Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,511,772	0	A	C	48.0%	66.1 / 20.5	50	V312G (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

GCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCTCATCAAGATCGGCAACACCAGTATGACCGGAAA  >  NC_000913/2511625‑2511919                                                                                                                                                    |                                                                                                                                                    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                                                   >  2:749666/1‑151 (MQ=255)                                                                                                tGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGc                                                   >  2:384658/1‑151 (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)                                                                                                                                                   caccTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCTCATCAAGATCGGCAACACCAGTATGACCGGaaa  >  1:859999/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                    GCGATACCAAAACTTAACAGTACCTGACTCATAACCAGAATCCGTGTCGGATCTAATCCCATCAGAATGACAATAAATGACGGCAACATGGTGACTGTACGACGCACCCACAGCGGGATATGAAAGCGAATGAAGCCCTGCATCACCACCTGCCCCGCCAGTGTCCCCACCACCGTTGAAGACAGCCCCGCAGCAACCAGGCTTAATCCAAAGACCGTTGCCGCAGCGTGGCTTAACAGCGGTTGCAGCGTCAGATAAGCCTCATCAAGATCGGCAACACCAGTATGACCGGAAA  >  NC_000913/2511625‑2511919

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: ‑