Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,435,727	0	G	A	45.6%	46.7 / 35.7	46	intergenic (‑108/+33)	uspF/ompN	stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific
Reads supporting (aligned to +/- strand):  ref base G (23/2);  new base A (0/21);  total (23/23)
Fisher's exact test for biased strand distribution p-value = 7.29e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACAT  >  NC_000913/1435579‑1435876                                                                                                                                                       |                                                                                                                                                       gAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAg                                                                                                                                                        <  1:531766/149‑1 (MQ=255)      ggAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑c                                                                                                                                                >  1:168538/1‑151 (MQ=255)      ggAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑c                                                                                                                                                >  1:505311/1‑151 (MQ=255)          atatCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGc                                                                                                                                            <  1:746988/151‑1 (MQ=255)          atatCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGc                                                                                                                                            <  2:462573/151‑1 (MQ=255)                 tAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAAc                                                                                                                                      >  2:444421/1‑150 (MQ=255)                      aaaaGAATCGTTCTTTTAAAAAACCCTCCTTTTTTAGTACCCGAAAAAAGTTTAACGCCAGATGACTTTTTTTGTG‑TAAGGACGGATTTCACATTTTTAATTTAGATA‑AAGGGAGAAAAAAAAAGCAAAAAAAG‑CCCGCCATAACAGCggg                                                                                                                                <  1:452004/149‑1 (MQ=255)                      aCAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCggg                                                                                                                                >  1:782675/1‑151 (MQ=255)                        aaGAATTTTTCTGTACAAAAACCCTCTTGTTTTATTATCCAAAAAAAGTGTAACGCAAGAAAACTTTTTTTGTG‑AAATGACGGATTTCACATTTTTAATTAAGAGA‑AAGGGAGAAAAAATAAGAAAAAAAAG‑CCCGCCATAACAGCg                                                                                                                                  <  2:1036836/147‑1 (MQ=255)                          aaaTCTTTCTGTTAAAAAACCCCCTTGTTTAATTATCCGAAAAAGGTGTACCCCCAGATGACTTTTTTTTTG‑TAATGAGGGATTTCACTTTTTTAATTAAGAAA‑AAAGGAGAAAAAAAAAGAAAAAAAAG‑CCCGCCATAACAGCGGGCagg                                                                                                                            <  1:581287/150‑1 (MQ=255)                                ttttGTTAATAAACCCTCCTTTTTTTGTACCCGAAAAAAGTGTACCGCCAGATGACTTTTTTTGTG‑TAATGACGGATTTCATTTTTTTAATTTAAAAC‑AAAGGAGAAAAAAAAAGCAAAAAAAG‑CCCGCCATAACAGCGGGCaggagg                                                                                                                         <  1:639831/145‑1 (MQ=255)                                 tCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGAttt                                                                                                                     >  2:441024/1‑151 (MQ=255)                                        aaaaacCCTCTTTTTTTAGTATCCGCAAAAAGTGAACCGCCAGATGACATTTTTTGTG‑TAAGGACGGATTCCATATTTTTAATTTAGAAA‑AAGGGAGAAAAAAAAAGAAAAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGaa                                                                                                                 <  1:195787/146‑1 (MQ=255)                                         aaaacCCTCTTGTTTTAGTACCCGAAAAAAGTGAAACCCCAGATGACTCTTTTTGTG‑AAAGGACGGATTTCACTTTTTTAATTTAAACA‑AAAGGAGGAAGAAAAAGAAAAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGa                                                                                                             <  1:539399/150‑1 (MQ=255)                                           aaaCCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGAt                                                                                                            >  2:807766/1‑150 (MQ=255)                                                 cctGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAAcc                                                                                                       >  1:749891/1‑149 (MQ=255)                                                     ttttAGTATCCGCAAAAAGTGTAACGCAAGATAACTCTTTTTGTG‑TAAGGCGGGAGTTCACATTTTTAATTTAGATA‑AAAGGAGAAAAAAAAACAAAAAAAAC‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGAcc                                                                                                  <  2:642975/150‑1 (MQ=255)                                                     ttttAGTACCCGAATAAAGTGTAACGCAAGATGACCTTTTTTGTG‑TAAGGACGGAGTCCACTTTTTTAATTAAGAAA‑AAAGGAGAAAAAAAAAGAAAAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGAc                                                                                                   <  1:34648/149‑1 (MQ=255)                                                            aTCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCg                                                                                           >  1:276166/1‑150 (MQ=255)                                                                 cATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAat                                                                                      >  1:653951/1‑150 (MQ=255)                                                                    aaaGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATatc                                                                                   >  2:790944/1‑150 (MQ=255)                                                                       gtgtAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCg                                                                               >  1:57914/1‑151 (MQ=255)                                                                         gaaaCGCCAGATGACTTTTTTTGTG‑TAATGACGGAGTTCACTTTTTAAATTAAGAAA‑AAAGGAGAAAAAAAAAGAAAAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCg                                                                               <  1:653644/147‑1 (MQ=255)                                                                           aaCCCCAGATAAC‑CTTTTTTTGTTAATGACGGATTTAACTTTTTTAATTAAGAGA‑AAAGGAGAAAAAAAAAGAAAAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTag                                                                           <  1:941315/151‑1 (MQ=255)                                                                             cGCCAAATAACATTTTTGGTG‑AAATGAGGAAATACACTTTTTTATTTAAGAAA‑AAGGGAGGAAAAAAAAGAAAAAAACC‑ACCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTa                                                                            <  2:226851/148‑1 (MQ=255)                                                                                cAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATg                                                                      >  1:100527/1‑151 (MQ=255)                                                                                     gACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCAtt                                                                 >  2:83070/1‑151 (MQ=255)                                                                                          tttttGTG‑AAAGGAGGGGTTTCATTTTTTAAATTAAGAAA‑AAAGGAGAAAAAAAAAGAAAAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCAtt                                                                 <  2:920475/146‑1 (MQ=255)                                                                                            tttGTG‑TAAGGAGGGAGTTCATTTTTTAAATTAAGAAA‑AAGGGAGAAAAAAAAAGAAAAAAAAC‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGc                                                           <  2:803138/150‑1 (MQ=255)                                                                                                   tAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGa                                                      >  2:754139/1‑149 (MQ=255)                                                                                                     attgccggagtcctaTTTTTAATTTAAAACAAAAGGAGAAAAAATAGGAAAAAAAAT‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGaa                                                     <  2:673976/135‑1 (MQ=255)                                                                                                        acgaggTTCACATTTTTAATTTA‑AAC‑AAAGAAGGAAAAAAAAGAAAAAAAAGCCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGt                                                <  1:402705/145‑1 (MQ=255)                                                                                                         cGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTc                                               >  1:1008123/1‑150 (MQ=255)                                                                                                             gTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCtt                                          >  2:349648/1‑151 (MQ=255)                                                                                                                    tttttAATTAAGATA‑AAGGAAAGAAAAATAACGAAAAAAAC‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCa                                    <  2:301045/150‑1 (MQ=255)                                                                                                                        tAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAgg                               >  1:572770/1‑151 (MQ=255)                                                                                                                         aaTTAAGAAA‑AAAGGAGAAAAAAAAAGAAAAAAACG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGt                              <  2:198247/151‑1 (MQ=255)                                                                                                                          aTTAAGATA‑AAAGGAGAAAAAAAAAGAAAAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGtt                             <  2:612899/151‑1 (MQ=255)                                                                                                                           tttAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTg                            >  1:1030809/1‑151 (MQ=255)                                                                                                                              aGATA‑AAAGGAGGAAAAATAAGAAAAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGAt                          <  1:865611/150‑1 (MQ=255)                                                                                                                                aTC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGAtttt                       >  1:991453/1‑151 (MQ=255)                                                                                                                                    aaaGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTtat                     >  2:829473/1‑150 (MQ=255)                                                                                                                                    aaaGGAGAAAAAAAAAGCAAAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTtat                     <  1:145865/150‑1 (MQ=255)                                                                                                                                            aaaaaaaaGCAAAAAAGG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACg             <  2:513907/144‑1 (MQ=255)                                                                                                                                               aaTAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAgg         >  1:102079/1‑151 (MQ=255)                                                                                                                                                  aaGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTgg      >  1:920816/1‑151 (MQ=255)                                                                                                                                                      aGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACAt  >  1:58036/1‑151 (MQ=255)                                                                                                                                                       |                                                                                                                                                       GAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTG‑TAATGACGGAGTTCACATTTTTAATTTAGATC‑AAAGGAGGAAGAATAAGCAGAAAAAG‑CCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGACAT  >  NC_000913/1435579‑1435876

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑