Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,982,513	0	C	G	63.2%	11.7 / 42.5	39	intergenic (‑126/+41)	otsB/araH	trehalose‑6‑phosphate phosphatase, biosynthetic/L‑arabinose ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base C (3/11);  new base G (24/0);  total (28/11)
Fisher's exact test for biased strand distribution p-value = 3.02e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.09e-08

CGGTTAACGGTTCTGTCACCCGGTTCTCCTCCTTCTCTTTTCTTATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGT‑GGGAAAAAACGCT‑AAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGC  >  NC_000913/1982369‑1982656                                                                                                                                                  |                                                                                                                                                  cGGTTAACGGTTCTGTCACCCGGTTCTCCTCCTTCTCTTTTCTTATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTAtggt                                                                                                                                             <  2:524169/151‑1 (MQ=255)                       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)                                                                                                                                                  |                                                                                                                                                  CGGTTAACGGTTCTGTCACCCGGTTCTCCTCCTTCTCTTTTCTTATTGTGTTGCGCAGAACGCGCTTTACAGACATGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGTT‑GGCTATGGT‑GGGAAAAAACGCT‑AAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGC  >  NC_000913/1982369‑1982656

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑