Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,943,488	0	T	G	57.1%	1.0 / 10.7	15	noncoding (54/76 nt)	gltU	tRNA‑Glu
Reads supporting (aligned to +/- strand):  ref base T (2/4);  new base G (8/0);  total (11/4)
Fisher's exact test for biased strand distribution p-value = 1.50e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.80e-01

CACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGGAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAGGGGTTCGAATCCCCTAGGGGACGCCACTTGCTGGTTTGTGAGTGAAAGTCACCTGCCTT  >  NC_000913/3943340‑3943543                                                                                                                                                     |                                                        cACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGGAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAGGGGtt                                                        <  2:381398/150‑1 (MQ=31)     tcctTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGGAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCACAGGACACCGCCCTTTCACGGCGGTAACAAGGGGTCGaa                                                    >  2:130160/1‑150 (MQ=9)         taccttaAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGGAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAGGGGGTCGAATcccc                                               >  2:33760/1‑151 (MQ=14)           ccttaAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGGAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAGGGGATCGAATcccc                                               >  2:607205/1‑149 (MQ=14)                aagaagCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGGAAGTGAATAGCAAGGCGACTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCGTTCACGGCGGGAAAATGGGGTCGAAGccccataagg                                         >  2:115429/1‑144 (MQ=11)                   aagCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGGAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAGGGGGTCGAATCCCCTAGGGGACGc                                     >  2:600172/1‑151 (MQ=14)                               cAGTGCTCACACAGATTGTCTGATAGGAAGGGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTTCCCTTCGTCCAGAGGCCCAGGACACCGCCCTTTCACGGCCGCAGCCAGGGGTGGAATCCCAAAgggggccaccactactgg                           >  2:241031/1‑135 (MQ=11)                                aGTGCTCACACAGATTGTCTGATAGGAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAGGGGTTCGAATCCCCTAGGGGACGCCACTTGCTGGttt                        <  1:277634/151‑1 (MQ=31)                                   gCTCACACAGATTGTCTGATAGGAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAGGGGGTCGAATCCCCTAGGGGACGCCACTTGCTGGTTtgt                      >  2:658738/1‑150 (MQ=14)                                          caGATTGTCTGATAGGAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAGGGGTTCGAATCCCCTAGGGGACGCCACTTGCTGGTTTGTGAGTGaaa              <  1:291907/151‑1 (MQ=31)                                           aGATTGTCTGATAGGAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAAGGGGTCGAATCCCCTAGGGGACGCCACTTTCTGGGTTGTGAGGGaaa              >  2:392453/1‑150 (MQ=255)                                               tGTCTGATAGGAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAGGGGTTCGAATCCCCTAGGGGACGCCACTTGCTGGTTTGTGAGTGAAAGTCAc         >  1:577544/1‑151 (MQ=31)                                                  cTGATAGGAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAGGGGTTCGAATCCCCTAGGGGACGCCACTTGCTGGTTTGTGAGGGAAAGTCACCt       >  1:538741/1‑150 (MQ=14)                                                    gATAGGAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAGGGGTTCGAATCCCCTAGGGGACGCCACTTGCTGGTTTGTGAGTGAAAGTCACCt       <  2:571998/148‑1 (MQ=31)                                                    gATAGGAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAGGGGTTCGAATCCCCTAGGGGACGCCACTTGCTGGTTTGTGAGTGAAAGTCACCTGc     <  2:277678/150‑1 (MQ=31)                                                       aGGAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAGGGGGTCGAATCCCCTAGGGGACGCCACTTGCTGGTTTGTGAGTGAAAGTCACCTGCCtt  >  1:297295/1‑150 (MQ=14)                                                                                                                                                     |                                                        CACCTCCTTACCTTAAAGAAGCGTTCTTTGCAGTGCTCACACAGATTGTCTGATAGGAAGTGAAAAGCAAGGCGTCTTGCGAAGCAGACTGATACGTCCCCTTCGTCTAGAGGCCCAGGACACCGCCCTTTCACGGCGGTAACAGGGGTTCGAATCCCCTAGGGGACGCCACTTGCTGGTTTGTGAGTGAAAGTCACCTGCCTT  >  NC_000913/3943340‑3943543

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑