Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,702,745	0	A	C	63.3%	24.0 / 63.3	49	S42A (TCG→GCG)	dppF	dipeptide/heme ABC transporter ATPas
Reads supporting (aligned to +/- strand):  ref base A (6/12);  new base C (11/20);  total (17/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.18e-02

AGATCCTGCCCCTGGTAATACAGCTCGCCACCGGTGGGCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGAAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTCGATAGCCTGCAACAGCGGTTGTTGCAGGGTGGCCTCTTGCGTACTCATAGTGTCGGCCTCCCGGCAT  >  NC_000913/3702612‑3702887                                                                                                                                      |                                                                                                                                               aGATCCTGCCCCTGGTAATACAGCTCGCCACCGGTGGGCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGAAACGCCATCCAGCGCtt                                                                                                                               <  1:284804/151‑1 (MQ=255)     ccTGCCCCTGGTAATACAGCTCGCCACCGGTGGGCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAAc                                                                                                                           <  1:259984/151‑1 (MQ=255)        gCCCCTGGTAATACAGCTCGCCACCGGTGGGCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCa                                                                                                                         <  2:68574/150‑1 (MQ=255)        gCCCCTGGTAATACAGCTCGCCACCGGTGGGCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGAAACGCCATCCAGCGCTTTAAcc                                                                                                                          >  2:756424/1‑149 (MQ=255)        gCCCCTGGTAATACAGCTCGCCACCGGTGGGCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGAAACGCCATCCAGCGCTTTAACCAg                                                                                                                        <  2:737303/151‑1 (MQ=255)         ccccTGGTAATACAGCTCGCCACCGGTGGGCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGa                                                                                                                       <  2:873633/151‑1 (MQ=255)           ccTGGTAATACAGCTCGCCACCGGTGGGCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGAAACGCCATCCAGCGCTTTAACCAGACg                                                                                                                     >  2:235180/1‑151 (MQ=255)             tGGTAATACAGCTCGCCACCGGTGGGCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGtt                                                                                                                   >  2:243237/1‑151 (MQ=255)                     cAGCTCGCCACCGGTGGGCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGcgcg                                                                                                           <  1:713137/151‑1 (MQ=255)                         tCGCCACCGGTGGGCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAAc                                                                                                        >  1:842856/1‑150 (MQ=255)                          cGCCACCGGTGGGCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGAAACGCCATCCAGCGCTTTTACCAGACGTTCCGGCGCGAACAt                                                                                                      <  1:100889/151‑1 (MQ=255)                          cGCCACCGGTGGGCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGAAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAAc                                                                                                        <  2:259601/149‑1 (MQ=255)                           gCCACCGGTGGGCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGAAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACAt                                                                                                      <  2:332890/150‑1 (MQ=255)                             cACCGGTGGGCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGcc                                                                                                   >  2:191527/1‑151 (MQ=255)                             cACCGGTGGGCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGAAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGcc                                                                                                   >  2:557381/1‑151 (MQ=255)                              aCCGGTGGGCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCt                                                                                                  >  1:77713/1‑151 (MQ=255)                              aCCGGTGGGCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGAAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCt                                                                                                  >  1:342448/1‑151 (MQ=255)                                cGGTGGGCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCTAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGAAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCttt                                                                                                <  1:835374/151‑1 (MQ=255)                                cGGTGGGCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCttt                                                                                                <  1:227918/151‑1 (MQ=255)                                  gTGGGCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTttct                                                                                              <  1:125511/151‑1 (MQ=255)                                  gTGGGCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTttct                                                                                              <  1:475766/151‑1 (MQ=255)                                    gggCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGAAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTttcttc                                                                                            >  1:423659/1‑151 (MQ=255)                                             aaTCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATa                                                                                    >  1:813136/1‑150 (MQ=255)                                              atcatcGTCAGCAACCGACCGAGGTTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAAt                                                                                  <  2:43039/151‑1 (MQ=255)                                                    gTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGttttt                                                                            <  2:202420/151‑1 (MQ=255)                                                      cAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTc                                                                          <  2:16857/151‑1 (MQ=255)                                                      cAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGAAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTc                                                                          <  2:577458/151‑1 (MQ=255)                                                           accgaccgAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGAAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTc                                                                     <  2:743573/151‑1 (MQ=255)                                                            ccgaccgaGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTCg                                                                    <  1:746781/151‑1 (MQ=255)                                                                  gaGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGAAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTCGATAGcc                                                              <  1:612567/151‑1 (MQ=255)                                                                        cGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGAAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTCGATAGCCTGCaa                                                         <  1:671544/150‑1 (MQ=255)                                                                             tACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGCTACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTCGATAGCCTGCAACAGCg                                                    <  2:746345/150‑1 (MQ=255)                                                                                 gCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTCGATAGCCTGCAACAGCGgttgt                                               <  1:123905/151‑1 (MQ=255)                                                                                  cAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTCGATAGCCTGCAACAGCGgttgtt                                              <  2:452907/151‑1 (MQ=255)                                                                                   aGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGAAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTCGATAGCCTGCAACAGCGGttgttg                                             <  1:903956/151‑1 (MQ=255)                                                                                    gCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTCGATAGCCTGCAACAGCGGttgttg                                             <  2:624873/150‑1 (MQ=255)                                                                                     ccAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAGCCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTCGATAGCCTGCAACAGCGGTTGTTGc                                            >  1:699210/1‑150 (MQ=255)                                                                                        gATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGAAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTCGATAGCCTGCAACAGCGGTTGTTGCAggg                                        <  1:553372/151‑1 (MQ=255)                                                                                              cccACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTCGATAGCCTGCAACAGCGGTTGTTGCAGGGTGGCct                                  <  2:69344/151‑1 (MQ=255)                                                                                                cACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGAAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTCGATAGCCTGCAACAGCGGTTGTTGCAGGGTGGCctct                                >  1:491926/1‑151 (MQ=255)                                                                                                  ctactGCCAGCGTTTTGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTCGATAGCCTGCAACAGCGGTTGTTGCAGGGTGGCCTCtt                               <  2:644305/150‑1 (MQ=255)                                                                                                             gTTTTGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTCGATAGCCTGCAACAGCGGTTGTTGCAGGGTGGCCTCTTGCGTACTCAt                     >  1:857780/1‑149 (MQ=255)                                                                                                                tttccACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTCGATAGCCTGCAACAGCGGTTGTTGCAGGGTGGCCTCTTGCGTACTCATAgtgt                >  1:526242/4‑151 (MQ=255)                                                                                                                 tGCCACGTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTCGATAGCCTGCAACAGCGGTTGTTGCAGGGTGGCCTCTTGCGTACTCATAgtgt                <  1:510633/150‑1 (MQ=255)                                                                                                                       gTTCAAGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTCGATAGCCTGCAACAGCGGTTGTTGCAGGGTGGCCTCTTGCGTACTCATAGTGTCGGCCTc         >  2:719637/1‑151 (MQ=255)                                                                                                                           aaGGTTAAACGCAACGCTATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTCGATAGCCTGCAACAGCGGTTGTTGCAGGGTGGCCTCTTGCGTCCTCATAGTGTCGGCCTccag      <  2:98408/150‑3 (MQ=255)                                                                                                                           aaGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTCGATAGCCTGCAACAGCGGTTGTTGCAGGGTGGCCTCTTGCGTACTCATAGTGTCGGCCTCCCgg     >  1:117336/1‑151 (MQ=255)                                                                                                                            aGGTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTCGATAGCCTGCAACAGCGGTTGTTGCAGGGTGGCCTCTTGCGTACTCATAGTGTCGGCCTCCCGGc    >  1:222171/1‑151 (MQ=255)                                                                                                                              gTTAAACGCAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTCGATAGCCTGCAACAGCGGTTGTTGCAGGGTGGCCTCTTGCGTACTCATAGTGTCGGCCTCCCGGcat  <  2:675700/151‑1 (MQ=255)                                                                                                                                      |                                                                                                                                               AGATCCTGCCCCTGGTAATACAGCTCGCCACCGGTGGGCATTTCAATCATCGTCAGCAACCGACCGAGGGTCGATTTACCGCAGCCAGATTCGCCCACTACTGCCAGCGTTTTGCCACGTTCAAGGTTAAACGAAACGCCATCCAGCGCTTTAACCAGACGTTCCGGCGCGAACATGCCTTTCTTCACCGGATAATGTTTTTTCAGGTCGATAGCCTGCAACAGCGGTTGTTGCAGGGTGGCCTCTTGCGTACTCATAGTGTCGGCCTCCCGGCAT  >  NC_000913/3702612‑3702887

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑