Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	987,494	0	T	G	54.5%	17.2 / 30.1	22	intergenic (‑512/+91)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
Reads supporting (aligned to +/- strand):  ref base T (1/9);  new base G (12/0);  total (13/9)
Fisher's exact test for biased strand distribution p-value = 2.01e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.45e-04

CATCCAGAATGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCA  >  NC_000913/987355‑987643                                                                                                                                            |                                                                                                                                                      cATCCAGAATGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGAt                                                                                                                                            <  1:285792/151‑1 (MQ=255)                  aaTAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTaacaaac                                                                                                                           <  1:172646/151‑1 (MQ=255)                                 gtgCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGGAAAAAAATTTGTTTTCTTAAAAAAAAAAAAAATTgagaga                                                                                                            >  2:277951/1‑151 (MQ=255)                                   gCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGGAAAAAAATTGCTTTACTTAAAAAAAAAATAAATTTACAGaaa                                                                                                          >  1:512204/1‑151 (MQ=255)                                         aGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGCAAAAAGATTGCTTGACTTAACAAAAAAAAAAATTTACAGaaaaaaaaa                                                                                                    >  1:31967/1‑146 (MQ=255)                                                 aaaaaCTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGGAAAAAAAATGCTTGAATTTAAAAAAAAAAAAATTTACAGaaaaaaaaaaaaaaaaa                                                                                            >  1:552556/1‑148 (MQ=255)                                                              cAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTTTAAATATATTGCTTGACTTTACAAAAAAAAATATTCAAAACAAAGATAAAAAAAGAACCCGCggggg                                                                                  >  1:19195/1‑146 (MQ=255)                                                                    gAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTTCAAAAAGAATTTTTTACTTTAAAAAAACAAAAAATGACAGAAAAGAAAAAAAAAAAGCCAGCGGGCGCTGGCGCtt                                                                         >  1:320187/1‑151 (MQ=255)                                                                    gAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGGAAATAAAATTCTTTTCTTTAAAAAAAAATAAATTTTCAGAAAAAATAAAAAAAAAAACAACGGGCGCAGGgtc                                                                           >  2:444056/1‑149 (MQ=255)                                                                         cGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAg                                                                     <  2:512194/150‑1 (MQ=255)                                                                           gATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGAc                                                                   <  2:31967/150‑1 (MQ=255)                                                                                         cgTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGc                                                     <  1:46104/150‑1 (MQ=255)                                                                                                gTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGCAAATAGATTTCTTGACTTAACAAAAAGATAAATTTACAGAAAAAATAAAAAAAAAACCAGCGGGCGCTGGCTCTTTAAGACGCTAAATTaaaaaatgggggtt                                             >  1:620789/1‑141 (MQ=255)                                                                                                    cAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTAcgc                                          <  1:266224/150‑1 (MQ=255)                                                                                                      aTGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGCAAATAGATTTCTTGACTTAAAAAACAGAAAAATTGACAGAAAAAATAAAAAAAAAGCCAGCGGGGGCTGGCTCTTGAAGAAGCTAAATTAGAAGCTGGCGGTACGCGGa                                       >  1:166150/1‑151 (MQ=255)                                                                                                      aTGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGCAAAAAGATTTGTTGACTTTACAAAAAGATAAATTTACAGAAAAGAAAAAAAAAAAACCAGCGGGGGCTGGGTCTTTAAGAAGCTAAATTAAAAAAGGGGGTTACGCggg                                       >  1:2391/1‑150 (MQ=255)                                                                                                        gTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGCAAATAAATTGCTTGACTTAACAAAAAAAAAACTTGACAGAAAAGATAAAAAAAAAGCCAGCGGGCGCCGGCTCTTTAAGAAGCTAAATTAAAAGCTGGCGTTACGCGGAgg                                     >  1:444538/1‑150 (MQ=255)                                                                                                        gTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGCAAAAAAAATTTTTGATTTAAAAAAAAAATAAATTGAGAGAAAAAAAAAAAAAAAAGACAGCGGGGGCTGGGTCTTTAAGAAGCAAAAATAAAAAATGGGGGTACGCggggg                                     >  2:502333/1‑148 (MQ=255)                                                                                                             atTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTg                                <  1:352371/151‑1 (MQ=255)                                                                                                             atTCCGCAACAGGATGATCGTTATTTCGTGTTAGTAAATAGATTGCTTGACTTAACTTACAGATATCTTGACATAAAAGATATAAACCAACCCATCGGGCTCCTGCTCTTGATGACGCTATATTAGAAGCTGGCGATACGCGCAGTAcctt                                <  2:292320/151‑4 (MQ=255)                                                                                                                  gTAACAGGATGATCGTTATGGCGGGGGTGCAAATAGAATGCTTGACTTAAAAAAAAGAAAAATTGACAGAAAAGAAAAAAAAAAAAACAGAGGGCGCCGGCTCTTTAAGACGCCAAATTAAAAACTGGCGGTACGCGGAGGACGTggggag                           >  2:303015/1‑148 (MQ=255)                                                                                                                             atCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAatcacat                 <  1:519969/150‑1 (MQ=255)                                                                                                                                            ttGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCa  <  1:618867/150‑1 (MQ=255)                                                                                                                                            |                                                                                                                                                      CATCCAGAATGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCA  >  NC_000913/987355‑987643

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑