Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,536,197	0	A	T	48.9%	32.2 / 47.1	47	intergenic (+166/+417)	yjhR/nanS	pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase
Reads supporting (aligned to +/- strand):  ref base A (4/20);  new base T (23/0);  total (27/20)
Fisher's exact test for biased strand distribution p-value = 1.27e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCA  >  NC_000913/4536053‑4536347                                                                                                                                                  |                                                                                                                                                       acgggAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATg                                                                                                                                                  <  2:3776/148‑1 (MQ=255)  cAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATga                                                                                                                                                 <  2:787745/151‑1 (MQ=255)  cAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATga                                                                                                                                                 <  1:475269/151‑1 (MQ=255)         agtaAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGaaaa                                                                                                                                          <  2:614658/151‑1 (MQ=255)           taAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑GTTTTATGAATGAAAGaaaa                                                                                                                                          >  2:310032/1‑149 (MQ=255)                  cATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑GGTTTTTGAGTTAAAAAAAAAgaaagca                                                                                                                                  >  1:131751/1‑150 (MQ=255)                   atatTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCaat                                                                                                                                <  2:392509/151‑1 (MQ=255)                     atTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑CTTTTTTGAATGAAAAAAAAAacaaacaaa                                                                                                                                >  1:242137/1‑148 (MQ=255)                      ttttACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑GTTTTTTTGATGAAAAAAAAAGAAAACaataa                                                                                                                              >  1:202696/1‑150 (MQ=255)                       tttACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑GTTTTTTGAATGAAAAAAAAAGAAAACaaaaa                                                                                                                              >  2:7221/1‑149 (MQ=255)                             aaTGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑CTTTTTGGAATGAAAGAAAAAACAAACAAaaaaataata                                                                                                                       >  2:1035966/1‑150 (MQ=255)                                   aaGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑GTTTTTGGAATGAAAAAAAAAGAAAACAAAAATAtaaaaaaaggc                                                                                                                 >  2:953860/1‑145 (MQ=255)                                   aaGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑CTTTTTTGAATGAAAAAAAAAACAAACAAAAAAAAAATAATAGcc                                                                                                                 >  1:423492/1‑150 (MQ=255)                                    aGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑CTTTTTTGAATTAAAAAAAAAGTAAACAAAAAAAtaaaaaaaggct                                                                                                                >  1:154983/1‑144 (MQ=255)                                        gACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑GTTTTTGGGATGAAAAAAAAAGAAAGCAAAAATATAAAAATGGCCTAAttt                                                                                                           >  2:824770/1‑151 (MQ=255)                                           tttCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCCTTTTTTGAAT‑TAAGAAAAAGCAAACAAAAAAAtaaaaaaagaactaattttt                                                                                                        >  2:436504/1‑137 (MQ=255)                                            ttCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCtt                                                                                                        <  2:186686/150‑1 (MQ=255)                                            ttCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCt                                                                                                         <  1:526295/149‑1 (MQ=255)                                              ccGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGa                                                                                                     <  2:756965/151‑1 (MQ=255)                                              ccGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGa                                                                                                     <  1:270450/151‑1 (MQ=255)                                               cGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGaa                                                                                                    <  2:567324/151‑1 (MQ=255)                                                    tATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑GCTTTTTGAAAGAAAAAAAAAACAAACAAAAATATAAAAAAAGCCTAATttttttttaaa                                                                                                  >  2:616622/1‑143 (MQ=255)                                                         cGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑GTTTTTTTAATTAAAAAAAAAAAAAACAATAATATAAAAAAAGGCTCATttttttttaaaaca                                                                                               >  1:701372/1‑138 (MQ=255)                                                            gTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCat                                                                                       <  2:643511/151‑1 (MQ=255)                                                              cGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCatat                                                                                     <  1:302784/151‑1 (MQ=255)                                                              cGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCatat                                                                                     <  2:363400/151‑1 (MQ=255)                                                                    tCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATatcatca                                                                                <  2:549848/150‑1 (MQ=255)                                                                     ccTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATatcatcat                                                                               <  2:699169/150‑1 (MQ=255)                                                                     ccTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑CTTTTTTGGATGAAAAAAAAAGGAAGAAAAAAAATAATAAAAGCCTCATTTTTTTTGACATTATTaaaaat                                                                                       >  2:19387/1‑138 (MQ=255)                                                                                  cTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTTGGGATGAAAGAAAAAGCAAGCAATAATATAAAAAAAGCCTAATTTTTTTTAAAATAATTAAAAATATCATCATCGTCTAtttttc                                                                   >  2:159952/1‑146 (MQ=255)                                                                                    tATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑CTTTTTGGGATTAAAAAAAAAGCAAACAAAAATATAAAAAAAGCCTAATTTTTTTTTAAATCATTAAAAATATTATCATCCTCTATTTTCCAGa                                                                >  2:395696/1‑150 (MQ=255)                                                                                         tttACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑CTTTTTTGAATGAAAAAAAAAGCAAGCAAAAAAATAAAAAAGGGCTAATTTTTTTTAAAAAAATTTAACAAATCATTAACCTCTTATTTTCAGAATcc                                                            >  2:916568/1‑149 (MQ=255)                                                                                           tACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTc                                                         <  2:914751/150‑1 (MQ=255)                                                                                           tACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTc                                                         <  2:242140/150‑1 (MQ=255)                                                                                              cTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑TTTTTTTGGATTTAAAAAAAAACAAGAAAAAAAATAAAAAAAGCCTAATTTTTTTTTAAATAATTAAAAATATAATTATAGTCTATTTTTCAGAAACCGt                                                          >  1:23003/1‑146 (MQ=255)                                                                                                 aTCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑GTTTTTTGGATTAAAAAAAAAGCAAGGAAAAAAATAAAAAAAGGCTAATTTTTTTTTAAATCATTAAACATATTATTATAGTTTATTTTTCAGAAACCGTCGACtt                                                    >  1:7273/1‑149 (MQ=255)                                                                                                    aTTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAAt                                               <  2:210260/151‑1 (MQ=255)                                                                                                      tttCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGG‑GTTTTTTGGATTAAAAAAAAAGCAAGAAAAAATATAATAATAGGCTAATTTTTTTTTAAATCATTAAACAAAATATCATCGTTTTTTTTTCAGAAACCGTCGACTTATaa                                                >  1:864155/1‑148 (MQ=255)                                                                                                               cATAATGCGCCTGGGATTAATGGCGGGGG‑GTTTTTTGGATGAAAAAAAAAACAAGGAATAAAATAAAAATAGGCCAATTTTTTTTTAAATCATTAAACATATTATCATCGTCTATTTTTCAGAATTCGTCGGCTTATAATAACCAGAAAgg                                    >  1:245961/1‑151 (MQ=255)                                                                                                                aTAATGCGCCTGGGATTAATGGCGGGGG‑GTTTTTGGGATGCAAAAAAAAACAAGCAAAAATATAAAAAAGGGCTTATTTTTTTTTACATCATTAAATATATTATTATTGTCTCTTTTTCTAAATCCGTCGACCTTTAATAGcc                                           >  1:486282/1‑143 (MQ=255)                                                                                                                         cTGGGATTAATGGCGGGGG‑CTTTTTTGAATGAAAGAAAAAACAAGCAAAAAAATAATAAAAGGCTAATTTTTTTTTAAAACATTTAACATATCATCATCGTCTATTTTTCAGAAACCCTCGCCTTATaaattcccgaa                                       >  1:352851/1‑129 (MQ=255)                                                                                                                          tGGGATTAATGGCGGGTG‑CTTTTTTGTATGAAAAAAAAAAAAAGCAAAAAAAAAAAAATAGGCTAATTTTTTTTTAAATCATTAAAAATAACATCATCCTCTTTTTTTCAGCATACGTCCTCTTATAATcaacaaca                                       >  1:819375/1‑130 (MQ=255)                                                                                                                                tAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGtgc                    <  1:293857/150‑1 (MQ=255)                                                                                                                                   tGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCg                >  2:147489/1‑151 (MQ=255)                                                                                                                                    ggCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGa               <  2:98604/151‑1 (MQ=255)                                                                                                                                         gTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCt          >  2:13380/1‑151 (MQ=255)                                                                                                                                              ttttAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTgg      >  1:185428/1‑151 (MQ=255)                                                                                                                                                  aGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGccc   <  1:518410/150‑1 (MQ=255)                                                                                                                                                  aGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCa  <  1:310028/151‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                       ACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTG‑CTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGGCCCA  >  NC_000913/4536053‑4536347

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑