Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,511,772	0	A	C	41.8%	84.3 / 17.1	55	V312G (GTG→GGG)	mntH	manganese/divalent cation transporter
Reads supporting (aligned to +/- strand):  ref base A (26/6);  new base C (0/23);  total (26/29)
Fisher's exact test for biased strand distribution p-value = 4.88e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCTCATCAAGATCGGCAACACCAGTATG  >  NC_000913/2511625‑2511911                                                                                                                                                    |                                                                                                                                            gCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCt                                                                                                                                          <  1:64140/151‑1 (MQ=255) gCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCt                                                                                                                                          <  2:951132/151‑1 (MQ=255)  cGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCt                                                                                                                                          >  1:838958/1‑150 (MQ=255)   gATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGc                                                                                                                                        <  2:656544/151‑1 (MQ=255)      aCCAAAACTTAACAGTACCTGACTCATAACCAGAACCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGcccc                                                                                                                                     >  2:400665/1‑151 (MQ=255)                 aCAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTccc                                                                                                                          >  1:294704/1‑151 (MQ=255)                               aTAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGAAAATAAATGACGGCAACAGGGTGACTGTACGCCGCCCCCACAGCGGGATATAAAAGCGAATGAAGCCCTGCATCCCCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGaa                                                                                                             <  2:351928/150‑1 (MQ=255)                                 aaCCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGAc                                                                                                          >  2:836724/1‑151 (MQ=255)                                 aaCCAAAACCCGTGTCGGATCTAACCCCATCAAAATGAAAAAAAATGACGGCAACATGGTGACTGTCCGACGCCCCCACAGCGGGATATAAAAGCGAATAAAGCCCTGCATCCCCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAg                                                                                                            <  2:88424/149‑1 (MQ=255)                                   ccAGAATCCGTGTCGGATCTAACCCCAACAGAATGACAAAAAATGACGGCACCATGGTGACTGTCCGACGCCCCCACAGCGGGATAGGAAAGCAAATAAGCCCCTGCATCACCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGAc                                                                                                          <  2:106378/149‑1 (MQ=255)                                   ccAAAACCCGTGTGGGATCTAACCCCACCAAAATGAAAAAAAATGACGGAAACAGGGTGACTTTACGCCGCCCCCACAGCGGAATATGAAAGCAAATAAAGCCCGCCATCACCCCCGGCCCCGCCAGTGTCCCCACCACCGTTGAAGACa                                                                                                         <  1:284534/150‑1 (MQ=255)                                     aaaaccggtgtCGAATCTAACCCCACCAAAATAAAAAAAAATGACGGAAACATGGTGACGGTACGCCCCCCCCACAGCGGGATATGAAAGCAAATAAACCCCGCCACCCCCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGcc                                                                                                      <  1:716900/144‑1 (MQ=255)                                     aGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGcc                                                                                                      >  2:774078/1‑151 (MQ=255)                                      gAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGccc                                                                                                     >  2:510627/1‑151 (MQ=255)                                       aaTCCGTGTCGGATCTAACCCCAACAGAATGAAAAAAAATGACGGCAACATGGTGACTGTACGACGCCCCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCCCCGGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGccc                                                                                                     <  2:736864/150‑1 (MQ=255)                                           cGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCgc                                                                                                  >  2:566142/1‑149 (MQ=255)                                             tgtCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCgcagc                                                                                               >  1:348675/1‑150 (MQ=255)                                                   aTCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAgg                                                                                        >  1:89973/1‑151 (MQ=255)                                                     cTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCt                                                                                      >  1:914176/1‑151 (MQ=255)                                                       aaTCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCtt                                                                                     >  2:694027/1‑150 (MQ=255)                                                       aaTCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCtt                                                                                     >  1:732236/1‑150 (MQ=255)                                                        acccaaTCAGAATGAAAAAAAAAGACGGCAACATGGTGACTGTCCGCCCCCCCCACGGCGGAATAAAAAACAAAAGGAGCCCCTGCATCACCCCCGCCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAgg                                                                                        <  1:934901/141‑1 (MQ=255)                                                        aTCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTa                                                                                    >  1:907204/1‑150 (MQ=255)                                                          cccACCAAAATGAAAATAAATGACGGAAACATGGTGACTGTCCGACCCCCCCACAGCGGGATATGAAAGCGAATGAACCCCTGCATCACCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAAt                                                                                  <  2:802154/150‑1 (MQ=255)                                                           ccATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATcc                                                                                >  2:476832/1‑151 (MQ=255)                                                             accaaaacaaCAATAAAGGCCGCCAACATGGTCCCTGAACGACCCCCCCACAGGGGGATAGGAACGCGAAAGAAGCCATGCACCCCCACCGCCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCaa                                                                              <  1:209685/142‑1 (MQ=255)                                                               cAGAATTAAAATAAACAACGATATCATGGTGCCGGTCCTCCCCCCCCACAGCGGGATAAAAAAGCAAATGACGCCCTCCACCCCCCCCGCCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAg                                                                            <  1:335373/151‑1 (MQ=255)                                                                agaagaaCAAAAAATGCCGGCAACATGGTGACTGTACGCCGCCCCCCCGGCGGTATATAAAAGCGAATAAGGCCCTGCACCCCCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAg                                                                            <  2:577457/144‑1 (MQ=255)                                                                aaaaTGAAAAAAAATGACGGAAACAGGGTGACTGTACGACCCACCCACAGCGGAATATAAAAGAAAAGGAACCCCTCCACCCCCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCaaa                                                                             <  1:390296/147‑1 (MQ=255)                                                                aaaaTGAAAAAAAATGACGACAACATGGTGACTGTACGCCCCCCCCACGGCGGGATATGAAAGCAAAAGAAGCCCTCCACCCCCCCCGCCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGa                                                                           <  1:821336/149‑1 (MQ=255)                                                                     gACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACATCCCCGCAGCAACCAGGCTTAATCCAAAGACCGtt                                                                      >  1:836741/1‑151 (MQ=255)                                                                        aaaaaaGGACGGCAACATGGTGACTGTACGCCGCCCCCACAGCGGGATAGAAAAGCAAATGAACCCCTGCACCCCCCCCTCCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGtt                                                                      <  2:436766/145‑1 (MQ=255)                                                                           aaaGGACGGCAACGGGGTGACTGTCCGACGCCCCCACAGGGGGATAGGAAAGCGAAAGAACCCGTCCACCCCCCCCCGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGc                                                                 <  2:616997/150‑1 (MQ=255)                                                                                  ggCAACAGGGTGACTGTACGCCGCCCCCACAGCGGTATATGAAAGCGAATGAACCCCTCCACCCCCCCCTCCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGt                                                            <  1:259617/148‑1 (MQ=255)                                                                                     aaCATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCtt                                                       >  1:537405/1‑150 (MQ=255)                                                                                          ggTGACTGTACGACGCCCCCACAGCGGGATATGAAAGCGAATGAACCCCTGCATCCCCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAg                                                  <  2:293574/150‑1 (MQ=255)                                                                                          ggTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGc                                                 >  2:751827/1‑151 (MQ=255)                                                                                               cTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTg                                            >  2:595066/1‑151 (MQ=255)                                                                                                tGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGc                                           >  1:664465/1‑151 (MQ=255)                                                                                                 gTACGACGCCCCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCACCCCCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGc                                           <  2:354173/150‑1 (MQ=255)                                                                                                 gTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGc                                           >  1:798134/1‑150 (MQ=255)                                                                                                  tACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGc                                           >  2:750002/1‑149 (MQ=255)                                                                                                       cgCCCCCACTGCGGTATATAAAAGATTATAAACCCCTCAACCCCCCCCTCCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTc                                     <  1:767395/150‑1 (MQ=255)                                                                                                       cccACCCACAGCGGAATAGGAAGGCGAAGGAACCCTTGCGCCACCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCa                                    <  2:838990/149‑1 (MQ=255)                                                                                                           ccccCAGGGGGATAGGAAAGCGAAGGAGCCCCTGCACCCCCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATa                                <  2:686567/151‑1 (MQ=255)                                                                                                             cacaGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATa                                >  2:871141/1‑149 (MQ=255)                                                                                                                 gCGGGATATGAAAGCGAAGGAAGCCCTGCATCCCCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCt                           <  2:552275/150‑1 (MQ=255)                                                                                                                 gCGGGATATAAAAGCGAATGACGCCCGGCACCCCCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAg                              <  2:662756/147‑1 (MQ=255)                                                                                                                   gggATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCtcat                        >  1:856831/1‑151 (MQ=255)                                                                                                                   gggATAACAAAGCAAATAAACCCCTGCACCCCCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCtc                          <  1:395998/149‑1 (MQ=255)                                                                                                                    ggATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCtcatc                       >  2:513427/1‑151 (MQ=255)                                                                                                                        atGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCtcatca                      >  2:23379/1‑148 (MQ=255)                                                                                                                           aaaGCAAATGACCCCCTCCACCCCCCCCTCCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCTCATCAAGAtt                 <  1:566120/150‑2 (MQ=255)                                                                                                                                       gCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCTCATCAAGATCGGCAACACCAGt     >  2:485871/1‑150 (MQ=255)                                                                                                                                        cccTCCACCCCCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCTCATCAAGATCGGCAACACCAGTa    <  1:395979/150‑1 (MQ=255)                                                                                                                                                ccccaccTCCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCTCATCAAGATCGGCAACACCAGTATg  <  1:510612/142‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                            GCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCTCATCAAGATCGGCAACACCAGTATG  >  NC_000913/2511625‑2511911

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑