Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,228,272	0	A	C	60.0%	7.3 / 14.1	15	pseudogene (338/1287 nt)	mdtQ	pseudogene; putative channel/filament proteins
Reads supporting (aligned to +/- strand):  ref base A (3/3);  new base C (0/9);  total (3/12)
Fisher's exact test for biased strand distribution p-value = 4.40e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.38e-03

GCTCTTTTTCTATTTGCTGCAAGACCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGCCCCATTAAGCCTTCTGCCGACATTT  >  NC_000913/2228126‑2228413                                                                                                                                                   |                                                                                                                                              gCTCTTTTTCTATTTGCTGCAAGACCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAAcc                                                                                                                                             <  2:307055/149‑1 (MQ=255)                  tgcAAGACCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGGGTTTCCCCCGTTTCCCCCCCCGCGCCTTTAACGTACCCCGGGGGGGAGGAACCCCCCCCCGCTTTTTTtccc                                                                                                                          >  2:245301/1‑151 (MQ=255)                   gcAAGACCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCa                                                                                                                         <  2:215348/151‑1 (MQ=255)                                                     cTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATGGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTACCCGTCCCCAGGGGGGCAGTACCCCCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCaaa                                                                                        <  2:69991/150‑1 (MQ=255)                                                                ggCGGGCTACGCTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCGGTGCTTTAACCGTACCCAGGCGGGCAGTACCCCCCGCCCGTTTTTTCCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTgg                                                                             <  2:197521/150‑1 (MQ=255)                                                                              ccagccagCAATGGGCGGGTTTGCTCGCGTCCCGCCGCCCGTGCTTTACCCGTCCCCGGGCGGGCAGTACCCCCCGCCCGATTCTTCCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCgg                                                              <  1:265315/151‑1 (MQ=255)                                                                                            gCGGTTTTGCTCGCGTCCCGCCGCCCGTGCTTTACCCGTCCCCAGGCGGGCAGTACCCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGcc                                                <  2:188374/151‑1 (MQ=255)                                                                                                  ttGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCg                                          >  2:364758/1‑151 (MQ=255)                                                                                                     cTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTc                                       >  2:158893/1‑151 (MQ=255)                                                                                                           tcccgcccCCCCTGCTTTACCCGTACCCGGGCGGGAAGTAACCTCCCCCCGATTCTTTCCCCAAATATCGAGATGCCACCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCaga                                    <  2:204862/146‑1 (MQ=255)                                                                                                             ccgccgCCCGTTCTTAACCCGTCCCCGGGGGGGCAGTACCCCCCCCCCGATTCTTCCCCCAGATTTCACGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGtt                                        <  1:159172/142‑1 (MQ=255)                                                                                                                       tGCTTAACCCGTCCCCAGGCGGGCAGTACCCTCCCCCCGATTCTTCCCCCAGATATCGAGAGGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGCCCCa                       <  1:469160/149‑1 (MQ=255)                                                                                                                             acccttccccAGGGGGGCATTACCCCCCGCCCTATTCTTCCCCCAGATACCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGCCCCATTAAGcc                <  1:78250/143‑1 (MQ=255)                                                                                                                             acccGTCCCCAGGCGGGCAGAACCCTCCGCCCGATTCTTCCCCCAGATAGCGAGATGCCACCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGCCCCATTAAg                  <  1:75847/146‑1 (MQ=255)                                                                                                                                           gggAAGTACCCCCCCCCCGATTCTTCCCCCAGATACCGAGAGGCCCGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGCCCCATTAAGCCTTCTGCCGACAttt  <  1:354348/150‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                              GCTCTTTTTCTATTTGCTGCAAGACCGTGTTTAACGCCGCCTGGGTTTGCCACTCCCAGTACAGGCGGGCTACGCTGCCAGCCAGCAATTGGCGGGTTTGCTCGCGTTCCGCCGCCCGTGCTTTAACCGTACCCAGGCGGGCAGTAACCTCCGCCCGATTCTTTCCCCAGATATCGAGATGCCAGCCCGCCGTTAAGCCAAAAGTACCGTTGGTGTACCACGGGCCGGTCGTACCTGCGGCCGGATCGTTCAGAGCAAACGGCCCCATTAAGCCTTCTGCCGACATTT  >  NC_000913/2228126‑2228413

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑