Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,982,523	0	A	G	60.0%	9.8 / 21.0	20	intergenic (‑136/+31)	otsB/araH	trehalose‑6‑phosphate phosphatase, biosynthetic/L‑arabinose ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base A (1/7);  new base G (12/0);  total (13/7)
Fisher's exact test for biased strand distribution p-value = 1.03e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.77e-05

CACCCGGTTCTCCTCCTTCTCTTTTCTTATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTC  >  NC_000913/1982385‑1982662                                                                                                                                           |                                                                                                                                            cACCCGGTTCTCCTCCTTCTCTTTTCTTATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGGTGTGGTGGGgaaaaaaacaaaa                                                                                                                                 >  1:220293/1‑144 (MQ=255)  aCCCGGTTCTCCTCCTTCTCTTTTCTTATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGGTATGGTGGGGAAAAAAGCTaaaa                                                                                                                                >  1:539093/1‑150 (MQ=255)  aCCCGGTTCTCCTCCTTCTCTTTTCTTATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGCTATGGGGGGGAAAAAAGcctaaa                                                                                                                                >  2:108706/1‑146 (MQ=255)           tcctccTTCTCTTTTCTTATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGCTATGGTGGGGAAAAAAGCTAAAATGTTGCAGa                                                                                                                       >  2:150234/1‑151 (MQ=255)               cctTCTCTTTTCTTATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGaaaaa                                                                                                                   <  1:245154/151‑1 (MQ=255)                         tCTTATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGAc                                                                                                         <  2:326291/151‑1 (MQ=255)                                gtgtTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGCTATGGGGGGGAAAAAAGCTAAAATTTTTCAGAAAAAAACATccaaaaaggcgg                                                                                                  >  2:202147/1‑140 (MQ=255)                                             cgcgCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCt                                                                                     <  2:152465/151‑1 (MQ=255)                                                   ttACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTTGGTATGGGGGGGAAAAAAGCTAAATTTTTTCAGAAAAAAAAATCAGACAGTGCGTTTTGCTTTTTTGTTGTaaa                                                                               >  2:378654/1‑150 (MQ=255)                                                             gTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGCTATGGTGGGGAAAAAAGCTAAAATGTTTCAGAAAAAAACATCAGACAGTGCGTTTTGCTTTTTGCTTGTAAAGGTCggaaat                                                                     >  2:431668/1‑146 (MQ=255)                                                               aaGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGGTGGGTATGGTGGGGAAAAAAACTAAAAATTTGCAGAAAAAAAAAACAAACAGTGCGGTTCGCTTTTTTTTTTTTACGGGTGAAGAACa                                                                   >  1:83368/1‑151 (MQ=255)                                                                aGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGGTATGGGGGGGAAAAAAGCTAAATTTTTGTAGAAAAAAAAATCAGACAATGCGGTTTGCTTTTTTTTTTTTACGGGCGGAGAACa                                                                   >  2:23668/1‑150 (MQ=255)                                                                aGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGGTATGGGGGGGAAAAAAGCTAAAATGTTGCAGAAAAAAACATCAGACAGTGGGTTTTGCTTTTTTTTTGTAACGGGCGAAGATCa                                                                   >  2:407213/1‑150 (MQ=255)                                                                 gTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGCTGTGGTGGGGGAAAAAACTAAAATGTTGTGGAAAAAAGAATAACACCATGCGTTTCGCTTTTTGTTTGTTACGGTCGAAGATCaa                                                                  >  1:313376/1‑149 (MQ=255)                                                                            gtgACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGGTATGGGGGGGAAAAAAGCTAAAATTTTTCAGAAAAAAACATCAGACAGTGCGTTTTGCTTTTTTCTTTTAACGGGCGAAGATCACCCCTGCcagcag                                                      >  2:214254/1‑151 (MQ=255)                                                                               aCGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGAt                                                   <  2:539103/151‑1 (MQ=255)                                                                                     gTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGc                                              <  1:214250/150‑1 (MQ=255)                                                                                                  aCGAAGAACAGCCAACCGTTATGGCGGTTGGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTAc                                <  2:206781/151‑1 (MQ=255)                                                                                                    gaagaaCAGCCAACCGTTATGGCGGTTGGCTATGGGGGGGAAAAACGCTAAATTGTTGGAGAAAAAAACATCAGAAAGGGGGGTTTGCTTTTTTTTTTTTAAGGGCGAAGATCACCGCCGCCAGCAGGGTTAAGCCGCGAAACACgga                                 >  1:209999/1‑146 (MQ=255)                                                                                                                            gTTGGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAg      >  1:238150/1‑151 (MQ=255)                                                                                                                                 cTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTc  <  2:439499/150‑1 (MQ=255)                                                                                                                                           |                                                                                                                                            CACCCGGTTCTCCTCCTTCTCTTTTCTTATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTC  >  NC_000913/1982385‑1982662

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑