Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,433,952	G→T	100%	intergenic (‑278/+39)	pinR ← / ← ynaE	Rac prophage; putative site‑specific recombinase/cold shock protein, Rac prophage

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,433,952	0	G	T	54.2%	‑6.6 / 2.0	6	intergenic (‑278/+39)	pinR/ynaE	Rac prophage; putative site‑specific recombinase/cold shock protein, Rac prophage
Reads supporting (aligned to +/- strand):  ref base G (0/2);  new base T (1/2);  total (1/5)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.07e-02

GGCGGACTCAAGGAAGAAGAATAGTGTTGCGTGTTATTTTAACCAGATTTCAAGTTGTTTGGTCGTGGAAAAGTGGAGCAAAATGTTGTTAAAGTGGAAAAATGATAAAAAAGTAAGTTTATTATATTACATTTTACCATTTAAATTTTGGTTGTCTTTAAGAACTG  >  NC_000913/1433865‑1434031                                                                                        |                                                                                ggaggAATCAAGGAAGAAGAATAGTGTTTCGTGTGATTTTAACCAGATTTAAAGTTGTTTGGTCGTGGAAAAGGGGAGCAAAATGTTGTTAAAGTGGa                                                                       <  1:2479957/95‑1 (MQ=1)                                 gataatttAACAAAATTTCAAGTAGATTGATAGTGGAAAAGTGGAGCAAAATGTTAAAAAAAAAAAAAAATGATAAAAAAGTAAGTttatt                                              <  1:530652/86‑1 (MQ=0)                                           cccgATTTCAAGTTGTTTGGTCGTGGAAAAGTGGAGCAAAGTGTTTTTAAAGTGGAAAACTGGTAGAAAAGTAAGTTTATTATATTACATTTTACCAtt                            >  1:820939/4‑99 (MQ=1)                                                 tttaaGTTGTTTGGTAGTGGAAAAGTGGACCAAAATGTTTTTAAAGTTGAAAAATGATATAAAAGTTAGTTTATTATATTACATTTTACCATTTAAAttt                     <  1:2319671/97‑1 (MQ=1)                                                       ttttttGGTCGTGGAAAATTGGAGCAAAATGTTTTTAAATTGGAAAAATGATAAAAAAGTAAGTTTATTATATTACATTTTACCATTTAAATTTTg                   <  1:2295725/93‑1 (MQ=1)                                                                    gagaaGTGGAGCAAAATGTTGTTAAAGTGGAAAAATGATAAAAAAGTAAGTTTATTATATTACATTTTACCATTTAAATTTTGGTTGTCTTTAAGAACTg  <  1:561465/97‑1 (MQ=1)                                                                                        |                                                                                GGCGGACTCAAGGAAGAAGAATAGTGTTGCGTGTTATTTTAACCAGATTTCAAGTTGTTTGGTCGTGGAAAAGTGGAGCAAAATGTTGTTAAAGTGGAAAAATGATAAAAAAGTAAGTTTATTATATTACATTTTACCATTTAAATTTTGGTTGTCTTTAAGAACTG  >  NC_000913/1433865‑1434031

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑