Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,065,580	0	T	A	46.4%	48.5 / 34.7	56	T63S (ACC→TCC)	yihO	putative sulphoquinovose importer
Reads supporting (aligned to +/- strand):  ref base T (22/8);  new base A (0/26);  total (22/34)
Fisher's exact test for biased strand distribution p-value = 3.66e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAACAAAAGGTGGTGGCGATAAACTGGAGCGTTGCAATTAACGCCGCCGGAACCGCTGCATATAAAATAAAGGGACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAGATAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTGAGGAGATACAGAGTACCGATGCAGAGCATTAAATTCGAACCGACGTCGCCCATACCATAGGCGA  >  NC_000913/4065432‑4065717                                                                                                                                                       |                                                                                                                                          aaacaaaAGGTGGTGGCGATAAACTGGAGCGTTGCAATTAACGCCGCCGGAACCGCTGCATATAAAATAAAGGGACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTaa                                                                                                                                         >  2:599548/1‑151 (MQ=255)  aacaaaAGGTGGTGGCGATAAACTGGAGCGTTGCAATTAACGCCGCCGGAACCGCTGCATATAAAATAAAGGGACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTaaa                                                                                                                                        >  2:121926/1‑151 (MQ=255)    caaaAGGTGGTGGCGATAAACTGGAGCGTTGCAATTAACGCCGCCGGAACCGCTGCATATAAAATAAAGGGACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTaaaaa                                                                                                                                      >  1:1033495/1‑151 (MQ=255)    caaaAGGTGGTGGCGATAAACTGGAGCGTTGCAATTAACGCCGCCGGAACCGCTGCATATAAAATAAAGGGACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTaaaaa                                                                                                                                      >  1:439836/1‑151 (MQ=255)      aaaGGTGGTGGCGATAAACTGGAGCGTTGCAATTAACGCCGCCGGAACCGCTGCATATAAAATAAAGGGACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAAc                                                                                                                                    <  2:246371/151‑1 (MQ=255)          gtggtgGCGATAAACTGGAGCGTTGCAATTAACGCCGCCGGAACCGCTGCATATAAAATAAAGGGACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCg                                                                                                                                >  1:405730/1‑151 (MQ=255)                gCGATAAACTGGAGCGTTGCAATTAACGCCGCCGGAACCGCTGCATATAAAATAAAGGGACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGccacca                                                                                                                          >  2:590259/1‑151 (MQ=255)                     aaaCTGGAGCGTTGCAATTAACGCCGCCGGAACCGCTGCATATAAAATAAAGGGACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAg                                                                                                                     >  1:1035480/1‑151 (MQ=255)                      aaCTGGAGCGTTGCAATTAACGCCGCCGGAACCGCTGCATATAAAATAAAGGGACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAGa                                                                                                                    >  2:374111/1‑151 (MQ=255)                      aaCTGGAGCGTTGCAATTAACGCCGCCGGAACCGCTGCATATAAAATAAAGGGACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAGa                                                                                                                    <  2:716194/151‑1 (MQ=255)                       aCTGGAGCGTTGCAATTAACGCCGCCGGAACCGCTGCATATAAAATAAAGGGACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAGAt                                                                                                                   <  1:208888/151‑1 (MQ=255)                       aCTGGAGCGTTGCAATTAACGCCGCCGGAACCGCTGCATATAAAATAAAGGGACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAGAt                                                                                                                   >  2:1056144/1‑151 (MQ=255)                       aCTGGAGCGTTGCAATTAACGCCGCCGGAACCGCTGCATATAAAATAAAGGGACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAGAt                                                                                                                   <  2:229654/151‑1 (MQ=255)                              cGTTTCAATTAACGCCGCCGGAACCGCTGCATATAAAATAAAGGGACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAGATAATcc                                                                                                              <  2:389649/149‑1 (MQ=255)                                          cgccgcCGAAACCTCTGCATATAAAAAAAAGGGAGAAAATTTGCCTTTGGGCCC‑AATATTTTTCC‑CCGATTCAAAAAAAAATCCGGGGGGCATATCGGAAACCGCGAAAAAAACCTTCGCCCCAAGAAAGATAATCCCGCCATAGTAAGCa                                                                                                <  2:423620/151‑1 (MQ=255)                                           cccgccgGAACCGATGCATAAAAAATAAGGGGACGAATTTTGATTTTAGGCAC‑AATATTTTTCC‑GCGAGTCGAAAAAAACCCGGGTGAGCATACCGGAAAACGCGGTAAAAATCTTCGCCACCAGAAAGAAAATCCCGCCATAGTAAGCAg                                                                                               <  1:392113/150‑1 (MQ=255)                                             cgcggGACCCGCTGCAAAAAAAATAAAGGGAAAAAATTGGCCTTGAGGCAA‑AATTTTTTCCC‑GGGAGTCGAGAAAAAACCCGGGGAGCATATCGGTAACCGGGGAAAAAAACTCCCCCACAAAAAAAAAAACCCCGCCATAGTAAGCAGGc                                                                                             <  1:83429/151‑1 (MQ=255)                                                   aacccttacATAAAAAAAAAAGGGACGAAATTTGCTTTTAGGCCA‑AATATTTTCCC‑GGGAGACGATAAAAAATCCGGGGAGCATACGGGAAAACGCGAAAAAAACCTCCCCCCCAAAAAAAATAATCCCGCCATAGTAAGCAGGCATCCCt                                                                                       <  2:55798/143‑1 (MQ=255)                                                   aacccgtagataaAAAAAAAAGGGAAAAAAGTTGCGTTTAGCCCA‑AATATTTTCCC‑GCGAGTAGAGAAAAAACCGGGTGATCATATGGGAAAACGGGGAAAAAACCTTCGCCACCAGAAAAAAAATCCCGCCATAGTAAGCAGGCATCCCt                                                                                       <  2:440000/142‑1 (MQ=255)                                                        cttcATAAAAAAAAAAGGGAAAAAATGTCCCTTTGGGCCA‑AATTTTTTCCC‑GCGAGTCGAGAAAAAACCGGGGGAGCTTATCGGAAACCGGGGAAAAAACCTCCCCCCCCAAAAAGATAACCCCGCCATAGTAAGCAGGCATCCCTAAtt                                                                                   <  1:812654/147‑1 (MQ=255)                                                        ctgattaaaaaaaaaaGGAACGAAATTGGCCTTAATCCCA‑ATTATTTTCCC‑GCGAGTCGAGAAAAAATCCGGTAAGCATATCGGAAAACGCGGAAAAAATCTTCCCCCCCAAAAAGATAACCCCGCCATAGTAAGCAGGCATCCCTAATTc                                                                                  <  1:572211/143‑1 (MQ=255)                                                        ctcaaaaaaaaaaaaaGGAAAAAAATTTGCTTTTAGGCCA‑AATATTTTCCC‑GAAAGCCAAGAAAAAATCCGGTGAGCATTTCGGTAAACGCGGTAAAAACCTCCGCCACCAAAAAAATAATCCCGCCATAGTAAGCAGGCATCCCTAAtt                                                                                   <  2:84722/142‑1 (MQ=255)                                                        cTGAATAAAAAAAAAGGGGACAAATTTTGCTTTTAGGCTA‑ATTTTTTTCCC‑GCGAGTCGAAAAAAACCCCGGAGGCAATACCGGAAACCGCGGAAAAAACCTCCCCCACAAAAAAAAAAATCCCGCCATAGTAAGCAGGCATCCCTAATTc                                                                                  <  1:202759/151‑1 (MQ=255)                                                        cTGAATAAAAAAAAAAGGGACAAATTTTGCTTTTGGGCCA‑AATTTTTTTCC‑GCGAGTGAAGTAAAAACCCGGGGAGCATATCGGTAAACGGGGTAAAAACCTTCGCCACCAGAAAGATAATCCCGCCATAGTAAGCAGGCATCCCTAATTc                                                                                  <  2:232408/151‑1 (MQ=255)                                                            atatAAAATAAAGGTACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAGATAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCg                                                                              >  1:18456/1‑151 (MQ=255)                                                            atatAAAATAAAGGGACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAGATAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCg                                                                              >  2:601576/1‑151 (MQ=255)                                                            atatAAAATAAAGGGACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAGATAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCg                                                                              >  2:1058155/1‑151 (MQ=255)                                                            atatAAAATAAAGGGACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAGATAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCg                                                                              >  2:918365/1‑151 (MQ=255)                                                                aaaataaaGGGACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGCGTCGAGTAAAAATCCGGTGCGCAGATCGGAAACCGCGGTAAAAAACTTCGCCCCCCGACAGATAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGtat                                                                          >  2:714528/1‑151 (MQ=255)                                                                aaaataaaGGGACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAGATAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGtat                                                                          >  1:332680/1‑151 (MQ=255)                                                                 aaataaaGGGACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAGATAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGtata                                                                         >  2:674861/1‑151 (MQ=255)                                                                 aaataaaGGGACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAGATAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGtata                                                                         >  2:53407/1‑151 (MQ=255)                                                                         ggACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAGATAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTga                                                                 >  2:570842/1‑151 (MQ=255)                                                                           acaaaaTTTCCCTTTAGCCCA‑ATTATTTTCCC‑GCGAGTCGAGAAAAAACCCGGTGAGAATACGGGAAACCGCGAAAAAAACCTCCGCCACCAAAAAAATAACCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTgagg                                                               <  2:737419/148‑1 (MQ=255)                                                                            aaaaaTTTTCCTTTAGGCCCAAATTTTTTCCC‑GAAACTCAAAAAAAAACCGGGAAAGCATTTCGTAAAACGGGGAAAAAACCTCCCCCCCAAAAAAAAAAACCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTgagg                                                               <  1:686937/149‑1 (MQ=255)                                                                             aaaaTTTGCCTTTAGGCCA‑AATATTTTCCC‑GCGAGTAAATAAAAAACCCGGTGAGAATATCGATAACGGCGGAAAAAACCTCCCCCACAAAAAAAAAAACCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTgagg                                                               <  1:121908/148‑1 (MQ=255)                                                                              aaaTTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAGATAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTGAGgaga                                                            >  2:743723/1‑151 (MQ=255)                                                                                 tttACCTTTAGCCCA‑ATTATTTTCCC‑GCGAGTAGAGAAAAAACCGGGTGAGCAAATCGATAAACGGGGAAAAAAACTCCGCCCCAAGAAAGAAAACCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTGAGGAGATAc                                                         <  1:935221/151‑1 (MQ=255)                                                                                   tcccTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAACCCGGTGAGCATTTCGGAAAACGCGGAAAAAACCTTCCCCACAAGAAAGAAAACCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTGAGGAGATACag                                                       <  1:17208/149‑1 (MQ=255)                                                                                   tGCCTTAGGGCCA‑AATATTTTCCC‑GGGAGTGAAAAAAAAACCCGGGGAGCATACGGGAAAACGCGGAAAAAAACTCCCCCCCAAAAAAAAAAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTGAGGAGATACag                                                       <  1:108222/151‑1 (MQ=255)                                                                                    gCCTTTAGGCCA‑AATATTTTCCC‑GCGAGTCGAGTAAAAATCGGGTGAGCATGCCGATAAAGGCGGAAAAAAACTCCGCCACAAAAAAAAAAACCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTGAGGAGATACag                                                       <  1:480030/150‑1 (MQ=255)                                                                                     ctttgagcccc‑AATATTTTCCC‑GCGAGTCGAGAAAAAATCCGGTGAGCATATCGGAAAACGGGGAAAAAAACTCCGCCCCAAAAAAAAAAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTGAGGAGATACagag                                                     <  1:260566/143‑1 (MQ=255)                                                                                      tttcagcccc‑AATATTTTCCC‑GCGAGGAGAGTAAAAATCCGGGGGGCATATGGATAAAGGGGAAAAAAACCTCCGCCACAAGAAAAAAAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTGAGGAGATACAGAGt                                                    <  1:263947/144‑1 (MQ=255)                                                                                           accac‑AATATTTGTCC‑GCAATGCGATTAAAAACCCGGTGAGGATATGGGAAAATGCGAAAAAAACCTCCCCCACAAAAAAGAAAAAACCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTGAGGAGATACAGAGTACCGa                                               <  1:561296/147‑1 (MQ=255)                                                                                            gCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAGATAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTGAGGAGATACAGAGTACCGAt                                              >  1:749323/1‑151 (MQ=255)                                                                                              ccaaaTTTTTTCCC‑GCGAGTCGAAAAAAAACCCGGTGAGCATACCGGAAACCGCGGAAAAAAACTCCCCCACAAAAAAAATAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTGAGGAGATACAGAGTACCGATg                                             <  1:1057773/148‑1 (MQ=255)                                                                                               caaaTTTTTTCCC‑GGGAGTCGAGAAAAAACCGGGTGAGCATATCGGAAAACGCGAAAAAAACCTTCCCCACCAAAAAAAAAACCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTGAGGAGATACAGAGTACCGATGc                                            <  1:373988/149‑1 (MQ=255)                                                                                               caaaTATTTTCCC‑GAGAGTCGAGAAAAAACCCGGTGAGCATATCGAAAAACGCGGAAAAAAACTCCCCCACAAAAAAAAAAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTGAGGAGATACAGAGTACCGATGc                                            <  1:50326/149‑1 (MQ=255)                                                                                               c‑AATTTTTTTCCGGCAAGTCGAAAAAAAACCCGTGAACCATACCGTAAACCGCGGAAAAAACCTCCCCCACAAAAAAAAAAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTGAGGAGATACAGAGTACCGATGc                                            <  1:351342/151‑1 (MQ=255)                                                                                                                                  tgcgaatctCGGAAAACGAGGAAAAAACCTCCCCCACAAAAAAAAAAACCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTGAGGAGATACAGAGTACCGATGCAGAGCATTAAATTCGAACCGACGTCGCccatacc          <  1:620379/143‑1 (MQ=255)                                                                                                                                  tGAACATATGGGAAAACGGGGAAAAAAACTTCCCCACAAAAAAAAAAACCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTGAGGAGATACAGAGTACCGATGCAGAGCATTAAATTCGAACCGACGTCGCccatacc          <  2:882059/151‑1 (MQ=255)                                                                                                                                   gagaATATCGTTAACCGCGGAAAAAACCTTCGCCACAAGAAAAAAAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTGAGGAGATACAGAGTACCGATGCAGAGCATTAAATTCGAACCGACGTCGCccatacc          <  1:1001127/150‑1 (MQ=255)                                                                                                                                     gCATATCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAGATAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTGAGGAGATACAGAGTACCGATGCAGAGCATTAAATTCGAACCGACGTCGCccataccata       >  1:86114/1‑151 (MQ=255)                                                                                                                                     acATATCGTAAAACGCGGAAAAAAACTTCGCCACCAAAAAGATAACCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTGAGGAGATACAGAGTACCGATGCAGAGCATTAAATTCGAACCGACGTCGCccataccat        <  2:410781/149‑1 (MQ=255)                                                                                                                                         atggtaaaaCGCGGAAAAAAACTCCGCCACAAAAAAAATAACCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTGAGGAGATACAGAGTACCGATGCAGAGCATTAAATTCGAACCGACGTCGCCCATACCATAGGCg   <  2:371030/145‑1 (MQ=255)                                                                                                                                          tCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAGATAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTGAGGAGATACAGAGTACCGATGCAGAGCATTAAATTCGAACCGACGTCGCCCATACCATAGGCGa  >  2:974764/1‑151 (MQ=255)                                                                                                                                                       |                                                                                                                                          AAACAAAAGGTGGTGGCGATAAACTGGAGCGTTGCAATTAACGCCGCCGGAACCGCTGCATATAAAATAAAGGGACGAAATTTGCCTTTAGGCCC‑AATATTTTTCC‑GCGAGTCGAGTAAAAATCCGGTGAGCATATCGGTAAACGCGGTAAAAAACTTCGCCACCAGAAAGATAATCCCGCCATAGTAAGCAGGCATCCCTAATTCATCGGTATAAAATTTGAGGAGATACAGAGTACCGATGCAGAGCATTAAATTCGAACCGACGTCGCCCATACCATAGGCGA  >  NC_000913/4065432‑4065717

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑