Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,511,769	0	A	C	48.0%	76.5 / 10.8	50	V313G (GTG→GGG)	mntH	manganese/divalent cation transporter
Reads supporting (aligned to +/- strand):  ref base A (22/4);  new base C (0/24);  total (22/28)
Fisher's exact test for biased strand distribution p-value = 1.72e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGAGCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCTCATCAAGATCGGCAACACCAGTATGACCGG  >  NC_000913/2511622‑2511916                                                                                                                                                    |                                                                                                                                                    agagCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGAACTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATcacc                                                                                                                                                   >  1:949357/1‑150 (MQ=255)    gCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCt                                                                                                                                               <  1:597728/151‑1 (MQ=255)    gCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCt                                                                                                                                               <  2:873944/151‑1 (MQ=255)     cGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTg                                                                                                                                              >  1:23764/1‑151 (MQ=255)         aCCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGccca                                                                                                                                          <  1:467455/151‑2 (MQ=255)          ccAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCg                                                                                                                                         >  2:20774/1‑151 (MQ=255)                 ttAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAgtgt                                                                                                                                  >  1:815459/1‑151 (MQ=255)                 ttAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAgtgt                                                                                                                                  >  2:843619/1‑151 (MQ=255)                     cAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTcccc                                                                                                                              >  2:88063/1‑151 (MQ=255)                          ccTGACCAATACCCAGAACCCTGGCCGAACCAAACCCCAACAAAATAACAAAAAATGCCGCCAACATGGTGACTGTCCGCCCCCCCCACGGCGGAATATGAAGGCGAAGGAAGCCCTGCATCCCCCCCGGCCCCGCCAGTGTCCccacc                                                                                                                           <  1:173454/149‑1 (MQ=255)                                tCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTg                                                                                                                    >  1:414327/1‑150 (MQ=255)                                     aCCAGAACCCGTGTGGGATCTAACCCCAACAGAAAAAAAAAAAATGACGGCAACAGGGTGACTGACCGCCGCCCCCACAGCGGGATAAGAAAGAGAAAGAAGCACTGCATCCCCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGAc                                                                                                               <  1:214478/150‑1 (MQ=255)                                        aaaacccGTGTCGGATCTAACCCCATCAGAATGACAAAAAATGACGGCAACATGGTGACTGTACGCCGCCCCCACAGCGGGATATGAAAGCGAATAAGGCCCTGCATCACCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAg                                                                                                             <  2:109543/144‑1 (MQ=255)                                             cggtgtCGGATCTAATCCCACCAAAATGAAAATAAAGGACGCCAACATGGTGCCTGTACGCCCCCCCCACAGCGGAATATAAAAGCAAATGAAGCCCTCCACCCCCCCCGCCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCgca                                                                                                      <  1:196521/149‑1 (MQ=255)                                             ccGTGTCGTATATAACCCCACCAAAATAAAAAAAAAGGACGGAAACAGGGTGACTGTACGACCCCCCCCCGGGGGGATATAAAAGCGAATGAAGCCCTCCACCCCCCCCTCCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCg                                                                                                        <  1:18654/149‑1 (MQ=255)                                             ccGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCgc                                                                                                       >  2:750670/1‑150 (MQ=255)                                              cGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCgc                                                                                                       >  1:47024/1‑149 (MQ=255)                                                   cGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAAcc                                                                                                >  1:584800/1‑151 (MQ=255)                                                    ggATCTAATCCCATCAGAAGAAAAAAAAAGGAGGGAAACAGGGTGACTGTACGCCCCCCCCACGGGGGGATATAAAAGCAAATGAAGCCCTCCACCCCCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCgca                                                                                                      <  1:527540/144‑1 (MQ=255)                                                    ggATCTAACCCCATAAAAATGAAAAAAAATGCCGGCAACAGGGTGACTGTACGACCCCCCCCCGGCGGGATATAAAAGCGAATGAGCCCCTGCACCCCCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCa                                                                                               <  1:602693/151‑1 (MQ=255)                                                    ggATCAAACCCCACCAAAATAAAAAAAAATGACGGCAACAGGGTGACTGTACGCCGCCCCCACAGCGGGATATAAAAGCGAATGAACCCCTGCACCCCCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAAcc                                                                                                <  2:743782/150‑1 (MQ=255)                                                    ggATCAAACCCAACCAGAATGAAAAAAAATGCCGACAACAGGGTGACTGTACGCCCCCCCCACGGCGGGATAGAAAAGCAAATGACGCCCTGCACCCCCCCCGCCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCa                                                                                               <  1:707632/151‑1 (MQ=255)                                                          actCCCAACAGAATAACAAAAAATGACGGCAACATGGTGCCTGTGCGACGCCCCCCCAGCGGGATAGGAAGGAGAATAACGCCCGGCACCCCCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTa                                                                                         <  2:641511/149‑1 (MQ=255)                                                          aaccccATCAAAATAAAAAAAAATGACGCCAAAATGGTGACTGTACGCCCCCCCCACAGGGGGATAGGAAAGCAAATGAAGCCCTGCACCCCCCCCGGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAgg                                                                                             <  1:862907/144‑1 (MQ=255)                                                            ccccATCAGAAGGAAAAAAAAAGCCGGAATCGTGGTGTTTTTACGACCCCCCCACAGCGGGATACAAAACCAAGAGAAGCCCAGCACCCCCCCCTCCCCCGCCAGTGTCCCCTCCACCGTTGAAGACAGCCCCGCAGCAAcc                                                                                                <  1:815162/141‑1 (MQ=255)                                                               cATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATcc                                                                                     >  1:592884/1‑150 (MQ=255)                                                                aTCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCa                                                                                    >  2:68579/1‑150 (MQ=255)                                                                         aaaaaaaaGGACGGCAACAGGGTGACTTTACGCCCCCCCCACGGCGGAATAAAAAAGCAAAGGACCCCCTCCACCCCCCCCTCCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGtt                                                                           <  1:1018324/145‑1 (MQ=255)                                                                               atggcaggCAACTGGGTGACGGTAGGCCACCCCCCCGGGGGAATTTAAAGGCTAATGAAACCCCCCTCCCCCACCGCCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAg                                                                    <  1:700850/145‑1 (MQ=255)                                                                                    cGGCAACATGGTGATTGTCCGACGCCCCCACGGCGGAATATAAAAGCGAATGAACCCCTGCATCCCCCCCGGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGt                                                                 <  2:794808/149‑1 (MQ=255)                                                                                        aaCAGGGGGACTGTACGCCCCCCCCCCGGGGGAATAGAAAGGCAAATAAACCCCGGCACCCCCCCCTCCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCt                                                             <  1:941231/149‑1 (MQ=255)                                                                                          cagggTGCCTGTACGCCGCCCCCACAGGGGGTTATGAAAGAGAATGAAGCCCTGCATCCCCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTaa                                                          <  2:363324/147‑1 (MQ=255)                                                                                           aTGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAAc                                                         >  1:300716/1‑150 (MQ=255)                                                                                             ggggACTGTACGCCCCCCCCACAGGGGGATATAAAGGCAAAGGAACCCCGGCACCCCCCCCTCCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAAc                                                         <  1:873731/145‑1 (MQ=255)                                                                                             ggTGACTTTACGACGCCCCCACAGCGGGATATGAAGGCGAATGAACCCCTGCACCCCCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGc                                                      <  2:210449/151‑1 (MQ=255)                                                                                             ggTGACTGTCCGACCCCCCCACAGCGGAATATAAAAGCGAATGAAGCCCTGCACCCCCCCCTCCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACa                                                        <  2:417042/149‑1 (MQ=255)                                                                                              gTGACTGTACGACGCACCCACAGCGGGATATAAAAGCGAAGAAAGCCCTGCTCCCCCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCg                                                     <  2:51443/151‑1 (MQ=255)                                                                                                 aCTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGtt                                                  >  2:234073/1‑151 (MQ=255)                                                                                                  cTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTg                                                 >  2:88872/1‑151 (MQ=255)                                                                                                   tGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGc                                                >  2:384658/1‑151 (MQ=255)                                                                                                   tGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGc                                                >  2:749666/1‑151 (MQ=255)                                                                                                    gTACGCCCCCCCCCCAGGGGAATAGAAAGGCGAATGAACCCCTGCACCCCCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGtt                                                  <  1:962743/148‑1 (MQ=255)                                                                                                               ccACAGGGGAATTTAAAGGCGAATGAACCCGGGCATCCCCCCCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATaa                                    <  2:702757/151‑1 (MQ=255)                                                                                                                        gATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCtcatc                            >  1:586769/1‑150 (MQ=255)                                                                                                                         atatGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCtcatca                           >  2:792724/1‑150 (MQ=255)                                                                                                                           agaaaggCGAAGCAAACCCTGCATCCCCCCCCGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCTCATCaa                          <  1:88046/143‑1 (MQ=255)                                                                                                                                 gCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCTCATCAAGATCGGc                   >  2:875310/1‑150 (MQ=255)                                                                                                                                    aaTGACCCCCTCCACCCCCCCCTCCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCTCATCAAGATCGGc                   <  1:469324/147‑1 (MQ=255)                                                                                                                                    aaTGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCTCATCAAGATCGGCAac                >  1:68239/1‑150 (MQ=255)                                                                                                                                      tGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCTCATCAAGATCGGCAACAcc             >  2:203987/1‑151 (MQ=255)                                                                                                                                                  tCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCTCATCAAGATCGGCAACACCAGTATGACCgg  >  1:29055/1‑150 (MQ=255)                                                                                                                                                    |                                                                                                                                                    AGAGCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCTCATCAAGATCGGCAACACCAGTATGACCGG  >  NC_000913/2511622‑2511916

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑