Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,556,207	0	T	C	41.2%	71.5 / 13.9	53	S215G (AGT→GGT)	rtcA	RNA 3'‑terminal phosphate cyclase
Reads supporting (aligned to +/- strand):  ref base T (24/6);  new base C (0/21);  total (24/29)
Fisher's exact test for biased strand distribution p-value = 5.11e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTCTGTTCATGCAG‑GGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGCCACCAC  >  NC_000913/3556061‑3556354                                                                                                                                                     |                                                                                                                                                    cGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGT‑CGCGCGGCGGGTTATGAATATTCTGTTCATGCAG‑GGAAAAACTcccc                                                                                                                                                 <  1:812481/151‑1 (MQ=255) cGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTCTGTTCATGCAG‑GGAAAAACTcccc                                                                                                                                                 >  1:851096/1‑151 (MQ=255)    aaCCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTCTGTTCATGCAG‑GGAAAAACTCCCCGcc                                                                                                                                              >  2:457643/1‑151 (MQ=255)      cccgcTCGGCCCTGTCGCGCTTTTCACCGCGGACAAAAAAGCGTCCGGTGATATTTTCACTTTCGACTAAAAGGGCATGGGTATTACCCGGACCATGTT‑GGCGCGGCATGTTATGAAGATTCCGTTCATGCAG‑GGCAAAACTCCCCGCCa                                                                                                                                             <  2:480316/146‑1 (MQ=255)                 cTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTCTGTTCATGCAG‑GGAAAAACTCCCCGCCAGTGTAGCGAttt                                                                                                                                 >  2:480947/1‑151 (MQ=255)                       cgcTTTTCACCGACAAAAAAAAAGTGTTGGGTGATATTTCCACTTTCCTCTTAAAGCAAGACGGTATTCCCCGCCCCCTGGT‑CGCGCGGCAGTTTAAAATTATTTTGTTCATGGAG‑GAAAAACCTCCCCGCCAGTGTAGCGATTTc                                                                                                                                <  1:965178/146‑1 (MQ=255)                          ttttCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTCTGTTCATGCAG‑GGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTc                                                                                                                          >  1:634564/1‑149 (MQ=255)                          ttttCACCAACAAAAAAAAAGCGTTCGGTAATTTTTTCCTTTTCGACTTAAAGCGAGAGGGTATTCCCCGGCCCCGGGT‑CGCGCGGCAGTTTATAAATATTCTGTTCATGCGG‑GGAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTc                                                                                                                          <  1:293864/149‑1 (MQ=255)                            ttCCCCGACGAAAAAAAAGCGTTCGGTGATTTTTTCCCTTTCGACTTCAAGCGAGACGGTTTTCCCCGGCCCCTGGC‑CGCGCGGCAGTTTATGAATATTCTGTTCATGAAG‑GAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGc                                                                                                                       <  1:737013/150‑1 (MQ=255)                                   acgacAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTCTGTTCATGCAG‑GGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGgc                                                                                                               >  1:578497/1‑151 (MQ=255)                                   acgaaAAAAAAGCGTTCGGTTATATTTTCCCTTCCGACTTCAAGCGAGACGGTTTTCCCCGCCCCCGGGT‑CGCGCGGCAGTTTATGAATATTCTGTTCATGCAG‑GAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATgg                                                                                                                <  1:702251/150‑1 (MQ=255)                                    cgacAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTCTGTTCATGCAG‑GGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGgcg                                                                                                              >  1:983964/1‑151 (MQ=255)                                       cAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTCTGTTCATGCAG‑GGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCgg                                                                                                           >  1:902027/1‑151 (MQ=255)                                        aaaaagGCGTTGGGTGATTTTTTCCCTTTCGCCTACAAGCGAGACGTTATTCCCCGCCCCCGGGT‑CGCGCGGCAGTTTATAAATATTCTGTTCAGGCAG‑GAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCgg                                                                                                           <  1:56646/150‑1 (MQ=255)                                        aaaaaaGCGTTCGGTAATATTTTCCCTTCCGACTTCAAGCGAGACGGTATTCCCCGCCCCCGGGC‑CGCGGGGCGGGTTATGAATATTCTGTTCATGCAG‑GAAAAAACCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATg                                                                                                                 <  2:825558/144‑1 (MQ=255)                                         aaaaaGCTTGGGGTTATATTTTCTCTTCCGATTTCAAGCGAGAGGTTATTACCCGGCCCCGGGC‑CGCGCGGGAGGTTATGAATATTCGGTGCTGGAAG‑GAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGca                                                                                                         <  2:903540/151‑1 (MQ=255)                                               cGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTCTGTTCATGCAG‑GGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACAcc                                                                                                     >  1:13885/1‑149 (MQ=255)                                                        atatTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTCTGTTCATGCAG‑GGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGa                                                                                           >  2:1052500/1‑150 (MQ=255)                                                         tatTTTCCCTTCCACCTTAAAGCGAGAGGGTTTTCCCCGCCCCGTGGT‑CGCGCGGCAGTTTATAAATTTTCTGTTCAGGCGG‑GAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGaa                                                                                          <  1:1022472/150‑1 (MQ=255)                                                          atTTTCCCTTTCGACTTAAAGCGAGACGTTATTACCCGGCCCCTGGT‑CGGGCGGCAGGTTATGAATTTTTTTTTATTGCAG‑GAAAAATCTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGaa                                                                                          <  1:679671/149‑1 (MQ=255)                                                                aCTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTCTGTTCATGCAG‑GGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTcc                                                                                   >  1:74497/1‑150 (MQ=255)                                                                 cTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTCTGTTCATGCAG‑GGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCAc                                                                                 >  2:363173/1‑151 (MQ=255)                                                                 cTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTCTGTTCATGCAG‑GGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCAc                                                                                 >  1:91166/1‑151 (MQ=255)                                                                        cTTCAAGCGAGACGGTATTACCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTCTGTTCATGCAG‑GGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTg                                                                          >  1:768175/1‑151 (MQ=255)                                                                         ttCAAGCGAGACGGTATTACCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTATGTTCATGCAG‑GGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGc                                                                         >  2:60478/1‑151 (MQ=255)                                                                          tCAAGCGAGACGGTATTACCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTCTGTTCATGCAG‑GGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGc                                                                         >  1:25881/1‑150 (MQ=255)                                                                          tCAAGCGAGACGGTATTACCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTCTGTTCATGCAG‑GGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGc                                                                         >  2:157899/1‑150 (MQ=255)                                                                           cAAGCGAGACGGTATTCCCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTCTTTTCATGCAG‑GAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTg                                                                          <  1:788758/148‑1 (MQ=255)                                                                              gCGAGAGGTTATTCCCCGCCCCCTGGC‑CCCGCGGCGGTTTATAATTATTCTGTTCTTGCAG‑GAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTg                                                                          <  2:801251/145‑1 (MQ=255)                                                                               cgcgccGGTATTGCCCCCCCGCCGCT‑CGCGCGGAAGGTTTCGTATATGTCGTTCAT‑CAGTGCAAAACCACCCCGCCAGTGTAGCGCTTTCCCGCTCATCCCCACGGCGCGCCACACCAGCTAATAGAACTTCTCCACGCATCTCCACAATg                                                                   <  2:432271/146‑1 (MQ=255)                                                                                    cGGTATTACCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTCTGTTCATGCAG‑GGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTccc                                                              >  2:1097208/1‑151 (MQ=255)                                                                                       tATTACCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTCTGTTCATGCAG‑GGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCcgcg                                                           >  2:322793/1‑151 (MQ=255)                                                                                              ccgCCCCCGGTGCGCGCGGCAGGATATGAATATTCGGTCCCTGCAG‑GGAAAAACCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGcc                                                     <  2:267539/149‑1 (MQ=255)                                                                                                 ccctTGGC‑CGCGCGGCAGGTTATGAATATTCTGTTCAGGCAG‑GAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGt                                                 <  2:970543/151‑1 (MQ=255)                                                                                                 cccgTGGC‑CGCGCGCGTGTTTATAAATTTTCTTTCCAGCCAG‑GAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAg                                                  <  2:144616/150‑1 (MQ=255)                                                                                                 ccccTGGC‑CGCGGGGCAGTTTATAAATTTTCTTTTCATGCAG‑GAAAAAACCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAg                                                  <  1:551596/150‑1 (MQ=255)                                                                                                   ccTGGT‑CGCGCGGCAGTTTATAAATATTCTGTTCATGCAG‑GAAAAAACCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTg                                               <  1:457811/151‑1 (MQ=255)                                                                                                      ggT‑CGCGCGGCGGGTTATAAATATTCTGTTCATGCAG‑GAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCa                                             <  1:2723/150‑1 (MQ=255)                                                                                                             ggggCAGGTTATGAATATTCTTTCCAGGAGG‑GAAAAAACCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGTCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGtt                                      <  1:525279/149‑1 (MQ=255)                                                                                                             gcgGCAGGTTATAAATATTCTGTTCATGCAG‑GGAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAg                                           <  1:768725/146‑1 (MQ=255)                                                                                                               ggCAGTTTATAAATATTCTTTTCATGCAG‑GAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAgg                                          <  1:190043/145‑1 (MQ=255)                                                                                                                  aGGTTATGAATATTCTGTTCATGCAG‑GGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACg                                 >  2:784281/1‑151 (MQ=255)                                                                                                                   ggTTATGAATATTCTGTTCATGCAG‑GGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACg                                 >  1:572114/1‑150 (MQ=255)                                                                                                                      tATGAATTGTCTGTTCAGGCAG‑GAAAAAGCACCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATg                              <  2:694740/150‑1 (MQ=255)                                                                                                                        tttattttCTGTCCAGGCAG‑GGAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGc                             <  2:27605/143‑1 (MQ=255)                                                                                                                              ttCTGTTCATGCAG‑GGAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACggg                       <  1:202709/149‑1 (MQ=255)                                                                                                                               tCTGTTCATGCAG‑GGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCg                     >  1:739801/1‑150 (MQ=255)                                                                                                                                  gTTCATGCAG‑GAAAAACCTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCga                    <  2:81751/148‑1 (MQ=255)                                                                                                                                   ttCAGGCAG‑GAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCga                    <  1:603088/147‑1 (MQ=255)                                                                                                                                          aG‑GGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTg         >  1:1085577/1‑151 (MQ=255)                                                                                                                                               aaaacCTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGccac     <  1:296191/151‑1 (MQ=255)                                                                                                                                                   aCTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGCcaccac  >  2:413062/1‑150 (MQ=255)                                                                                                                                                   aCTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGCcaccac  >  2:135194/1‑150 (MQ=255)                                                                                                                                                     |                                                                                                                                                    CGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTCTGTTCATGCAG‑GGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGCCACCAC  >  NC_000913/3556061‑3556354

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑