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%	179.9 / NA	50	I142I (ATT→ATC)	nikA	nickel/heme ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (26/24);  total (26/24)

GAACCGTTCGATGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGA  >  NC_000913/3613961‑3614221                                                                                                                                    |                                                                                                                                  gAACCGTTCGATGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGa                                                                                                                            <  2:1593064/139‑1 (MQ=255)       ttCGATGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAgcg                                                                                                                      >  1:161271/1‑139 (MQ=255)                      gcggcAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGa                                                                                                                            >  2:1467421/1‑118 (MQ=255)                      gcggcAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGa                                                                                                                            <  1:1467421/118‑1 (MQ=255)                               aaCTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAAc                                                                                              <  2:621953/139‑1 (MQ=255)                                              cTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTc                                                                               >  1:1285939/1‑139 (MQ=255)                                                        gTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGttt                                                                     >  2:1721163/1‑139 (MQ=255)                                                            aCGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATc                                                                 >  1:409667/1‑139 (MQ=255)                                                                cACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGcc                                                                                         >  1:50497/1‑111 (MQ=255)                                                                cACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGcc                                                                                         <  2:50497/111‑1 (MQ=255)                                                                cACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCt                                                              <  2:1805102/138‑1 (MQ=255)                                                                cACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCt                                                              >  1:1805102/1‑138 (MQ=255)                                                                 aCGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGcc                                                                                         >  1:420771/1‑110 (MQ=255)                                                                 aCGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGcc                                                                                         <  2:420771/110‑1 (MQ=255)                                                                         ctggAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGt                                                    >  2:1815037/1‑139 (MQ=255)                                                                           ggAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGttt                                                  <  1:1815037/139‑1 (MQ=255)                                                                                  gCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCC‑GCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAaaacca                                          >  1:380337/1‑139 (MQ=255)                                                                                               ttgATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTAt                                                                  <  2:1435581/103‑1 (MQ=255)                                                                                               ttgATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTAt                                                                  >  1:1435581/1‑103 (MQ=255)                                                                                               ttgATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAaccatgaaaccatgaa                              <  2:409667/139‑1 (MQ=255)                                                                                               ttgATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAaccatgaaaccatgaa                              <  2:161271/139‑1 (MQ=255)                                                                                                     ttAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGcc                                                                                                                    <  2:564041/47‑1 (MQ=255)                                                                                                     ttAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGcc                                                                                                                    >  1:564041/1‑47 (MQ=255)                                                                                                         aGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGc                                                       <  1:1729237/104‑1 (MQ=255)                                                                                                         aGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGc                                                       >  2:1729237/1‑104 (MQ=255)                                                                                                             cTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTAt                                                                  <  1:1554485/89‑1 (MQ=255)                                                                                                             cTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTAt                                                                  >  2:1554485/1‑89 (MQ=255)                                                                                                             cTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAgcgc                >  2:1341510/1‑139 (MQ=255)                                                                                                              tCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGcc                                                                                         <  1:736401/65‑1 (MQ=255)                                                                                                              tCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGcc                                                                                         >  2:736401/1‑65 (MQ=255)                                                                                                              tCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGcc               >  2:927434/1‑139 (MQ=255)                                                                                                                aGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATGGCTCCCTCGCAGTTTaaaa                                              >  2:1244526/1‑106 (MQ=255)                                                                                                                aGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCAGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTaaaa                                              <  1:1244526/106‑1 (MQ=255)                                                                                                                 gTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGAt            <  2:1285939/139‑1 (MQ=255)                                                                                                                     aaCAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGc                                                                                     >  2:850394/1‑62 (MQ=255)                                                                                                                     aaCAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGc                                                                                     <  1:850394/62‑1 (MQ=255)                                                                                                                          agCTGCAAATCACCCTGATAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCgg   >  1:1044582/1‑139 (MQ=255)                                                                                                                          agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCa                                                                                                   >  2:1132139/1‑43 (MQ=255)                                                                                                                          agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCa                                                                                                   <  1:1132139/43‑1 (MQ=255)                                                                                                                          agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAAc                                                                                              <  2:1745052/48‑1 (MQ=255)                                                                                                                          agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAAc                                                                                              >  1:1745052/1‑48 (MQ=255)                                                                                                                          agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCg                                                                <  2:360155/78‑1 (MQ=255)                                                                                                                          agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCg                                                                >  1:360155/1‑78 (MQ=255)                                                                                                                          agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAaaaccatg                                        >  1:763139/1‑102 (MQ=255)                                                                                                                          agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAaaaccatg                                        <  2:763139/102‑1 (MQ=255)                                                                                                                          agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCC‑GCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGa  <  2:380337/139‑1 (MQ=255)                                                                                                                           gCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGc                                                                                                    >  1:804825/1‑41 (MQ=255)                                                                                                                           gCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGc                                                                                                    <  2:804825/41‑1 (MQ=255)                                                                                                                           gCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGc                                                                                                    <  2:1010163/41‑1 (MQ=255)                                                                                                                           gCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGc                                                                                                    >  1:1010163/1‑41 (MQ=255)                                                                                                                                    |                                                                                                                                  GAACCGTTCGATGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGA  >  NC_000913/3613961‑3614221

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑