Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,982,523	0	A	G	52.4%	27.4 / 47.8	42	intergenic (‑136/+31)	otsB/araH	trehalose‑6‑phosphate phosphatase, biosynthetic/L‑arabinose ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base A (6/14);  new base G (22/0);  total (28/14)
Fisher's exact test for biased strand distribution p-value = 7.33e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.26e-04

GTTCTCCTCCTTCTCTTTTCTTATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGT‑GGGAAAAAACGCT‑AAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATGGC  >  NC_000913/1982391‑1982667                                                                                                                                       |                                                                                                                                                  gTTCTCCTCCTTCTCTTTTCTTATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑TGGTTTGGT‑GGGGAAAAAAACC‑AAAatgttt                                                                                                                                >  1:601800/1‑150 (MQ=255)        tcctTCTCTTTTCTTATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTTTGGT‑GGGGAAAAAAGCC‑AAATTGTTGCAGaaaa                                                                                                                         >  2:487878/1‑151 (MQ=255)         cctTCTCTTTTCTTATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTCTTGG‑GGGGAAAAACCCTCAAAtttttctcaaaaa                                                                                                                         >  1:368476/1‑143 (MQ=255)            tctcTTTTCTTATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑TGGTATGGTGGGGAAAAAAGCCA‑AAATTGTTGAGGaaaaaaa                                                                                                                      >  2:667090/1‑150 (MQ=255)                   tCTTATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGT‑GGGAAAAAACGCT‑AAATTGTTGCAGAAAAAAGCATCAGAc                                                                                                              <  2:54890/151‑1 (MQ=255)                     ttATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑TGGTATGGG‑GGGGAAAAAAGCC‑AAATTTTTGCAGAAAAAAACAACAGaaaa                                                                                                            >  2:35962/1‑148 (MQ=255)                                             ttACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTATGGT‑GGGGAAAAAAGCC‑AAAATTTTGCAGAAAAAAAAAACAGAAAGTGCGTTTTGCCTTTTTCtttttaa                                                                                    >  2:345888/1‑146 (MQ=255)                                                  gACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTATGGT‑GGGGAAAAAAACT‑AAAATTTTGTAGAAAAAAAAAACAGAAAGTGCGTTTTGCTTTTTTCTTGTAACGGGCg                                                                               >  2:16167/1‑151 (MQ=255)                                                   aCATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGCT‑TGGGATGGT‑GGGGAAAAAAGAT‑CAATTTTCGCCCAAAAAAACAACAAACAACGCGGTTCGCTTTTTTCTTGTAAAgggtg                                                                               >  1:182082/1‑147 (MQ=255)                                                    cATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGT‑GGGAAAAAAAGCT‑AAAATGTTGCAGAAAAAAACATCAAAAAGTGCGGTTTGCTTTTTTCTTGTAAAGGTCGaa                                                                             >  2:415465/1‑151 (MQ=255)                                                    cATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGGT‑GGGGATGGG‑GGGGAAAAAAGAT‑AAAATTTTGGAGGAAAAAACATCAAAAAGAGCGTTTCGCTTTTTTCTTGTAAAGGGCGaa                                                                             >  1:557447/1‑151 (MQ=255)                                                      tGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGG‑GGGGAAAAACGCT‑AAATTGTTGCAGAAAAAAACAACAGACAGTGCGGTTCGCTTTTTTTTTTTAAAGGTCGAAGa                                                                           >  1:27025/1‑151 (MQ=255)                                                        tAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGT‑GGGAAAAAACGCT‑AAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGAt                                                                          <  2:530178/150‑1 (MQ=255)                                                        tAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGT‑GGGAAAAAACGCT‑AAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGAt                                                                          <  2:127199/150‑1 (MQ=255)                                                          attctctcctttgtgATGTGGGTCTTCTTTTGTAATGAAGAACAGCCAACCGTTATGGCGGGT‑GGGTATGGT‑GGGGAAAAAAGCT‑AAATTGTTTCAGAAAAAAGCAACAGACAATGCGGTTCGCTTTTTTGTTGTAACGGGCGGAGAACa                                                                        >  2:655375/12‑150 (MQ=255)                                                          aGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTTGGGGTATGGG‑GGGAAAAAA‑ACT‑AAATTATTTGAGAAAAAAAAAACAAAAAAGGGGTTTTGCTTTTTTTTTTTGACGGTGGaaaaaaca                                                                       >  2:368975/1‑145 (MQ=255)                                                          aGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTATGGT‑GGGGAAAAACGCT‑AAAATGTTGCAGAAAAAAACATCAGACAGGGCGTTTTGCTTTTTTCTTGTAACGGGCGAAGATCa                                                                        >  2:293908/1‑150 (MQ=255)                                                          aGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTATGGT‑GGGGAAAAACACC‑AAATTATTGCTGAAAAAAGCATCAGACAGAGCGTTTCGCTTTTTGCTTTTAACGGGCGAAGAACa                                                                        >  1:135963/1‑150 (MQ=255)                                                          aGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTATGGT‑GGGGAAAAAAGCT‑AAAATGTTTCAGAAAAAAACATCAGACAGTGCGTTTTGCTTTTTTTTTTTTACGGTCGAAGATCa                                                                        >  2:436428/1‑150 (MQ=255)                                                          aGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTATGGG‑GGGGAAAAAAGCT‑CAATTGTTGCAGAAAAAAACATCAGACAGTGGGGTTTGCTTTTTGCTTGTTAAGGGCGGAGAACa                                                                        >  2:95367/1‑150 (MQ=255)                                                          aGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTATGGG‑GGGGAAAAAAGCC‑AAAATGTTGCAGAAAAAAAAAAAAGACAGAGGGGTTTGCTTTTTTCTTGTTAAGGGCGAAGAACa                                                                        >  1:184122/1‑150 (MQ=255)                                                          aGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGGATGGG‑GGGAAAAAAAGGG‑AAAATGTTGCAGAAAAAAGAAACAGACAAGGGGTTTTGGTTTTTGCTTGTAAAGGGCGAAGaataa                                                                       >  2:183982/1‑147 (MQ=255)                                                          aGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGG‑GGGGAAAAAAGCT‑AAAATGTTGCAGAAAAAAACAACAGACAGGGCGGTTTGGTTTTTGTTTGTAACAGTAGAAGAACa                                                                        >  2:356409/1‑150 (MQ=255)                                                          aGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGGT‑GGTGATGGG‑GGGGAAAAAAAAT‑AAAATGTTGTAGAAAAAAAAATAAAACAGCGGGGTTTGGTTTTTTTTTTTAAAGGTCGaaagaca                                                                        >  1:604159/1‑145 (MQ=255)                                                          aGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGGT‑GGGGATGGT‑GGGGAAAAAAACT‑AAAATTTTGCAGAAAAAAAAATCAAACAATGGGGTTTGCTTTTTTTTTGTTAAGGTCGgagaaaa                                                                        >  1:122498/1‑147 (MQ=255)                                                           gTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑TGGCATGGT‑GGGGAAAAAACCT‑AAAATTTTGCAGAAAAAAACATCATACAGTGCGTTTTGCTTTTTTTTTTTAAAGGTCGAAGATCAc                                                                       >  2:89375/1‑150 (MQ=255)                                                           gTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTATGGT‑GGGAAAAAAACCT‑AAATTTTTGCAGAAAAAAACATCAGACAGTGCGTTTCGCTTTTTTCTTTTTAAGGGCGAAGATCAc                                                                       >  2:264210/1‑150 (MQ=255)                                                           gTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTATGGG‑GGGGAAAAACACT‑AAATTGTTTCAGAAAAAAAGATCAGACAGGGGGTTTTGCTTTTTTCTTGTAAAGGTCGAAGAACaa                                                                       >  2:428476/1‑149 (MQ=255)                                                                    gtgtGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTATGGG‑GGGGAAAAAAGCC‑AAATTGTTGCAGAAAAAAACATCAGACAGTGCGTTTTGCTTTTTTCTTGTAACGGGCGAAGATCACCGCTGCcag                                                              >  2:283265/1‑150 (MQ=255)                                                                    gtgtGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGGATGGG‑GGGAAAAAACACA‑CAAATTTTGTAGAAAAAAAAAACAGACACCGCGTGTCGCTTTTTTCTTTTTACGGTCGAAGATAAcaccgtcccg                                                              >  1:541579/1‑141 (MQ=255)                                                                         aCGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGT‑GGGAAAAAACGCT‑AAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGAt                                                        <  2:601812/151‑1 (MQ=255)                                                                         aCGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGT‑GGGAAAAAACGCT‑AAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGAt                                                        <  1:151625/151‑1 (MQ=255)                                                                               gTCGACGTTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGT‑TGGAAAAAACGCT‑AAAGTGTTGAAGAAAAAAGCATCAGACAGGGCGTTTCGCTTTTTTCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGCTTAAgt                                                   <  1:530448/150‑2 (MQ=255)                                                                                       ttGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGGTATGGT‑GGGGAAAAAAACC‑AAAATTTTGCAGAAAAAAAAATAAGACAAGGGGTTTTTCTTTTTTTTTTTTAAGGTCGGAGATCACCCCCGCCCGCAGGGTTAATCCGCGGAcc                                           >  1:73706/1‑150 (MQ=255)                                                                                            aCGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGT‑GGGAAAAAACGCT‑AAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTAc                                     <  1:459163/151‑1 (MQ=255)                                                                                            aCGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGT‑GGGAAAAAACGCT‑AAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTAc                                     <  1:442847/151‑1 (MQ=255)                                                                                                       ccAACCGTTATGGCGGTT‑GGCTATGGT‑GGGAAAAAACGCT‑AAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAgg                          <  2:615473/151‑1 (MQ=255)                                                                                                                    cGGTT‑GGCTATGGT‑GGGAAAAAACGCT‑AAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGc             <  2:37904/151‑1 (MQ=255)                                                                                                                               tggt‑ggGAAAAAACGCT‑AAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATgg   <  2:426618/151‑1 (MQ=255)                                                                                                                               tggt‑ggGAAAAAACGCT‑AAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATgg   <  1:436425/151‑1 (MQ=255)                                                                                                                               tggt‑ggGAAAAAACGCT‑AAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATgg   <  2:27025/151‑1 (MQ=255)                                                                                                                                 gt‑ggGAAAAAACGCT‑AAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATGGc  <  1:205339/150‑1 (MQ=255)                                                                                                                                       |                                                                                                                                                  GTTCTCCTCCTTCTCTTTTCTTATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGT‑GGGAAAAAACGCT‑AAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATGGC  >  NC_000913/1982391‑1982667

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑