Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,253,775	0	T	C	40.0%	76.0 / 10.3	50	D147G (GAT→GGT)	yhaJ	LysR family putative transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (26/4);  new base C (0/20);  total (26/24)
Fisher's exact test for biased strand distribution p-value = 2.25e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TATTTCACACGCGTCACTTCAGATAACGGTTCCGGCTCCTGATGAATCGGGTGATCAGGCGCGGCAACGTAGACGTTCATTAACGTATAGAGCTTGCGCGAGTTGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTGGGTATTGGCTTTTGCCGCCAGTTTGTCGATTAACGGGAAAAAGGCAGGTGTCGGTACCAGCGCTTCGGTCACAATGGTG  >  NC_000913/3253625‑3253918                                                                                                                                                        |                                                                                                                                                tatTTCACACGCGTCACTTCAGATAACGGTTCCGGCTCCTGATGAATCGGGTGATCAGGCGCGGCAACGTAGACGTTCATTAACGTATAGAGCTTGCGCGAGTTGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAatat                                                                                                                                                 >  1:120708/1‑151 (MQ=255)  atTTCACACGCGTCACTTCAGATAACGGTTCCGGCTCCTGATGAATCGGGTGATCAGGCGCGGCAACGTAGACGTTCATTAACGTATAGAGCTTGCGCGAGTTGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATc                                                                                                                                                >  2:952042/1‑151 (MQ=255)            cgTCACTTCAGATAACGGTTCCGGCTCCTGATGAATCGGGTGATCAGGCGCGGCAACGTAGACGTTCATTAACGTATAGAGCTTGCGCGAGTTGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGcccc                                                                                                                                      >  1:862180/1‑151 (MQ=255)                aCTTCAGATAACGGTTCCGGCTCCTGATGAATCGGGTGAGCAGGCGCGGCAACGTAGACTTTCATTAACGTATAGAGCTTGCGGGAGTTAACCCCCGACGAGAAACAAAAATGC‑ATACCCGGCGCAATAACAATACCCGCCCGCCCCt                                                                                                                                     <  1:109488/148‑1 (MQ=255)                   tCAGATAACGGTTCCGGCTCCTGATGAATCGGGTGATCAGGCGCGGCAACGTAGACGTTCATTAACGTATAGAGCTTGCGCGAGTTGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATACCCGCCCGCCCCTGCTcc                                                                                                                                <  1:408226/150‑1 (MQ=255)                    cAGATAACGGTTCCGGCTCCTGATGAATCGGGTGATCAGGCGCGGCAACGTAGACGTTCATTAACGTATAGAGCTTGCGCGAGTTGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCa                                                                                                                               <  2:233047/150‑1 (MQ=255)                    cAGATAACGGTTCCGGCTCCTGATGAATCGGGTGATCAGGCGCGGCAACGTAGACGTTCATTAACGTATAGAGCTTGCGCGAGTTGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCa                                                                                                                               <  2:536995/150‑1 (MQ=255)                      gATAACGGTTCCGGCTCCTGATGAATCGGGTGATCAGGCGCGGCAACGTAGACGTTCATTAACGTATAGAGCTTGCGCGAGTTGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGcc                                                                                                                            >  1:787956/1‑151 (MQ=255)                        tAACGGTTCCGGCTCCTGATGAATCGGGTGATCAGGCGCGGCAACGTAGACGTTCATTAACGTATAGAGCTTGCGCGAGTTGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGCCGt                                                                                                                          >  2:1086356/1‑151 (MQ=255)                         aaCGGTTCCGGCTCCTGATGAATCGGGTGATCAGGCGCGGCAACGTAGACGTTCATTAACGTATAGAGCTTGCGCGAGTTGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGCCGtt                                                                                                                         >  2:1015456/1‑151 (MQ=255)                            gtttCCGGCTCCTGATGAATCGGGTGACCAGGCGCGGAAACGTAGACGTTCATTAACGTATAGAGCTGGCGCGAGTTGTTCCCCGCCGAGGACCGAAAAGGC‑ATTCCCGGCGCGATACCAATATCCGCCCGCCCCTGCTCCAGCCGTTccc                                                                                                                      <  1:376411/149‑1 (MQ=255)                              ttCCGGCTCCTGATGAATCGGGTGATCAGGCGCGGCAACGTAGACGTTCATTAACGTATAGAGCTTGCGCGAGTTGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGCCGTTCCCAc                                                                                                                    >  1:4164/1‑151 (MQ=255)                                ccGGCCCCTGATGAATCGGGTGATCAGGCGCGGCAACGTAGCCGTTCATTAACGTATAGAACTTGCGCGAGTGGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATACCCGCCCGCCCCTGCTCCAGCCGTTCCCAc                                                                                                                    <  2:235689/149‑1 (MQ=255)                                    cTCCTGATGAATCAGGTGATCAGGCGCGGCAACGTAGACGTTCATTAACGTATAGAGCTTGCGCGAGTTGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGCCGTTCCCACGccccc                                                                                                              >  2:178414/1‑151 (MQ=255)                                    cTCCTGATAAATCGGGTGATCAGGCGCGGCAACGTAGACGTTCATTAACTTATAGAGCTTGCGCGAGTTGTTCTCCGACGAGGAACAAAAAGGC‑ATACCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGCCGTTCCCACGcccc                                                                                                               <  2:662421/150‑1 (MQ=255)                                          atgaATCGGGTGATCAGGCGCGGCAACGTAGACGTTCATTAACGTATAGAGCTTGCGCGAGTTGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAg                                                                                                         >  2:117899/1‑150 (MQ=255)                                            gaATCGGGTGATCAGGCGCGGCAACGTAGACGGTCATTAACGTATAGAGCTTGCGCGAGTTGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCAc                                                                                                      >  1:683414/1‑151 (MQ=255)                                               tCGGGTGATCAGGCGCGGCAACGTAGACGTTCATTAACGTATAGAGCTTGCGCGAGTTGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTc                                                                                                   >  1:76844/1‑151 (MQ=255)                                                cGGGTGATCAGGCGCGGCAACGTAGACGTTCATTAACGTATAGAGCTTGCGCGAGTTGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTc                                                                                                   >  2:829570/1‑150 (MQ=255)                                                      aTCGGGCGCGGAAACGTAGCCGTTCATAAACGTATAGAGTTTGCGGGAGTTGATCCCCGACGAGGAACAAAAATGC‑ATACCCGGCGCGATAAAAATACCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGtgat                                                                                             <  2:1046093/150‑1 (MQ=255)                                                          ggCGGGGAAACGTAGCCTTCCATAACCGTATAGAGCTTGCGCGGTTTATTCCCCGCGGAGAAACAAAAAGGA‑ATACCGGGCGCGAAAAAAATACCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGtgatga                                                                                           <  2:175315/148‑1 (MQ=255)                                                          ggCGCGGAAAGGTAGATGTTCATAAACGTATAGAGTTGGCGGGAGTTGTTCCCCGAGGGGAAACAAAAATGC‑ATACCCGGCGCAATAAAAATACCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTg                                                                                        <  2:72501/151‑1 (MQ=255)                                                          ggCGCGGAAAGGAAGCCTTTAATTAACGTAAGGACTTGGCGGGGGTTATTCCCCG‑CGGGGAACCAAAAAGCAATACCCGGCGGAAAAACAATACCCCCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTg                                                                                        <  2:1030921/151‑1 (MQ=255)                                                          ggCGCGCAAACGTAGCTGTTCTTAAACGTATAGAGCTGGCGGGAGTTTACCCCCGGGGAGAAACAAAAAGCC‑ATCCCGGCCGCAAAAAAAATTCCCCCCCGCCCCTGCCCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGtga                                                                                              <  1:903836/145‑1 (MQ=255)                                                                  aatgtaaagtttCATTAACTTAAGGAACTTGCCCAGTTTGACCCCCAACGAGAAAGAAAAATCC‑ACACCCGCCGCAAAAAAAATGCCCCCCCGCCCCTGCTCCAGCCGTTCCCACCCCCCCGCCAGCACTTCTGTGATGATTGCCa                                                                                     <  1:147600/136‑1 (MQ=255)                                                                  aaCGTAGACTTTAATAACCGTATAGAGCTGGCGCGAGTTGATCTCCGAGGAGGAACAAAAAGGC‑ATCCCCGGCGCGATAAAAATCCCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTg                                                                                 <  2:906467/150‑1 (MQ=255)                                                                   aCGTAGACGTTCATTAACGTATAGAGCTTGCGCGAGTTGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTggg                                                                               >  1:1024081/1‑151 (MQ=255)                                                                    cGTAGACGTTCATTAACGTATAGAGCTTGCGCGAGTTGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTggg                                                                               >  2:841244/1‑150 (MQ=255)                                                                    cGTAGACGTTCATTAACGTATAGAGCTTGCGCGAGTTGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTggg                                                                               >  2:872582/1‑150 (MQ=255)                                                                        gACGTTCATTAACGTATAGAGCTTGCGCGAGTTGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTGGGTATTg                                                                          >  2:724254/1‑151 (MQ=255)                                                                               aTTAATGTATAGAGCTTGCGCGAGTTGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCAAGCACTTCTGTGATGATTGCCAGTTGGGTATTGGCTTTTg                                                                   >  2:1227095/1‑151 (MQ=255)                                                                                  acctaaaagggtttGCGCGATTTGATCCCCGACGAGAAAAAAAAAGCA‑ATACCCGGCGGAATAAAAAACCCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTGGGTATTGGCTTTTgccg                                                                <  2:866678/139‑1 (MQ=255)                                                                                  aaCGTATAGAGCTTGCGCGAGTTGATCTCCGCCGAGGAACAAAAATGC‑ATACCCGGCGCAAAAAAAATCCCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTGGGTATTGGCTTTTgc                                                                  <  2:484351/149‑1 (MQ=255)                                                                                                  gcgAGTTGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTGGGTATTGGCTTTTGCCGCCAGTTTGTCGATTa                                                 >  1:1141221/1‑150 (MQ=255)                                                                                                    gAGGTGTTCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCAAGTTGGGTATTGGCTTTTGCCGCCAGTTTGTCGATTAACg                                              >  1:1186598/1‑151 (MQ=255)                                                                                                      tttGATCCCCGGGGAGAAAGAAAAATCC‑ATCCCGGGCGCAAAAACAATCCCCCCCCGCCCCTGCTCCAGCCGTTCCCCCGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTGGGTATTGGCTTTTGCCGCCAGTTTGt                                                       <  1:362842/139‑1 (MQ=255)                                                                                                       ttGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTGGGTATTGGCTTTTGCCGCCAGTTTGTCGATTAACggg                                            >  2:415741/1‑150 (MQ=255)                                                                                                       tggATCTCCGCGGAGAAACGAAAATAC‑ATACCCGGCCAGATAAAAATACCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTGGGTATTGGCTTTTGCCGCCa                                                             <  2:903660/131‑1 (MQ=255)                                                                                                          aTCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTGGGTATTGGCTTTTGCCGCCAGTTTGTCGATTAACGGGa                                           >  1:1037849/1‑148 (MQ=255)                                                                                                          aTCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGATCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTGGGTATTGGCTTTTGCCGCCAGTTTGTCGATTAACGGGaaa                                         >  1:898503/1‑150 (MQ=255)                                                                                                                     gaaaCAAAAAGGC‑ATCCCCGGCGCAAAAAAAATTCCCCCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTGGGTATTGGCTTTTGCCGCCAGTTTGTCGATTAACGGGAAAAAGGCAGgtgt                              <  2:1143021/148‑1 (MQ=255)                                                                                                                       accaaaaaTCC‑ATACCCGGCGGAAAAAAATTACCCCCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTGGGTATTGGCTTTTGCCGCCAGTTTGTCGATTAACGGGAAAAAGGCAGgtg                               <  1:81640/143‑1 (MQ=255)                                                                                                                        aCGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTGGGTATTGGCTTTTGCCGCCAGTTTGTCGATTAACGGGAAAAAGGCAGGTGTCGGt                          >  2:179564/1‑151 (MQ=255)                                                                                                                           aaatTGC‑ATACCCGCCGCAATAAAAATCCCCCCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTGGGTATTGGCTTTTGCCGCCAGTTTGTCGATTAACGGGAAAAAGGCAGGTGTCgg                           <  1:258822/147‑1 (MQ=255)                                                                                                                            aaaGGC‑ATCCCCGGCCCTAAAAAAATACCCCCCCGCCCCGGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTGGGTATTGGCTTTTGCCGCCAGTTTGTCGATTAACGGGAAAAAGGCAGGTGTCGGTACCa                      <  2:417380/151‑1 (MQ=255)                                                                                                                                 c‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTGGGTATTGGCTTTTGCCGCCAGTTTGTCGATTAACGGGAAAAAGGCAGGTGTCGGTACCAGCGCt                 >  1:254365/1‑151 (MQ=255)                                                                                                                                     atCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTGGGTATTGGCTTTTGCCGCCAGTTTGTCGATTAACGGGAAAAAGGCAGGTGTCGGTACCAGCGCTTCg              >  2:787725/1‑151 (MQ=255)                                                                                                                                         ggCGCGAAAACAATACCCCCCCGCCCCGGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTGGGTATTGGCTTTTGCCGCCAGTTTGTCGATTAACGGGAAAAAGGCAGGTGTCGGTACCAGCGCTTCGGTc           <  2:862226/150‑1 (MQ=255)                                                                                                                                           cgcgATAACAATATCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTGGGTATTGGCTTTTGCCGCCAGTTTGTCGATTAACGGGAAAAAGGCAGGTGTCGGTACCAGCGCTTCGGTcac         >  1:590011/1‑150 (MQ=255)                                                                                                                                            gaaaaaaaaaTACCCCCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTGGGTATTGGCTTTTGCCGCCAGTTTGTCGATTAACGGGAAAAAGGCAGGTGTCGGTACCAGCGCTTCGGTcac         <  2:1151995/141‑1 (MQ=255)                                                                                                                                                  aCAATATCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTGGGTATTGGCTTTTGCCGCCAGTTTGTCGATTAACGGGAAAAAGGCAGGTGTCGGTACCAGCGCTTCGGTCACAATGGTg  >  2:802226/1‑150 (MQ=255)                                                                                                                                                        |                                                                                                                                                TATTTCACACGCGTCACTTCAGATAACGGTTCCGGCTCCTGATGAATCGGGTGATCAGGCGCGGCAACGTAGACGTTCATTAACGTATAGAGCTTGCGCGAGTTGATCTCCGACGAGGAACGAAAATGC‑ATATCCGGCGCGATAACAATATCCGCCCGCCCCTGCTCCAGCCGTTCCCACGCCCCCGCCAGCACTTCTGTGATGATTGCCAGTTGGGTATTGGCTTTTGCCGCCAGTTTGTCGATTAACGGGAAAAAGGCAGGTGTCGGTACCAGCGCTTCGGTCACAATGGTG  >  NC_000913/3253625‑3253918

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑