Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	987,529	0	C	A	53.8%	27.1 / 51.4	26	intergenic (‑547/+56)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
Reads supporting (aligned to +/- strand):  ref base C (3/9);  new base A (14/0);  total (17/9)
Fisher's exact test for biased strand distribution p-value = 7.04e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.53e-05

AAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCACGCCAGTTACGTAAGCAATC  >  NC_000913/987399‑987663                                                                                                                                   |                                                                                                                                       aaGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATaaaaaa                                                                                                                    <  2:475631/151‑1 (MQ=255)   gAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATaaaaaa                                                                                                                    <  1:568867/149‑1 (MQ=255)   gAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGGAAAAAAAATTGTTTACTTTACAAAAAAAAAAAATGACAGaaaaaaaaaaaaaa                                                                                                                   >  2:620767/1‑150 (MQ=255)    aaaaaaCTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGTAAAAAAAATTGTTTACTTAACAAAAAAAAAAATTTaaaaaaaaaaaaaaaaaaa                                                                                                                  >  2:653613/1‑149 (MQ=255)        aaCTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGGAAAAAAAATTCTTGACTTAAAAAACAAAAAAATTTTTCAAAAAAATaaaaaaaaa                                                                                                                 >  1:336039/1‑145 (MQ=255)            aaTCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCgg                                                                                                         <  1:390060/151‑1 (MQ=255)             aTCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGGAAATAGATTTCTTTTCTTTAAAAAAAAAAAAATTTACAGAAAAAAAAAAAAAAAAACCAGCggg                                                                                                        >  1:302854/1‑151 (MQ=255)                cGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGCAAAAAAAATGCTTGACTTTACAAAAAGAAAAATTGACAGAAAAGATAAAAAAAAAAACAGCggg                                                                                                        >  1:482709/1‑148 (MQ=255)                  cAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTg                                                                                                   <  2:558475/151‑1 (MQ=255)                                 ttAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGCAAAAAAAATTCTTTACTTTAAAAAAAAAAAAATTTACAGAAAAAAAAAAAAAAAAAACAGCGGGCGCCGGCTCCTGAAGaa                                                                                       >  1:328175/1‑147 (MQ=255)                                   aGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTaa                                                                                  <  1:620804/151‑1 (MQ=255)                                    gTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGATGCGAAAAAAATGTCTGATTTAACAAAAAAATAAATTGTAAGAAAAAATAAAAAAAAAGACAGCGGGGGGGGGGTCTTTAAGaggaaaa                                                                                  >  1:652862/1‑144 (MQ=255)                                           cgcgTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGGAAAAAAATTGTTTGACTTTAAAAAAAAAAAAATTTACAGAAAAAAAAAAAAAAAAACCAACGGGGGCCGGCTCTTTTAGACGCCAAAATaaaa                                                                           >  1:666271/1‑150 (MQ=255)                                                aaaTGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGc                                                                     <  1:478184/151‑1 (MQ=255)                                                aaaTGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGc                                                                     <  1:334216/151‑1 (MQ=255)                                                  aTGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAAATTTTTTGACTTAAAAAACAAATAAATTGTCAGAAAAAATAAAAAAAAAAACAGCGGGCGCTGGCTCTTTTAGAAGCTAAATTAAAAAATGGCg                                                                    >  1:536447/1‑150 (MQ=255)                                                          aTGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGTAAAAAAATTGCTTTGATTAAAAAAAAAATAAATTGAAAAAAAAAAAAAAAAAAAAAACAACGGGGGCCGGCTCTTTCAAACACCAAAATAAAAAATAGCGTTACGCgg                                                            >  2:350590/1‑150 (MQ=255)                                                            gTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGGTGAAAAAGATTGCTTTAATTTACAAAAAGATAAATTTAAAGAAAAAATAAAAAAAAAAACAGCGGGGGCTGGGTTTTTAAAACGCCAAATTAAAAAATTGCGGTTCGCGGAg                                                          >  1:405885/1‑150 (MQ=255)                                                                tatTCCGTAACAGGATGATCGTTATGGCGGGGTGGGGAAGACATTTCTTTATTTGACAAAAACAGAAATTGTCAGAAAAAAAAAAAAAAGAACGAACGGGCGCCGGGCCTTGGAGACACTTAATTAGAAGCTGGCggttccccgagt                                                         >  1:755499/1‑136 (MQ=255)                                                                    ccGTAACAGGATGATCGTTATGGCGGGGGGGCAAATATAATGCTTGAATTAAAAAAAAAATAAATTTACAGAAAAAATAAAAAAAAAAACAGCGGGCGCTGGCTCTTGAAGAAGCTAAAATAAAAAAAGGGGGTACGCGGAGGAAGTggg                                                  >  1:593697/1‑150 (MQ=255)                                                                     cGTAACAGGATGATCGTTATGGCGGGGGTGGAAAAAGAATGCTTTACTTTAAAAAAAGAAAAATTTACAGAAAAGAAAAAAAAAAAACCAGCCGGCGCTGGCTCTTTAAGACGCTAAAATAAAAAATGGCGTTACGCGGAGTACGgggg                                                  >  1:760140/1‑149 (MQ=255)                                                                                 atCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAatcacatc                                    <  2:336025/151‑1 (MQ=255)                                                                                               gTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCa                      <  2:302841/151‑1 (MQ=255)                                                                                                                tGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCACGCCAGTTACGTAAGc      >  1:304931/1‑150 (MQ=255)                                                                                                                    ttAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCACGCCAGTTACGTAAGCAATc  >  1:165025/1‑150 (MQ=255)                                                                                                                      aacaaacaGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCACGCCAGTTACGTAAGCAATc  >  2:21848/1‑148 (MQ=255)                                                                                                                                   |                                                                                                                                       AAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGCAAATAGATTGCTTGACTTAACAAACAGATAACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTTTTGCACGCCAGTTACGTAAGCAATC  >  NC_000913/987399‑987663

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑