Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,982,551	0	G	A	52.5%	13.2 / 48.1	40	intergenic (‑164/+3)	otsB/araH	trehalose‑6‑phosphate phosphatase, biosynthetic/L‑arabinose ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base G (5/14);  new base A (21/0);  total (26/14)
Fisher's exact test for biased strand distribution p-value = 5.01e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.18e-07

TCTTATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATGGCGTTTTCCACGGTGCCTAAAATTAAGATACCCGC  >  NC_000913/1982409‑1982700                                                                                                                                                |                                                                                                                                                      tCTTATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGAc                                                                                                                                               <  2:54890/151‑1 (MQ=255)   ttATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑TGGTATGGGGGGGAAAAAAGCCAAATTTTTGCAGAAAAAAACAACAGaaaa                                                                                                                                             >  2:35962/1‑148 (MQ=255)                           ttACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTATGGTGGGGAAAAAAGCCAAAATTTTGCAGAAAAAAAAAACAGAAAGTGCGTTTTGCCTTTTTCtttttaa                                                                                                                     >  2:345888/1‑146 (MQ=255)                                gACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTATGGTGGGGAAAAAAACTAAAATTTTGTAGAAAAAAAAAACAGAAAGTGCGTTTTGCTTTTTTCTTGTAACGGGCg                                                                                                                >  2:16167/1‑151 (MQ=255)                                 aCATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGCT‑TGGGATGGTGGGGAAAAAAGATCAATTTTCGCCCAAAAAAACAACAAACAACGCGGTTCGCTTTTTTCTTGTAAAgggtg                                                                                                                >  1:182082/1‑147 (MQ=255)                                  cATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGTGGGAAAAAAAGCTAAAATGTTGCAGAAAAAAACATCAAAAAGTGCGGTTTGCTTTTTTCTTGTAAAGGTCGaa                                                                                                              >  2:415465/1‑151 (MQ=255)                                  cATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGGT‑GGGGATGGGGGGGAAAAAAGATAAAATTTTGGAGGAAAAAACATCAAAAAGAGCGTTTCGCTTTTTTCTTGTAAAGGGCGaa                                                                                                              >  1:557447/1‑151 (MQ=255)                                    tGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGGGGGGAAAAACGCTAAATTGTTGCAGAAAAAAACAACAGACAGTGCGGTTCGCTTTTTTTTTTTAAAGGTCGAAGa                                                                                                            >  1:27025/1‑151 (MQ=255)                                      tAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGAt                                                                                                           <  2:127199/150‑1 (MQ=255)                                      tAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGAt                                                                                                           <  2:530178/150‑1 (MQ=255)                                        attctctcctttgtgATGTGGGTCTTCTTTTGTAATGAAGAACAGCCAACCGTTATGGCGGGT‑GGGTATGGTGGGGAAAAAAGCTAAATTGTTTCAGAAAAAAGCAACAGACAATGCGGTTCGCTTTTTTGTTGTAACGGGCGGAGAACa                                                                                                         >  2:655375/12‑150 (MQ=255)                                        aGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGGGTATGGGGGGAAAAAA‑ACTAAATTATTTGAGAAAAAAAAAACAAAAAAGGGGTTTTGCTTTTTTTTTTTGACGGTGGaaaaaaca                                                                                                        >  2:368975/1‑145 (MQ=255)                                        aGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTATGGTGGGGAAAAACGCTAAAATGTTGCAGAAAAAAACATCAGACAGGGCGTTTTGCTTTTTTCTTGTAACGGGCGAAGATCa                                                                                                         >  2:293908/1‑150 (MQ=255)                                        aGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTATGGTGGGGAAAAACACCAAATTATTGCTGAAAAAAGCATCAGACAGAGCGTTTCGCTTTTTGCTTTTAACGGGCGAAGAACa                                                                                                         >  1:135963/1‑150 (MQ=255)                                        aGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTATGGTGGGGAAAAAAGCTAAAATGTTTCAGAAAAAAACATCAGACAGTGCGTTTTGCTTTTTTTTTTTTACGGTCGAAGATCa                                                                                                         >  2:436428/1‑150 (MQ=255)                                        aGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTATGGGGGGGAAAAAAGCTCAATTGTTGCAGAAAAAAACATCAGACAGTGGGGTTTGCTTTTTGCTTGTTAAGGGCGGAGAACa                                                                                                         >  2:95367/1‑150 (MQ=255)                                        aGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTATGGGGGGGAAAAAAGCCAAAATGTTGCAGAAAAAAAAAAAAGACAGAGGGGTTTGCTTTTTTCTTGTTAAGGGCGAAGAACa                                                                                                         >  1:184122/1‑150 (MQ=255)                                        aGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGGATGGGGGGAAAAAAAGGGAAAATGTTGCAGAAAAAAGAAACAGACAAGGGGTTTTGGTTTTTGCTTGTAAAGGGCGAAGaataa                                                                                                        >  2:183982/1‑147 (MQ=255)                                        aGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGGGGGGAAAAAAGCTAAAATGTTGCAGAAAAAAACAACAGACAGGGCGGTTTGGTTTTTGTTTGTAACAGTAGAAGAACa                                                                                                         >  2:356409/1‑150 (MQ=255)                                        aGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGGT‑GGTGATGGGGGGGAAAAAAAATAAAATGTTGTAGAAAAAAAAATAAAACAGCGGGGTTTGGTTTTTTTTTTTAAAGGTCGaaagaca                                                                                                         >  1:604159/1‑145 (MQ=255)                                        aGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGGT‑GGGGATGGTGGGGAAAAAAACTAAAATTTTGCAGAAAAAAAAATCAAACAATGGGGTTTGCTTTTTTTTTGTTAAGGTCGgagaaaa                                                                                                         >  1:122498/1‑147 (MQ=255)                                         gTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑TGGCATGGTGGGGAAAAAACCTAAAATTTTGCAGAAAAAAACATCATACAGTGCGTTTTGCTTTTTTTTTTTAAAGGTCGAAGATCAc                                                                                                        >  2:89375/1‑150 (MQ=255)                                         gTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTATGGTGGGAAAAAAACCTAAATTTTTGCAGAAAAAAACATCAGACAGTGCGTTTCGCTTTTTTCTTTTTAAGGGCGAAGATCAc                                                                                                        >  2:264210/1‑150 (MQ=255)                                         gTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTATGGGGGGGAAAAACACTAAATTGTTTCAGAAAAAAAGATCAGACAGGGGGTTTTGCTTTTTTCTTGTAAAGGTCGAAGAACaa                                                                                                        >  2:428476/1‑149 (MQ=255)                                                  gtgtGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTATGGGGGGGAAAAAAGCCAAATTGTTGCAGAAAAAAACATCAGACAGTGCGTTTTGCTTTTTTCTTGTAACGGGCGAAGATCACCGCTGCcag                                                                                               >  2:283265/1‑150 (MQ=255)                                                  gtgtGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGGATGGGGGGAAAAAACACACAAATTTTGTAGAAAAAAAAAACAGACACCGCGTGTCGCTTTTTTCTTTTTACGGTCGAAGATAAcaccgtcccg                                                                                               >  1:541579/1‑141 (MQ=255)                                                       aCGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGAt                                                                                         <  1:151625/151‑1 (MQ=255)                                                       aCGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGAt                                                                                         <  2:601812/151‑1 (MQ=255)                                                             gTCGACGTTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGTTGGAAAAAACGCTAAAGTGTTGAAGAAAAAAGCATCAGACAGGGCGTTTCGCTTTTTTCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGCTTAAgt                                                                                    <  1:530448/150‑2 (MQ=255)                                                                     ttGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTATGGTGGGGAAAAAAACCAAAATTTTGCAGAAAAAAAAATAAGACAAGGGGTTTTTCTTTTTTTTTTTTAAGGTCGGAGATCACCCCCGCCCGCAGGGTTAATCCGCGGAcc                                                                            >  1:73706/1‑150 (MQ=255)                                                                          aCGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTAc                                                                      <  1:459163/151‑1 (MQ=255)                                                                          aCGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTAc                                                                      <  1:442847/151‑1 (MQ=255)                                                                                     ccAACCGTTATGGCGGTT‑GGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAgg                                                           <  2:615473/151‑1 (MQ=255)                                                                                                  cGGTT‑GGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGc                                              <  2:37904/151‑1 (MQ=255)                                                                                                             tggtggGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATgg                                    <  2:426618/151‑1 (MQ=255)                                                                                                             tggtggGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATgg                                    <  1:436425/151‑1 (MQ=255)                                                                                                             tggtggGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATgg                                    <  2:27025/151‑1 (MQ=255)                                                                                                               gtggGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATGGc                                   <  1:205339/150‑1 (MQ=255)                                                                                                                         aCGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATGGCGTTTTCCACgg                        >  1:307980/1‑151 (MQ=255)                                                                                                                                       cAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATGGCGTTTTCCACGGTGCCTAAAATTAAg          >  1:208428/1‑151 (MQ=255)                                                                                                                                                gCATCAGACCGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATCAAGCCGCGAAGCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATGGCGTTTTCCACGGTGCCTAAAATTAAGATACCCGc  >  2:244438/1‑150 (MQ=255)                                                                                                                                                gCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATGGCGTTTTCCACGGTGCCTAAAATTAAGATACCCGc  >  1:319390/1‑150 (MQ=255)                                                                                                                                                gCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATGGCGTTTTCCACGGTGCCTAAAATTAAGATACCCGc  >  1:94097/1‑150 (MQ=255)                                                                                                                                                |                                                                                                                                                      TCTTATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGTGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATGGCGTTTTCCACGGTGCCTAAAATTAAGATACCCGC  >  NC_000913/1982409‑1982700

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: ‑