Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,536,197	0	A	T	40.0%	64.6 / 51.6	55	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 (2/31);  new base T (22/0);  total (24/31)
Fisher's exact test for biased strand distribution p-value = 2.12e-13
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACG  >  NC_000913/4536056‑4536337                                                                                                                                               |                                                                                                                                              ggAGTAGTAAAGGTCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTTCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATgaaa                                                                                                                                      <  1:1125578/151‑1 (MQ=255)   agtagtAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTTGGGATgaaa                                                                                                                                      >  2:989512/1‑149 (MQ=255)    gtagtaAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATgaaagaa                                                                                                                                   <  2:1096748/151‑1 (MQ=255)      agtaAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATgaaagaaa                                                                                                                                  <  1:1084115/150‑1 (MQ=255)        taAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATAGC‑TGGTGCTTTTAGGAATGAAAGCAAAt                                                                                                                                >  1:277461/1‑150 (MQ=255)         aaaGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATg                                                                                                                               <  2:565507/150‑1 (MQ=255)          aaGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTTGGAAAGGAaaaaaaa                                                                                                                                >  2:794199/1‑147 (MQ=255)               cATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATgcaagcaa                                                                                                                        <  1:883757/151‑1 (MQ=255)               cATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCA‑TTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCaat                                                                                                                       <  1:927340/151‑1 (MQ=255)                      tACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAataatat                                                                                                                  <  1:105285/150‑1 (MQ=255)                          aaTGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGGTTTTTTGGATGAAAAAAAAAACAAGAAAaaatattat‑a                                                                                                             >  1:980285/1‑150 (MQ=255)                          aaTGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAAtaatataat‑a                                                                                                             <  1:741408/150‑1 (MQ=255)                           aTGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTTTGAATTAAAGAAAAAGGAAGACAAAATAtaaa‑aa                                                                                                            >  1:133351/1‑150 (MQ=255)                             gTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATg                                                                                                          <  1:921554/150‑1 (MQ=255)                               tAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGc                                                                                                        <  1:68341/150‑1 (MQ=255)                                aaGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGCCt                                                                                                      <  1:489631/151‑1 (MQ=255)                                aaGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGGGGTTTTTTGAATGAAAGAAAAAACAAGCAAAAATAtaaa‑aaaaacc                                                                                                       >  2:447606/1‑145 (MQ=255)                                    cGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGCCTAAtt                                                                                                  <  2:711986/151‑1 (MQ=255)                                    cGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGGGCTTTTTGGGATGAAAGAAAAAGCAAACAAAAAAAtaat‑aaaaggctaa                                                                                                    >  2:1078216/1‑141 (MQ=255)                                           ccGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTTGGGATGAAAAAAAAATCAAACAAAAATATAAA‑AAATGGCTAATttttttt                                                                                            >  2:277169/1‑149 (MQ=255)                                                ttATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGCCTAATTTCTTTGAAcat                                                                                       <  1:847926/150‑1 (MQ=255)                                                 tATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGGGCTTTTTTGAATGAAAAAAAAAACAAGAAAAAATATAAA‑AAAAGCCTAATttttttttaaa                                                                                        >  2:246865/1‑143 (MQ=255)                                                    tGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGGTTTTTTGGATGAAAAAAAAAAAAAACAATAAAATAATAAAAGGCCAAATtttttttac                                                                                          >  2:58521/1‑141 (MQ=255)                                                     gCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGCCTAATTTCTTTGAACATCATTaa                                                                                 <  2:448732/151‑1 (MQ=255)                                                     gCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGCCTAATTTCTTTGAACATCATTa                                                                                  <  2:620257/150‑1 (MQ=255)                                                       gAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGCCTAATTTCTTTGAACATCATTAAGc                                                                               <  2:595798/151‑1 (MQ=255)                                                       gAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGAGGCTTTTTTGTATTAAAAAAAAAGTAAGAAAAAAAAAAAT‑AAATGCCTTATtttttttataataaataa                                                                                 >  1:289948/1‑137 (MQ=255)                                                        aGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGCCTAATTTCTTTGAACATCATTAAGCa                                                                              <  2:746244/151‑1 (MQ=255)                                                             ccTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGGTTTTTTTAATTAAAAAAAAATCAAGAAATAATAATAA‑AATAGTCTAATTTTTTTTTAAATCATTAAACa                                                                              >  1:428319/1‑146 (MQ=255)                                                             ccTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGCCTAATTTCTTTGAACATCATTAAGCATatca                                                                         <  1:129873/151‑1 (MQ=255)                                                                  ccTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGCCTAATTTCTTTGAACATCATTAAGCATatcatcat                                                                     <  1:529208/150‑1 (MQ=255)                                                                   cTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTTTGTATGTAATAAAAAACAAGCAAAAAAATAAA‑AATTGGTTTATTTTTTTGTACATAATTAAGCAAataatc                                                                       >  1:389009/1‑147 (MQ=255)                                                                     gATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCg                                                                   <  2:807391/149‑1 (MQ=255)                                                                        tataAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGGTTTTTGGGATGAAAGAAAAAGCAAACAATAATATAAT‑AATAGCCTAATTTTTTTTTAAATCATTAAACATATCATCATCGTCTAt                                                              >  2:12624/1‑151 (MQ=255)                                                                        tataAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTTGGAATGAAAGAAAAAGCAAAAAATAAAATAAA‑AAAAGGCTAATTTTTTTTAACATTACTAAAAAAattatcattttct                                                                >  2:172901/1‑144 (MQ=255)                                                                         ataAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTAt                                                              <  1:766057/150‑1 (MQ=255)                                                                           aaaTCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTAttt                                                            <  2:373526/150‑1 (MQ=255)                                                                           aaaTCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTAttt                                                            <  2:913606/150‑1 (MQ=255)                                                                            aaTCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGATTTTTTTAATAAAAAAAAAAGTAAGAAATAAAATAAT‑AATAGGGTACTTTCTTTTAAAATCAATAAAAATATTATCTTTGTccttt                                                             >  1:562199/1‑144 (MQ=255)                                                                               cTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGTGTTTTTTGTATTAAAAAAAAAT‑CCAGCAAAAAAATAAT‑AATTGTCTAATTTTTTTTAACATCATTAAACATattatcatttttctatttt                                                          >  1:576995/1‑137 (MQ=255)                                                                                 tATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCa                                                        <  2:507084/148‑1 (MQ=255)                                                                                     gTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCg                                                 <  2:768868/151‑1 (MQ=255)                                                                                      tttACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGGGGTTTTTGGAAAGAAAAAAAAAGGAAGAAAAAAAATAAT‑AAATGGCTAATTTTTTTTAACAACATTAAACATATTATCATCGTCTATTTTCCCGAAt                                                    >  2:273805/1‑147 (MQ=255)                                                                                         aCCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCg                                              <  2:119683/150‑1 (MQ=255)                                                                                          ccTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGGGCTTTTTTGGAAGAAAAAAAAAACAAGCAAAAAAATAAA‑AAAAGCCTAAATTTTTTTAAAAACATTAAACAAATCATCATCGTCTATTTTTCAGAATCCCTCgcc                                            >  2:420428/1‑149 (MQ=255)                                                                                           cTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTTTTTATTAAAAAAAAAACAAGCAAAAAAATAAA‑AAATGTCTAATTTTTTTTTAAATAATTAAACATAATATCAATGTCTATTTTTCAGAAACAGTCGACt                                           >  1:193531/1‑151 (MQ=255)                                                                                            tAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGGGGTTTTTGGGATGAAAAAAAAAGCAAGGAAAAATATAAT‑AATTGGCTAATTTTTTTTAAAAACATTTAACAAATCATCATCCTCTATTTTCCAGAATACCTCg                                              >  2:301318/1‑147 (MQ=255)                                                                                                cATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATaa                                      <  2:978238/151‑1 (MQ=255)                                                                                                 aTTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAAt                                     <  1:995634/151‑1 (MQ=255)                                                                                                   tttCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGGGGTTTTTGGAATGAAAAAAAAATCAAACAAAAATATAAA‑AAATGACTAAATTTTTTTTAAATCATTAAACATATAATCAACCTCTTTTTTCCCGAAACCCTCCACTTATaa                                      >  2:389143/1‑148 (MQ=255)                                                                                                         ttGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAg                               <  2:928850/149‑1 (MQ=255)                                                                                                             aTAATGCGCCTGGGATTAATGGC‑GGGGGGTTTTTTGTATGAAAAAAAAAGAAAGAAAAAAAAAAAA‑AAAAACCTAATTTTTTTTTAAAACATTAAGCAAATAATAAACGTCCATTTTTCCGAAACCGTCGACCTATTATCAcccgca                             >  1:981109/1‑143 (MQ=255)                                                                                                                   cgcCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCa                   <  2:832152/151‑1 (MQ=255)                                                                                                                           aTTAATAGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑TATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGtg           <  2:277566/151‑1 (MQ=255)                                                                                                                                     gggTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACg  >  2:481964/1‑151 (MQ=255)                                                                                                                                               |                                                                                                                                              GGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGC‑GGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAAT‑AATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACG  >  NC_000913/4536056‑4536337

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑