Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,536,197	0	A	T	44.0%	48.4 / 42.9	50	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 (4/24);  new base T (22/0);  total (26/24)
Fisher's exact test for biased strand distribution p-value = 1.72e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGG  >  NC_000913/4536047‑4536343                                                                                                                                                       |                                                                                                                                                   cATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTa                                                                                                                                                    <  1:562017/151‑1 (MQ=255)  aTGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAg                                                                                                                                                   <  2:611091/151‑1 (MQ=255)  aTGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAg                                                                                                                                                   <  2:459239/151‑1 (MQ=255)    gATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAgg                                                                                                                                                  <  2:136331/150‑1 (MQ=255)    gATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAgg                                                                                                                                                  <  1:609556/150‑1 (MQ=255)     aTACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGaa                                                                                                                                                <  1:697979/151‑1 (MQ=255)            agtagtAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTTTAATgaaa                                                                                                                                           >  1:649496/1‑149 (MQ=255)                 taAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGGTTTTTTGGATTaaaaaaaaa                                                                                                                                     >  1:822599/1‑149 (MQ=255)                       gCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATgcaagca                                                                                                                              <  2:485506/151‑1 (MQ=255)                         atatTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTGGAATGAAAAAAAAAgaaaacaa                                                                                                                             >  2:899489/1‑150 (MQ=255)                           atTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGGTTTTTGGAAAAGGAGAAAAAACAAGAaata                                                                                                                           >  2:651348/1‑150 (MQ=255)                             tttACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTTGGATGGAAAAAAAAGGAAACaataa                                                                                                                          >  2:190575/1‑149 (MQ=255)                               tACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAataatat                                                                                                                       <  1:346747/150‑1 (MQ=255)                                aCCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTTGAATGAAAAAAAATGCAAGCaataa                                                                                                                          >  1:219560/1‑146 (MQ=255)                                   aaTGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGGTTTTTTGAATGAAAAAAAAAGCAAGCaataaaataa                                                                                                                     >  1:582286/1‑148 (MQ=255)                                                 tttCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTTGGATGAAAAAAAAAGCAAACAAAAATATAAAAAAGGGCTAAtttttt                                                                                                    >  2:349059/1‑151 (MQ=255)                                                  ttCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCtt                                                                                                    <  2:781298/150‑1 (MQ=255)                                                    ccGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGATTTTTTGTATGGAAAAAAAAAAAAAAAATAATAAAATAATGGTCCAATtttttt                                                                                                   >  2:180435/1‑149 (MQ=255)                                                             tGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTTGGATGAAAGAAAAAGCAAACAATAAAATAATAATTGGCTAATTTTTTTTAAAATCAtt                                                                                         >  2:778485/1‑150 (MQ=255)                                                              gCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTa                                                                                        <  2:659510/150‑1 (MQ=255)                                                                       cTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTTGGATGAAAAAAAAAGCAAGCAATAATATAAAAAAAGCCTAATTTTTTTTAACAACATTAAACatat                                                                                 >  2:638384/1‑148 (MQ=255)                                                                           ccTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATatcatcatc                                                                          <  2:290968/151‑1 (MQ=255)                                                                            cTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTGGAATGAAAGAAAAAGCAAGCAATAATATAATAATGGCCTAATTTTTTTGAACATCATTAAACatatta                                                                               >  2:532339/1‑143 (MQ=255)                                                                                   taAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTTGCATTAAAGAAAATATAAGCAAAAAAATAAAAATAGCATCATTTTTTTTAAAATCTTTAAGGATAACATTATCCTTTAttt                                                                  >  1:877411/1‑151 (MQ=255)                                                                                        cTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTTGTATTGAAAAAAAAGCAAGCAAAAATATAAAAATTGGCTAATTTTTTTTAAAAACATTAAAAAAATTATTATTCTCTAtttttc                                                               >  1:610139/1‑146 (MQ=255)                                                                                         ttATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTGGAATGAAAGAAAAAGGAAACAATAAAATAAAAATTGCCTAATTTTTTTTAACAACATTAAACATATTATTAACGTCTATTTTcc                                                               >  2:279181/1‑148 (MQ=255)                                                                                          tATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCa                                                              <  1:549431/148‑1 (MQ=255)                                                                                          tATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGa                                                            <  1:661776/150‑1 (MQ=255)                                                                                           aTTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTTGGATGAAAGAAAAAGCAAGCAAAAAAATAAAAATTGGCTAATTTTTTTGAAAATCATTAAACATATTATTATCTTCTTTTTTCCCGaa                                                           >  2:241208/1‑150 (MQ=255)                                                                                            ttGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTTGGATGAAAAAAAAAGCAAACAATAATATAATAATTGCCTAATTTTTTTTTAAATCATTAAGCATATCCTCATCGTCTTTTTTCCAGAAt                                                          >  2:453303/1‑150 (MQ=255)                                                                                              gTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATAGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCg                                                       >  1:680406/1‑151 (MQ=255)                                                                                                  aCCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGa                                                   <  2:820951/151‑1 (MQ=255)                                                                                                  aCCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGa                                                   <  1:586364/151‑1 (MQ=255)                                                                                                  aCCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATAGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCg                                                    <  2:680476/150‑1 (MQ=255)                                                                                                            tttCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATc                                          <  1:717479/150‑1 (MQ=255)                                                                                                               ccTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTTGTATTGAAGAAAAAACAAGCAAAAAAATAATAATGGGCTAATTTTTTTTTAAATCATTAAAAAAATCATAATTGTCTATTTTCCAGAAACCGTCGACTtat                                              >  1:408347/1‑143 (MQ=255)                                                                                                               ccTTTGCATAATGCGCCTGGGATTAATGGCGGGGGCTTTTTGGAATGGAAGAAAAAGCAAACAAAAATATAAAAATTGGCTAAATTTTTTTAACATCAATAAAAATATTATCATCGTCTATTTTTCAGAATCCGTCGACTTATAAtatcc                                       >  2:480724/1‑146 (MQ=255)                                                                                                                cTTTGCATAATGCGCCTGGGATTAATGGCGGGTGGTTTTTTGGATTAAAAAAAAAGCAAGCAATAATATAATAAAGGCCTAATTTTTTTTAACAACATTAAACATATAATCATCGTCTATTTTCCAAAATCCGTCGACTTATAATAGcc                                       >  1:330073/1‑149 (MQ=255)                                                                                                                cTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTTGGGATGAAAGAAAAAGCAAGCAAAAATATAAAAATGGGCTAATTTTTTTTTACATCATTAAACATATCATCATCGTCTATTTTTCAGAATCCGTCGACTTATAATCGcc                                       >  2:58001/1‑149 (MQ=255)                                                                                                                  ttGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGACCAGCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAAACGCCAGa                                    <  1:271982/150‑1 (MQ=255)                                                                                                                     cATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACgg                                <  1:265732/151‑1 (MQ=255)                                                                                                                      aTAATGCGCCTGGGATTAATGGCGGGTGCTCTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGc                               <  2:677995/151‑1 (MQ=255)                                                                                                                       tAATGCGCCTGGGATTAATGGCGGGGGGTTTTTGGGATGAAAAAAAAAGCAAACAAAAATAAAAAAATGGCCTAAATTTTTTTTAAAACATTAAACAAATACTCATCCTCTATTTTCCCGAAACCGTCGACTTTTAATTGccccga                                   >  2:520559/1‑142 (MQ=255)                                                                                                                        aaTGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCa                              <  1:903015/150‑1 (MQ=255)                                                                                                                        aaTGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCa                              <  1:831495/150‑1 (MQ=255)                                                                                                                         aTGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCata                            <  1:401228/151‑1 (MQ=255)                                                                                                                           gcgcCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATc                          <  1:655674/151‑1 (MQ=255)                                                                                                                                            cGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAAc         <  1:484694/151‑1 (MQ=255)                                                                                                                                                tGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCtg     >  2:473991/1‑151 (MQ=255)                                                                                                                                                   ttttAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTgg  >  1:388844/1‑151 (MQ=255)                                                                                                                                                   ttttAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTgg  >  1:386280/1‑151 (MQ=255)                                                                                                                                                       |                                                                                                                                                   CATGATACAGGAGTAGTAAAGGGCATATTTTACCAATGTTAAGGCGACTTTCCGTTTTATTGCGAGTCGCCTTTCCTGATTATAAATCTTATTGTTTACCTAATCATTTTCCTTTGCATAATGCGCCTGGGATTAATGGCGGGTGCTTTTAGGAATGAAAGAAAATGCAAGCAATAATATAATAATGGCCTAATTTCTTTGAACATCATTAAGCATATCATCATCGTCTATTTGCCAGAATCCGTCGACTTATAATCGCCAGAACGGCATATCAGGACGGTGCTGCGAACGCTGTGG  >  NC_000913/4536047‑4536343

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑