Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,528,563	0	A	C	53.3%	1.4 / 10.7	15	pseudogene (662/2037 nt)	rhsE	pseudogene, Rhs family
Reads supporting (aligned to +/- strand):  ref base A (4/3);  new base C (8/0);  total (12/3)
Fisher's exact test for biased strand distribution p-value = 7.69e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.22e-02

CTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCCTCGCACCAGACCTGGACATCCGCATCCCGTATGCCACGGACCCGGCGGGCAACCGGCTGCCGGACCCGGAGCTGCACCCGGACAGTACACTCACAGTGTGGCCGGATAACCGCATCGCGGAGGATGCGCACTATGTCTACCGCCACGATGAATACGG  >  NC_000913/1528315‑1528575                                                                                                                                                                                                                                                         |             cTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCCTCGCACCAGACCTGGACATCCGCATCCCGTATGCCACGGACCCGGCGGGCAACCGGCTGCCGGACCCGGAGCTGCACCCGGACAGTACACTCACAGTGTGGCCGGATAACCGCATCGCGGAGGATGCGCACTATGTCTACCGCCACg            >  2:1950091/1‑251 (MQ=31)      ggTGGAATTACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCCTCGCACCAGACCTGGACATCCGCATCCCGTATGCCACGGACCCGGCGGGCCACCGGCTGCCGGACCAGGAGCTGCACCCGGACAGAACACCCACAGTGTGGCCGGATAACCGCAGCGCGGCGGATGCGCACTATTTCTACCGCCCCGATGaa       >  2:298317/1‑251 (MQ=11)         ggAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCCTCGCACCAGACCTGGACATCCGCATCCCGTATGCCACGGACCCGGCGGGCAACCGGCTGCCGGACCCGGAGCTGCACCCGGACAGTACACTCACAGTGTGGCCGGATAACCGCATCGCGGAGGATGCGCACTATGTCTACCGCCACGATGAATAc    <  2:2475220/251‑1 (MQ=31)          gAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCCTCGCACCAGACCTGGACATCCGCATCCCGTATGCCACGGACCCGGCGGGCAACCGGCTGCCGGACCCGGAGCTGCACCCGGACAGTACACTCACAGTGTGGCCGGATAACCGCATCGCGGAGGATGCGCACTATGTCTACCGCCACGATGAATACg   <  2:1647329/251‑1 (MQ=31)           aaTGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCCTCGCACCCGACCTGGACATCCGCATCCCGTATGCCACGGACCCGGCGGGCAACCGGCTGCCGGACCCGGAGCTGCCCCCGGACAGTAAACTCCCCGTGTGGCCGGATAACCGCATCGCCGACGCGGCCCACTATGTCCACCGCCCCGGTGaaaccgg  >  1:1031032/1‑246 (MQ=11)           aaTGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCCTCGCACCAGACCTGGACATCCGCATCCCGTATGCCACGGACCCGGCGGGCAACCGGCTGCCGGACCCGGAGCTGCACCCGGTCAGTACACTCACAGTGTGGCCGGATAACCGCATCGCGGAGGATGCGCACTCTGCATACCGCCCCGATGaaaagcg  >  1:1526247/1‑246 (MQ=2)           aaTGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCCTCGCACCAGACCTGGACATCCGCATCCCGTATGCCACGGACCCGGCGGGCAACCGGCTGCCGGACCCGGAGCTGCACCCGGCCCGTACACTCACAGTGTGGCCGGATAACCGCATCGCGGAGGATGCGCACTATGTCCACCGCCCCGAAGAATCCgg  >  1:1758145/1‑251 (MQ=2)           aaTGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCCTCGCACCAGACCTGGACATCCGCATCCCGTATGCCACGGACCCGGCGGGCAACCGGCTGCCGGACCCGGAGCTGCACCCGGACCGTACACCCCCACTGTGGCCGGAAAACCGCCCCGCGGCGGAGGCGCACCATGCCTACCGCCCCGGCGAATAccg  >  1:133442/1‑249 (MQ=11)           aaTGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCCTCGCACCAGACCTGGACATCCGCATCCCGTATGCCACGGACCCGGCGGGCAACCGGCTGCCGGACCCGGAGCTGCACCCGGACAGTACACTCACAGTGTGGCCGGATAACCGCATCGCGGAGGATGCGCACTATGTCTACCGCCACGATGAATACgg  >  2:1003633/1‑251 (MQ=11)           aaTGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCCTCGCACCAGACCTGGACATCCGCATCCCGTATGCCACGGACCCGGCGGGCAACCGGCTGCCGGACCCGGAGCTGCACCCGGACAGTACACTCACAGTGTGGCCGGATAACCGCATCGCGGAGGATGCGCACTATGTCTACCGCCACGATGAATACgg  >  2:708651/1‑251 (MQ=11)           aaTGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCCTCGCACCAGACCTGGACATCCGCATCCCGTATGCCACGGACCCGGCGGGCAACCGGCTGCCGGACCCGGAGCTGCACCCGGACAGTACACTCACAGTGTGGCCGGATAACCGCACCGCGGAGGATGCGGACCATGTCTACCGCCCCGACGAATACgg  >  1:658650/1‑251 (MQ=2)           aaTGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCCTCGCACCAGACCTGGACATCCGCATCCCGTATGCCACGGACCCGGCGGGCAACCGGCTGCCGGACCCGGAGCCGCACCCGGACAGTACACTCACACTGTGGCCGGACAACCGCACCGCGGCGGGTGCCCCCCATGTCCACCGCCCCCATCAATACgg  >  1:1798848/1‑251 (MQ=11)           aaTGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCCTCGCACCAGACCTGGACATCCGCATCCCGTATGCCACGGACCCGGCGGGCAACCGGCTGCCGGACACGGGGCTGCACCCGGACAGTACACTCCAAGTGTGGCCGGATAACCGCCACGCGGAGGATGCGCACTATGTCTACCGCCACGATGAATACgg  >  2:2298663/1‑251 (MQ=2)           aaTGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCCTCGCACCAGACCTGGACATCCGCATCCCGTATGCCACGGACCCGGCGGGCAACCGGCTGCCCGACCCGGAGCTGCCCCCGGACAGTACACTCACAGCGTGGCCGGATAACCGCATCCCGGAGGATGCGCCCCTTGTCCCCCGCCCCGGAGAATAccg  >  1:2358876/1‑249 (MQ=11)           aaTGACAACGGCGACCGGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCCTCGCACCAGACCTGGACATCCGCATCCCGTATGCCACGGACCCGGCGGGCAACCGGCTGCCGGACCCGGAGCTGCACCCGGACAGTACACTCACAGTGTGGCCGGATAACCGCATCGCGGAGGATGCGCACTATGTCTACCGCCACGATGAATACgg  <  2:1887597/251‑1 (MQ=11)                                                                                                                                                                                                                                                         |             CTACGGGTGGAATGACAACGGCGACCTGGTGCGCATCAGCGGCCCGCGACAGACGCGGGAATACGGCTACAGCGCCACGGGCAGGCTGGAGAGTGTGCGCACCCTCGCACCAGACCTGGACATCCGCATCCCGTATGCCACGGACCCGGCGGGCAACCGGCTGCCGGACCCGGAGCTGCACCCGGACAGTACACTCACAGTGTGGCCGGATAACCGCATCGCGGAGGATGCGCACTATGTCTACCGCCACGATGAATACGG  >  NC_000913/1528315‑1528575

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑