Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,982,529	0	C	A	52.4%	19.9 / 36.0	21	intergenic (‑142/+25)	otsB/araH	trehalose‑6‑phosphate phosphatase, biosynthetic/L‑arabinose ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base C (2/8);  new base A (11/0);  total (13/8)
Fisher's exact test for biased strand distribution p-value = 2.21e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.06e-04

ACCCGGTTCTCCTCCTTCTCTTTTCTTATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATGGCGTTTTCCAC  >  NC_000913/1982386‑1982676                                                                                                                                                |                                                                                                                                                    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)                                                                                                                                             aaaCGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATGGCGTTTTCCAc  <  2:461459/151‑1 (MQ=255)                                                                                                                                                |                                                                                                                                                    ACCCGGTTCTCCTCCTTCTCTTTTCTTATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATGGCGTTTTCCAC  >  NC_000913/1982386‑1982676

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: ‑