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%	207.3 / NA	57	I142I (ATT→ATC)	nikA	nickel/heme ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (30/27);  total (30/27)

ACCGTTCGATGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGACCGT  >  NC_000913/3613963‑3614225                                                                                                                                  |                                                                                                                                       aCCGTTCGATGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGaaa                                                                                                                               <  1:400530/139‑1 (MQ=255)       cGATGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGcc                                                                                                                         <  1:162675/139‑1 (MQ=255)             cGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTAt                                                                                                                   <  1:447139/139‑1 (MQ=255)               aGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATcc                                                                                                                 >  2:453736/1‑139 (MQ=255)                         aGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCaa                                                                                                       >  2:404105/1‑139 (MQ=255)                             aaCTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAAc                                                                                                   <  2:1114037/139‑1 (MQ=255)                             aaCTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAAc                                                                                                   <  1:453736/139‑1 (MQ=255)                                              cGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCATCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCt                                                                                 <  1:1169919/139‑1 (MQ=255)                                                    ccGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCtt                                                                                                               <  1:837379/104‑1 (MQ=255)                                                    ccGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGCTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCtt                                                                                                               >  2:837379/1‑104 (MQ=255)                                                         aaCGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTAt                                                                      <  1:334356/139‑1 (MQ=255)                                                              cACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTATCGCTc                                                                 >  1:149971/1‑139 (MQ=255)                                                                   ctggctggAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCg                                                            <  1:404105/139‑1 (MQ=255)                                                                      gctggAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑cc                                                                                             <  1:190837/103‑1 (MQ=255)                                                                      gctggAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑cc                                                                                             >  2:190837/1‑103 (MQ=255)                                                                               ggCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTAt                                                                      <  1:1284710/117‑1 (MQ=255)                                                                               ggCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTAt                                                                      >  2:1284710/1‑117 (MQ=255)                                                                                 cAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAaaacca                                              >  1:656772/1‑139 (MQ=255)                                                                                   aaCCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAaaaccatg                                            <  2:149971/139‑1 (MQ=255)                                                                                               gATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGaa                                                                                                    <  2:1297378/72‑1 (MQ=255)                                                                                               gATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGaa                                                                                                    >  1:1297378/1‑72 (MQ=255)                                                                                                       aGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTaaa                        >  1:960307/1‑139 (MQ=255)                                                                                                          aCTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGc                                                                                                         >  2:1180297/1‑56 (MQ=255)                                                                                                          aCTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGc                                                                                                         <  1:1180297/56‑1 (MQ=255)                                                                                                           cTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCcta                                                                                                                       <  1:923632/41‑1 (MQ=255)                                                                                                           cTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCcta                                                                                                                       >  2:923632/1‑41 (MQ=255)                                                                                                           cTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAgcgc                    >  1:269347/1‑139 (MQ=255)                                                                                                            tCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTAt                                                                      <  1:83456/88‑1 (MQ=255)                                                                                                            tCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTAt                                                                      >  2:83456/1‑88 (MQ=255)                                                                                                            tCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAgcg                     >  1:53073/1‑137 (MQ=255)                                                                                                            tCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAgcg                     <  2:53073/137‑1 (MQ=255)                                                                                                            tCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTGTCCGTTTTATCCCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGcc                   >  2:1096970/1‑139 (MQ=255)                                                                                                                tAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGAtt               >  2:924202/1‑139 (MQ=255)                                                                                                                   aaCAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑c                                                                                              >  2:1419675/1‑57 (MQ=255)                                                                                                                   aaCAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑c                                                                                              <  1:1419675/57‑1 (MQ=255)                                                                                                                   aaCAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCttt                                                                               >  1:1149670/1‑72 (MQ=255)                                                                                                                   aaCAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCttt                                                                               <  2:1149670/72‑1 (MQ=255)                                                                                                                        agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAAc                                                                                                   >  1:917128/1‑48 (MQ=255)                                                                                                                        agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAAc                                                                                                   <  2:917128/48‑1 (MQ=255)                                                                                                                        agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTAt                                                                      >  2:1098119/1‑76 (MQ=255)                                                                                                                        agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTAt                                                                      <  1:1098119/76‑1 (MQ=255)                                                                                                                        agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCgg       >  2:1554466/1‑139 (MQ=255)                                                                                                                        agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCgg       >  1:464506/1‑139 (MQ=255)                                                                                                                          cTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCa                                                                                                        >  2:162019/1‑41 (MQ=255)                                                                                                                          cTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCa                                                                                                        <  1:162019/41‑1 (MQ=255)                                                                                                                          cTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCCTGCCCCGTCCTTTCCGTTTTAt                                                                      >  2:1551825/1‑75 (MQ=255)                                                                                                                          cTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCCTGCCCCGTCCTTTCCGTTTTAt                                                                      <  1:1551825/75‑1 (MQ=255)                                                                                                                          cTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGt                                                                           >  1:573537/1‑69 (MQ=255)                                                                                                                          cTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGt                                                                           <  2:573537/69‑1 (MQ=255)                                                                                                                          cTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGAt                >  2:1677507/1‑128 (MQ=255)                                                                                                                          cTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGAt                <  1:1677507/128‑1 (MQ=255)                                                                                                                          cTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGAc     >  2:1696339/1‑139 (MQ=255)                                                                                                                             cAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAaaaccatg                                            <  1:617705/97‑1 (MQ=255)                                                                                                                             cAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAaaaccatg                                            >  2:617705/1‑97 (MQ=255)                                                                                                                             cAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGACCGt  >  1:501262/1‑139 (MQ=255)                                                                                                                              aaaTCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCt                                                                                 >  2:765545/1‑59 (MQ=255)                                                                                                                              aaaTCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCt                                                                                 <  1:765545/59‑1 (MQ=255)                                                                                                                                  |                                                                                                                                       ACCGTTCGATGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGG‑CCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGACCGT  >  NC_000913/3613963‑3614225

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑