Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,614,092	T→C	I142I (ATT→ATC)	nikA →	nickel/heme ABC transporter periplasmic binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,614,092	0	T	C	100.0%	181.4 / NA	51	I142I (ATT→ATC)	nikA	nickel/heme ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (25/26);  total (25/26)

GAACCGTTCGATGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGACCGT  >  NC_000913/3613961‑3614225                                                                                                                                    |                                                                                                                                      gAACCGTTCGATGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGa                                                                                                                                <  2:446984/139‑1 (MQ=255)  aaCCGTTCGATGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGaa                                                                                                                               >  1:754672/1‑139 (MQ=255)       ttCGATGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAgcg                                                                                                                          >  2:1338295/1‑139 (MQ=255)           aTGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCcta                                                                                                                      <  1:1056947/139‑1 (MQ=255)           aTGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCcta                                                                                                                      <  1:1338295/139‑1 (MQ=255)              ccGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCctacta                                                                                                                   >  2:1717439/1‑139 (MQ=255)                               aaCTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAAc                                                                                                  <  1:1086781/139‑1 (MQ=255)                               aaCTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAAc                                                                                                  <  2:231662/139‑1 (MQ=255)                                        gcAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGc                                                                                         <  2:235737/139‑1 (MQ=255)                                          aGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGccc                                                                                       >  2:1543355/1‑139 (MQ=255)                                                    aaCCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTcc                                                                             >  2:1494899/1‑139 (MQ=255)                                                        gTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCt                                                                                                               >  1:966107/1‑101 (MQ=255)                                                        gTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACGCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCt                                                                                                               <  2:966107/101‑1 (MQ=255)                                                           aaCGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTAt                                                                      <  2:505153/139‑1 (MQ=255)                                                             cGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGcc                                                                                                                        >  1:1732097/1‑87 (MQ=255)                                                             cGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGcc                                                                                                                        <  2:1732097/87‑1 (MQ=255)                                                                      tggctggAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGc                                                           <  2:754672/139‑1 (MQ=255)                                                                                            ttgttgATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCg                                                            >  1:1361466/1‑116 (MQ=255)                                                                                            ttgttgATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCg                                                            <  2:1361466/116‑1 (MQ=255)                                                                                             tgttgATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAaaaccatgaaaccatg                                    <  2:1403309/139‑1 (MQ=255)                                                                                                    gTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGaa                             >  1:1140370/1‑139 (MQ=255)                                                                                                         aGCACTCAGTAAAACAGAGCTGCAAATCACCCTG‑AAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTAt                                                                      <  1:135891/92‑1 (MQ=255)                                                                                                         aGCACTCAGTAAAACAGAGCTGCAAATCACCCTG‑AAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTAt                                                                      >  2:135891/1‑92 (MQ=255)                                                                                                             cTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAgcgc                    >  1:265301/1‑139 (MQ=255)                                                                                                              tCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCa                                                                                                       >  1:1086183/1‑55 (MQ=255)                                                                                                              tCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCa                                                                                                       <  2:1086183/55‑1 (MQ=255)                                                                                                              tCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGccc                                                                                            >  2:1221097/1‑66 (MQ=255)                                                                                                              tCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGccc                                                                                            <  1:1221097/66‑1 (MQ=255)                                                                                                              tCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGCACGGAATTAAAGCGcc                   >  2:1098286/1‑139 (MQ=255)                                                                                                                aGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAaaaccatgaaaccatg                                    <  1:514218/120‑1 (MQ=255)                                                                                                                aGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAaaaccatgaaaccatg                                    >  2:514218/1‑120 (MQ=255)                                                                                                                 gTAAATCAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGAt                <  2:1138744/139‑1 (MQ=255)                                                                                                                          agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGc                                                                                                        <  1:583207/42‑1 (MQ=255)                                                                                                                          agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGc                                                                                                        >  2:583207/1‑42 (MQ=255)                                                                                                                          agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTa                                                     >  1:85060/1‑93 (MQ=255)                                                                                                                          agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTa                                                     <  2:85060/93‑1 (MQ=255)                                                                                                                          agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCgg       >  2:1637362/1‑139 (MQ=255)                                                                                                                          agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCgg       >  1:258358/1‑139 (MQ=255)                                                                                                                          agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCgg       >  1:1254204/1‑139 (MQ=255)                                                                                                                            cTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGcccc                                                                                      <  2:629258/58‑1 (MQ=255)                                                                                                                            cTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGcccc                                                                                      >  1:629258/1‑58 (MQ=255)                                                                                                                            cTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAaaaccatga                                           >  1:1749374/1‑101 (MQ=255)                                                                                                                            cTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAaaaccatga                                           <  2:1749374/101‑1 (MQ=255)                                                                                                                            cTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAgcg                     >  1:1542575/1‑123 (MQ=255)                                                                                                                            cTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAgcg                     <  2:1542575/123‑1 (MQ=255)                                                                                                                            cTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTACCCCGTCCt                                                                                 >  1:1387098/1‑63 (MQ=255)                                                                                                                            cTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTACCCCGTCCt                                                                                 <  2:1387098/63‑1 (MQ=255)                                                                                                                             tGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGAcc    <  2:258358/139‑1 (MQ=255)                                                                                                                               cAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGAt                <  1:1543762/125‑1 (MQ=255)                                                                                                                               cAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGAt                >  2:1543762/1‑125 (MQ=255)                                                                                                                               cAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGACCGt  <  1:1494899/139‑1 (MQ=255)                                                                                                                                    |                                                                                                                                      GAACCGTTCGATGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGACCGT  >  NC_000913/3613961‑3614225

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑