Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000964	2,579,564	0	T	A	34.8%	11.0 / 16.7	23	I52F (ATT→TTT)	pstA	phosphate ABC transporter (permease)
Reads supporting (aligned to +/- strand):  ref base T (9/6);  new base A (8/0);  total (17/6)
Fisher's exact test for biased strand distribution p-value = 5.82e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.14e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CGTATAACCCCAGCCTGTTAAGTTGACAAACATCAATAATCCAAACATCCCAATGACAATAGACGGAAGAGATGAAAGCACCTCTATACATGTTCTAATGAAGTCAGTTACTTTGTTATTAGGCGCGTATTCAGCCATGAAGACTCCGCCGCCCACACCGAGCGGGATTGTAATCAGCATTGTAATAAACAAAATATAAAAGGAGTTAAACAGCTGATCTCGTATGCCTCCTCCAGCTGCAATGGCGCTCGACTTTGTTGTAATAAATTGAAAACTGAGCTGAGAAACACCGTTTATAATAATATAGGAAAACAAACCTACTAAAATGGCAGCGATAATGGCTGCACACAAACCAAACATTCCGGTCGCCAGTTTATCTGTTATTTTGCGGTTCATTACACTTTCCTCCTAGATGACAAGTAGCGAATAAGCAGGATGAACAAGAATGACATCACCAGAAGCACAAGCCCCATTGACCACAGCGTATTGTTTT  >  NC_000964/2579322‑2579814                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                           cgaataaacacAGCCTGATAAGTTGACAAACATCAATAATCCAAACATCCCAATGAAAATAGACGGAAGAGATGAAAGCACCTCTATACATGTTCTAGTGAAGTCTGATACTTTGTTATTAGGCGCGTATTCGTCCATGAAGACTCCGCCGCCAACACCGTCCGGGACTGTAATCAGCATTGCAATAAACAAAATATAAAAGGAGTTAATCAGCTCATCTCGTATGCCTCCTCCAGCTTCAATTgcgcaa                                                                                                                                                                                                                                                     >  2:85624/11‑248 (MQ=255)                                                                                                    aaaGTCAGTTACTTTGTTATTAGGCGCGTATTCAGCCATGAAGACTCCGCCGCCCACACCGAGCGGGATTGTAATCAGCATTGTAATAAACAAAATATAAAAGGAGTTAAACAGCTGATCTCGTATGCCTCCTCCAGCTGCAATGGCGCTCGACTTTGTTGTAATAAATTGAAAACTGAGCTGAGAAACACCGTTTATAATAATATAGGAAAACAAACCTACTAAAATGGCAGCGATAATGGCTGcacaca                                                                                                                                                 <  2:46733/250‑1 (MQ=255)                                                                                                     aaGTCAGTTACTTTGTTATTAGGCGCGTATTCAGCCATGAAGACTCCGCCGCCCACACCGAGCGGGATTGTAATCAGCATTGTAATAAACAAAATATAAAAGGAGTTAAACAGCTGATCTCGTATGCCGTCTTCTGCTTGAATAAAACTCGACTTTGTTGTAATAAATTGAAAACTGAGCTGAGAAACACCGTTTATAATAATATAGGAAAACAAACCTACTaa                                                                                                                                                                           >  1:171710/1‑224 (MQ=255)                                                                                                        tCAGTTACTTTGTTATTAGGCGCGTATTCAGCCATGAAGACTCCGCCGCCCACACCGAGCGGGATTGTAATCAGCATTGTAATAAACAAAATATAAAAGGAGTTAAACAGCTGATCTCGTATGCCTCCTCCAGCTGCAATGGCGCTCGACTTTGTTGTAATAAATTGAAAAct                                                                                                                                                                                                                           <  1:118403/173‑1 (MQ=255)                                                                                                        tCAGTTACTTTGTTATTAGGCGCGTATTCAGCCATGAAGACTCCGCCGCCCACACCGAGCGGGATTGTAATCAGCATTGTAATAAACAAAATATAAAAGGAGTTAAACAGCTGATCTCGTATGCCTCCTCCAGCTGCAATGGCGCTCGACTTTGTTGTAATAAATTGAAAAct                                                                                                                                                                                                                           >  2:118403/1‑173 (MQ=255)                                                                                                         cagatACTTTGTTATTAGGCGCGTATTCAGCCATTAAGACTCCGCCGCCTACAACGAGCGGTATTGTAATCAGCATTATAATAAACAAAATATAAAAGGAGTTAAACAGCTGATCTCGTAGGCCTGCTCCAGCTTAAATGGTGCTCGACTTTGTTGTAATAAATTGAAAACTGAGCTGACATACGCCGATTATAAGAATATAGGAAAACAAACCTTCTAAAATGACAGCGATAATGGATGCACAcaatct                                                                                                                                             <  2:132029/246‑4 (MQ=255)                                                                                                          aGTTACTTTGTTATTAGGCGCGTATTCAGCCATGAAGACTCCGCCGCCCGCACCGAGCGGGATTGTAATCAGCATTGTAATAAACAAAATATAAAAGGAGTTAAACAGCTGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAGACTTTGTTGTAATAAATTGAAAACTGAGCTGAGAAACACCGTTTATAATAATATAGGAAAAAAAACCTACTAAAATGGCAGCGAAAATGGCTGCACAcaaacca                                                                                                                                            >  1:159820/1‑250 (MQ=255)                                                                                                                    ttattaGGCGCGTATTCAGCCATGAAGACTCCGCCGCCCACACCGAGCGGGATTGTAATCAGCATTGTAATAAACAAAATATAAAAGGAGTTAAACAGCTGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAGACTTTGTTGTAATAAATTGAAAACTGAGCTGAGAAACACCGTTTATAATAATATAGGAAAATAAACCTACTAAAATGGCAGCGATAATGGCTGCACACAAACCAAACATTCCGGt                                                                                                                                 >  1:241789/1‑251 (MQ=255)                                                                                                                         aGGCGCGTATTCAGCCATGAAGACTCCGCCGCCCACACCGAGCGGGATTGTAATCAGCATTGTAATAAACAAAATATAAAAGGAGTTAAACAGCTGATCTCGTATGCCTCCTCCAGCTGCAATGGCGCTCGACTTTGTTGTAATAAATTGAAAACTGAGCTGAGAAACACCGTTTATAATAATATAGGAAAACAAACCTACTAAAATGGCAGCGATAATGGCTGCCCACAAACCACACATTCCGGTCGcc                                                                                                                             >  2:109137/1‑250 (MQ=255)                                                                                                                            cgcgTATTCAGCCATGAAGACTCCGCCGCCCACACCGAGCGGGATTGTAATCAGCATTGTAATAAACAAAATATAAAAGGAGTTAAACAGCTGATCTCGTATGCCGCCTCCTGCTGCAATGACGCTCGACTTTGTTGTAATAAATTg                                                                                                                                                                                                                                 >  1:124696/1‑147 (MQ=255)                                                                                                                                tATTCAGCCATGAAGACTCCGCCGCCCACACCGAGCGGGATTGTAATCAGCATTGTAATAAACAAAATATAAAAGGAGTTAAACAGCTGATCTCGTATGCCGTCTTCTGCTTGAAAAAAACACGACTTTGTTGTAATAAATTGAAAACTGAGCTGAGAAACACAGTTTATAATAATATAGGAAAAAAAACCTACTAAAATGGCAGCGATAATGGCTGCACACAAACAAAAAATTCCGGTCGCCAGTTTAtg                                                                                                                     >  1:316422/1‑250 (MQ=255)                                                                                                                                            aaGACTCCGCCGCCCACACCGAGCGGGATTGTAATCAGCATTGTAATAAACAAAATATAAAAGGAGTTAAACAGCTGATCTCGTATGCCGTCTTCTGCTTGAAAAACAAACGACTTTGTTGTAATAAATTGAAAACTGAGCTGAGAAACATCGTTTATAATAATATAGGAAAACAAACCTACTAAAATGGCAGCGATAATGGCTGCACACAAACCAAACATTCCGGTCGCCAGTTTATCTGTTATTTTGCg                                                                                                         >  1:286568/1‑251 (MQ=255)                                                                                                                                                                gAGCGGGATTGTAATCAGCATTGTAATAAACAAAATATAAAAGGAGTTAAACAGCTGATCTCGTATGCCTCCTTCAGCTTGAATGGCGATCGACTTTGTTGTAGTAAATTGAAAACTGAGATGAGAAACACCGTTTATAATAATGTAGGAAAACAAACCTACTAAAATGGCAGCGATAATGGCTGCACACAAACCAAACATTCCGGTCGcaa                                                                                                                            >  1:110353/1‑210 (MQ=255)                                                                                                                                                                    gggATTGTAATCAGCATTGTAATAAACAAAATATAAAAGGAGTTAAACAGCTGATCTCGTATGCCTCCTCCAGCTGCAATGGCGCTCGACTTTGTTGTAATAAATTGAAAACTGAGCTGAGAAACACCGTTTATAATAATATAGGAAAACAAACCTACTAAAATGGCAGCGATAATGGCTGCACACAAACCAAACATTCCGGTCGCCAGTTTATCTGTTATTTTGCGGTTCATTACACTTTcctcct                                                                                     >  2:57104/1‑247 (MQ=255)                                                                                                                                                                    gggATTGTAATCAGCATTGTAATAAACAAAATATAAAAGGAGTTAAACAGCTGATCTCGTATGCCTCCTCCAGCTGCAATGGCGCTCGACTTTGTTGTAATAAATTGAAAACTGAGCTGAGAAACACCGTTTATAATAATATAGGAAAACAAACCTACTAAAATGGCAGCGATAATGGCTGCACACAAACCAAACATTCCGGTCGCCAGTTTATCTGTTATTTTGCGGTTCATTACACTTTCCTCCTAGAt                                                                                 <  1:125486/251‑1 (MQ=255)                                                                                                                                                                         tGTAATCAGCAATGTAATAAACAAAATATAAAATGAGTTAAACAGCGGGTATCGTATGCCTACGCCAGCTGTAATGACACACGACATTGTAGTAATAAAATGAAAACTAAGCAGAGAAACTCTGTTTATAATAATATAGGAAAACAGACCTACTAAAATGGCATCGATAATGGATGCACACACACCAAACATTCCGGTCGCCAGTTTATCTGTTAGTTTGCGGTTGATTacacgtttcgcccagaagaca                                                                             <  2:101024/250‑18 (MQ=255)                                                                                                                                                                               aaGCATTGTAATAAACAAAATATAAAAGGAGTTAAACAGCTTATCTCGTATGCCTCCTCAAGCTGCAATAGCGCTCGACTTAGTTGTAATAAATTGAAAACTGAGCTGAGAAACACCGTTTATAATAATATAGGAAAACAAACCTACTAAAATGGCAGCGATAATGGCTGCACACAAACCAAACATTCCGGTCGCCAGTTTATCTGTTATTTTGCGGTACATTACACTTTCCTCCTAGATTACAAGTAGCg                                                                      <  2:9392/250‑1 (MQ=255)                                                                                                                                                                                   aTTGTAATAAACAAAATATAAAAGGAGTTAAACAGCTGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAATTTGATGTAATAAATTGAAAACTGAGCTGAGAAACACCGTTTATAATAATATAGGAAAACAAACATACTAAAATGGCAGCGATAATGGCTGCACACAAACCAAACATTACGGCCGCCAGTTTATCTGTTATTATGCGGATCATTACACTTTCCTCCTAGATGACAAGAAGCGAAt                                                                   >  1:251720/1‑250 (MQ=255)                                                                                                                                                                                       taataaACAAAATATAAAAGGAGTTAAACAGCTGATCTCGTATGCCGCCTTCTGCTTCAATAACACTCGAATTTGTTGTAATAAATTGAAAACTGAGCTGAGAAACACCGTTTATTATAATATAGGAAAACAAACCTACTAAAATGGCAGCGAAACTGGCTGCACACAAACCATACATTCAGGTCGCCAGATTATCTGATATCTTGCGGTTAATTACAATTTACTACTAGATGACAAGTAGCGAATAAGc                                                               >  1:261637/1‑250 (MQ=255)                                                                                                                                                                                        aataaACAAAATATAAAAGGAGTTAAACAGCTGATCTCGTATGCCGTCTTCTGCTTGAAAAGAACACGACTTTGTTGTAATAAATTGAAAACTGAGCTGAGAAACACCGTTTATAATAATATAGGAAAACAAACCTACTAAAATGGCAGCGATAATGGCTGCACACAAACCAAACATTCCGGTCGCCAGTTTATCTGTTATTTTGCGGTTCATTACACTTTCCTCCTAGATGACAAGTAGCGAATAAGc                                                               >  1:58220/1‑249 (MQ=255)                                                                                                                                                                                           aaaCAAAATATAAAAGGAGTTAAACAGCTGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAATAGACTTTGTTGTAATAAATTGAAAACTGAGCTGAGAAACACCGTTTATAATAATATAGGAAAACAAACCTACTAAAATGGCAGCGATAATGGCTGCACACAAACCAAACATTCCGGTCGCCAGTTTATCTGTTATTTTTCGGTTCATTACACTTTCCTCCTAGATGACAAGTAGCGAATAAGCAGGAt                                                          >  1:93075/1‑251 (MQ=255)                                                                                                                                                                                                      aaaaGGAGTTAAACAGCTGATCTCGTATGCCGTCTTCTGCTTGAAAAAAACTCGACTTTGTTGTAATAAATTGAAAACTGAGCTGAGAAACACCGTTTATAATAATATAGGAAAACAAACCTACTAAAATGGCAGCGATAATGGCTGCACACAAACCAAACATACCGGTCGCCAGTTTATCTGTTATTTTCCGGTTCATTACACTTTCCTCCTAGATGACAAGTAGCGACTAAGCAGGATGAACAAGAATg                                               >  1:134483/1‑251 (MQ=255)                                                                                                                                                                                                                                       ctccAGCTGCAATGGCGCTCGACTTTGTTGTAATAAATTGAAAACTGAGCTGAGAAACACCGTTTATAATAATATAGGAAAACAAACCTACTAAAATGGCAGCGATAATGGCTGCACACAAACCAAACATTCCGGTCGCCAGTTTATCTGTTATTTTGCGGTTCATTACACTTTCCTCCTAGATGACAAGTAGCGAATAAGCAGGATGAACAAGAATGACATCACCAGAAGCACAAGCCCCATTGACcac               >  1:64285/1‑250 (MQ=255)                                                                                                                                                                                                                                                   tGGCGCTCGACTTTGTTGTAATAAATTGAAAACTGAGCTGAGAAACACCGTTTATAATAATATAGGAAAACAAACCTACTAAAATGGCAGCGATAATGGCTGCACACAAACCAAACATTCCGGTCGCCAGTTTATCTGTTATTTTGCGGTTCATTACACTTTCCTCCTAGATGACAAGTAGCGAATAAGCAGGATGAACAAGAATGACATCACCAGAAGCACAAGCCCCATTGACCACAGCGTATTGtttt  >  2:34083/1‑251 (MQ=255)                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                           CGTATAACCCCAGCCTGTTAAGTTGACAAACATCAATAATCCAAACATCCCAATGACAATAGACGGAAGAGATGAAAGCACCTCTATACATGTTCTAATGAAGTCAGTTACTTTGTTATTAGGCGCGTATTCAGCCATGAAGACTCCGCCGCCCACACCGAGCGGGATTGTAATCAGCATTGTAATAAACAAAATATAAAAGGAGTTAAACAGCTGATCTCGTATGCCTCCTCCAGCTGCAATGGCGCTCGACTTTGTTGTAATAAATTGAAAACTGAGCTGAGAAACACCGTTTATAATAATATAGGAAAACAAACCTACTAAAATGGCAGCGATAATGGCTGCACACAAACCAAACATTCCGGTCGCCAGTTTATCTGTTATTTTGCGGTTCATTACACTTTCCTCCTAGATGACAAGTAGCGAATAAGCAGGATGAACAAGAATGACATCACCAGAAGCACAAGCCCCATTGACCACAGCGTATTGTTTT  >  NC_000964/2579322‑2579814

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑