Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	4,356,445	A→T	33.4%	intergenic (‑34/+25)	dtpC ← / ← cadA	dipeptide and tripeptide permease/lysine decarboxylase, acid‑inducible

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,356,445	0	A	T	33.4%	7.8 / 8.5	12	intergenic (‑34/+25)	dtpC/cadA	dipeptide and tripeptide permease/lysine decarboxylase, acid‑inducible
Reads supporting (aligned to +/- strand):  ref base A (4/4);  new base T (2/2);  total (6/6)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.64e-01

GTGAGATAGAGAATGAGTAAGGCACGCATGCCGTAAAAACTGAAGTACTCCCAGATTTGGATCGCCACGATATAGTATATCGCGCGCGGCTGTGAGGGTGTTTTCATGTGTTCTCCTTATGAGCAAAAAAGGGAAGTGGCAAGCCACTTCCCTTGTACGAGCTAATTATTTTTTGCTTTCTTCTTTCAATACCTTAACGGTATAGCGGCCATCAGCCTGACGGTATGCACCGTGAATATCGGTTTCAAAGCCCGGATAGTGAGCGCCGA  >  NC_000913/4356305‑4356573                                                                                                                                             |                                                                                                                                 gTGAGATAGAGAATGAGTAAGGCACGCATGCCGTAAAAACTGAAGTACTCCCAGATTTGGATCGCCACGATATAGTATATCGCGCGCGGCTGTGAGGGTGTTTTCATGTGTTCTCCTTATGAGCAAAAAAGGGAAGTGGCTTGCCACt                                                                                                                           <  3:644709/148‑1 (MQ=255)             aTGAGTAAGGCACGCATGCCGTAAAAACTGAAGTACTCCCAGATTTGGATCGCCACGATATAGTATATCGCGCGCGGCTGTGAGGGTGTTTTCATGTGTTCTCCTTATGAGCAAAAAAGGGAAGTGGCa                                                                                                                                  >  1:156291/1‑129 (MQ=255)             aTGAGTAAGGCACGCATGCCGTAAAAACTGAAGTACTCCCAGATTTGGATCGCCACGATATAGTATATCGCGCGCGGCTGTGAGGGTGTTTTCATGTGTTCTCCTTATGAGCAAAAAAGGGAAGTGGCa                                                                                                                                  <  4:740019/129‑1 (MQ=255)             aTGAGTAAGGCACGCATGCCGTAAAAACTGAAGTACTCCCAGATTTGGATCGCCACGATATAGTATATCGCGCGCGGCTGTGAGGGTGTTTTCATGTGTTCTCCTTATGAGCAAAAAAGGGAAGTGGCa                                                                                                                                  >  3:740019/1‑129 (MQ=255)             aTGAGTAAGGCACGCATGCCGTAAAAACTGAAGTACTCCCAGATTTGGATCGCCACGATATAGTATATCGCGCGCGGCTGTGAGGGTGTTTTCATGTGTTCTCCTTATGAGCAAAAAAGGGAAGTGGCa                                                                                                                                  <  2:156291/129‑1 (MQ=255)                     ggCACGCATGCCGTAAAAACTGAAGTACTCCCAGATTTGGATCGCCACGATATAGTATATCGCGCGCGGCTGTGAGGGTGTTTTCATGTGTTCTCCTTATGAGCAAAAAAGGGAAGTGGCa                                                                                                                                  >  2:394080/1‑121 (MQ=255)                     ggCACGCATGCCGTAAAAACTGAAGTACTCCCAGATTTGGATCGCCACGATATAGTATATCGCGCGCGGCTGTGAGGGTGTTTTCATGTGTTCTCCTTATGAGCAAAAAAGGGAAGTGGCa                                                                                                                                  <  1:394080/121‑1 (MQ=255)                         cGCATGCCGTAAAAACTGAAGTACTCCCAGATTTGGATCGCCACGATATAGTATATCGCGCGCGGCTGTGAGGGTGTTTTCATGTGTTCTCCTTATGAGCAAAAAAGGGAAGTGGCAAGcc                                                                                                                              >  3:345948/1‑121 (MQ=255)                         cGCATGCCGTAAAAACTGAAGTACTCCCAGATTTGGATCGCCACGATATAGTATATCGCGCGCGGCTGTGAGGGTGTTTTCATGTGTTCTCCTTATGAGCAAAAAAGGGAAGTGGCAAGcc                                                                                                                              <  4:345948/121‑1 (MQ=255)                                                                 ccACGATATAGTATATCGCGCGCGGCTGTGAGGGTGTTTTCATGTGTTCTCCTTATGAGCAAAAAAGGGAAGTGGCAAg                                                                                                                                >  2:779852/1‑79 (MQ=255)                                                                 ccACGATATAGTATATCGCGCGCGGCTGTGAGGGTGTTTTCATGTGTTCCCCTTATGAGCAAAAAAGGGAAGTGGCAAg                                                                                                                                <  1:779852/79‑1 (MQ=255)                                                                  cACGATATAGTATATCGCGCGCGGCTGTGAGGGTGTTTTCATGTGTTCTCCTTATGAGCAAAAAAGGGAAGTGGCAAg                                                                                                                                >  3:257417/1‑78 (MQ=255)                                                                  cACGATATAGTATATCGCGCGCGGCTGTGAGGGTGTTTTCATGTGTTCTCCTTATGAGCAAAAAAGGGAAGTGGCAAg                                                                                                                                <  4:257417/78‑1 (MQ=255)                                                                   aCGATATAGTATATCGCGCGCGGCTGTGAGGGTGTTTTCATGTGTTCTCCTTATGAGCAAAAAAGGGAAGTGGCTTGCCACTTc                                                                                                                         >  2:1036931/1‑84 (MQ=255)                                                                   aCGATATAGTATATCGCGCGCGGCTGTGAGGGTGTTTTCATGTGTTCTCCTTATGAGCAAAAAAGGGAAGTGGCTTGCCACTTc                                                                                                                         <  1:1036931/84‑1 (MQ=255)                                                                                                       ttCATGTGTTCTCCTTATGAGCAAAAAAGGGAAGTGGCTTGCCAc                                                                                                                            >  3:26314/1‑45 (MQ=37)                                                                                                                                aaaGGGAAGTGGCAAGCCACTTCCCTTGTACGAGCTAATTATTTTTTGCTTTCTTCTTTCAATACCTTAACGGTATAGCGGCCATCAGCCTGACGGTATGCACCGTGAATATCGGTTTCAAAGCCCGGATAGTGAGCGCCGa  <  2:537700/142‑1 (MQ=255)                                                                                                                                aaaGGGAAGTGGCAAGCCACTTCCCTTGTACGAGCTAATTATTTTTTGCTTTCTTCTTTCAATACCTTAACGGTATAGCGGCCATCAGCCTGACGGTATGCACCGTGAATATCGGTTTCAAAGCCCGGATAGTGAGCGCCGa  >  1:537700/1‑142 (MQ=255)                                                                                                                                             |                                                                                                                                 GTGAGATAGAGAATGAGTAAGGCACGCATGCCGTAAAAACTGAAGTACTCCCAGATTTGGATCGCCACGATATAGTATATCGCGCGCGGCTGTGAGGGTGTTTTCATGTGTTCTCCTTATGAGCAAAAAAGGGAAGTGGCAAGCCACTTCCCTTGTACGAGCTAATTATTTTTTGCTTTCTTCTTTCAATACCTTAACGGTATAGCGGCCATCAGCCTGACGGTATGCACCGTGAATATCGGTTTCAAAGCCCGGATAGTGAGCGCCGA  >  NC_000913/4356305‑4356573

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑