGGCGGCAACGGGATGCAGTTTATGCGCTTTGCAGAACGCCAGGTAGGCTTCGTGACGTCGCTTACCGGTTGTCACGT  >  NC_000913/4466220‑4466687

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑