Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,556,200	0	G	A	40.0%	60.8 / 18.4	51	S217F (TCC→TTC)	rtcA	RNA 3'‑terminal phosphate cyclase
Reads supporting (aligned to +/- strand):  ref base G (22/8);  new base A (0/20);  total (22/29)
Fisher's exact test for biased strand distribution p-value = 1.26e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTCTGTTCATGCAG‑GGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTG  >  NC_000913/3556055‑3556347                                                                                                                                                    |                                                                                                                                                    cTGTGCCGCACCCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTCTGTTCATGCAG‑GGaaaa                                                                                                                                                 <  2:252567/150‑1 (MQ=255)       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)                                                                                                                                                    |                                                                                                                                                    CTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGT‑CGCGCGGCAGGTTATGAATATTCTGTTCATGCAG‑GGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTG  >  NC_000913/3556055‑3556347

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: ‑