Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	601,896	G→A	intergenic (+39/‑63)	cusA → / → pheP	copper/silver export system RND permease/phenylalanine:H(+) symporter PheP

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	601,896	0	G	A	100.0%	185.4 / NA	53	intergenic (+39/‑63)	cusA/pheP	copper/silver export system RND permease/phenylalanine:H(+) symporter PheP
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (25/28);  total (25/28)

GATTGGCGGCATGATCACCGCACCTTTGCTGTCGCTGTTTATTATCCCGGCGGCGTATAAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTGCGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAACCGTATCGGAAGATACTGCGTCGAATCAAGAGCCGACGCTTCATCGCGGATTACATA  >  NC_000913/601761‑602031                                                                                                                                        |                                                                                                                                        gatTGGCGGCATGATCACCGCACCTTTGCTGTCGCTGTTTATTATCCCGGCGGCGTATAAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTAcgac                                                                                                                                     >  1:566944/1‑140 (MQ=255)  atTGGCGGCATGATCACCGCACCTTTGCTGTCGCTGTTTATTATCCCGGCGGCGTATAAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTacgacg                                                                                                                                    <  1:264489/140‑1 (MQ=255)    tGGCGGCATGATCACCGCACCTTTGCTGTCGCTGTTTATTATCCCGGCGGCGTATAAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGAt                                                                                                                                  <  2:603026/140‑1 (MQ=255)           aTGATCACCGCACCTTTGCTGTCGCTGTTTATTATCCCGGCGGCGTATAAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACt                                                                                                                           <  2:280798/140‑1 (MQ=255)            tGATCACCGCACCTTTGCTGTCGCTGTTTATTATCCCGGCGGCGTATAAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTa                                                                                                                          <  1:95084/140‑1 (MQ=255)             gATCACCGCACCTTTGCTGTCGCTGTTTATTATCCCGGCGGCGTATAAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTaa                                                                                                                         <  2:449262/140‑1 (MQ=255)             gATCACCGCACCTTTGCTGTCGCTGTTTATTATCCCGGCGGCGTATAAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTaa                                                                                                                         <  2:345540/140‑1 (MQ=255)             gATCACCGCACCTTTGCTGTCGCTGTTTATTATCCCGGCGGCGTATAAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTaa                                                                                                                         <  2:175077/140‑1 (MQ=255)             gATCACCGCACCTTTGCTGTCGCTGTTTATTATCCCGGCGGCGTATAAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAACAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTaa                                                                                                                         <  1:681246/140‑1 (MQ=255)                 aCCGCACCTTTGCTGTCGCTGTTTATTATCCCGGCGGCGTATAAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGGTACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGt                                                                                                                     >  1:783267/1‑140 (MQ=255)                     cACCTTTGCTGTCGCTGTTTATTATCCCGGCGGCGTATAAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTaaa                                                                                                                 <  1:781718/140‑1 (MQ=255)                             cTGTCGCTGTTTATTATCCCGGCGGCGTATAAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGccc                                                                                                         <  1:793132/140‑1 (MQ=255)                                tCGCTGTTTATTATCCCGGCGGCGTATAAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTc                                                                                                      >  2:192837/1‑140 (MQ=255)                                             tCCCGGCGGCGTATAAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGGTACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGaca                                                                                         <  2:783267/140‑1 (MQ=255)                                             tCCCGGCGGCGTATAAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGaca                                                                                         <  2:407512/140‑1 (MQ=255)                                               ccGGCGGCGTATAAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGacaca                                                                                       <  2:566944/140‑1 (MQ=255)                                                  gcggcgTATAAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAg                                                                                            <  2:773064/132‑1 (MQ=255)                                                  gcggcgTATAAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAg                                                                                            >  1:773064/1‑132 (MQ=255)                                                  gcggcgTATAAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAg                                                                                    >  1:224781/1‑140 (MQ=255)                                                  gcggcgTATAAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAg                                                                                    >  1:394532/1‑140 (MQ=255)                                                    ggcgTATAAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAggg                                                                                  >  2:358411/1‑140 (MQ=255)                                                        tataAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGaaa                                                                              >  1:73015/1‑140 (MQ=255)                                                                 aTGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGaaa                                                                     <  1:635907/140‑1 (MQ=255)                                                                  tgtgGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGaaaa                                                                    >  1:767255/1‑140 (MQ=255)                                                                  tgtgGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGaaaa                                                                    >  2:128315/1‑140 (MQ=255)                                                                       cTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAAcgcg                                                               >  1:177542/1‑140 (MQ=255)                                                                        tGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGt                                                              >  1:487590/1‑140 (MQ=255)                                                                           aCCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCaa                                                           >  1:631468/1‑140 (MQ=255)                                                                           aCCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCaa                                                           <  1:192837/140‑1 (MQ=255)                                                                            ccGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAAc                                                          <  2:394532/140‑1 (MQ=255)                                                                            ccGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAAc                                                          <  2:224781/140‑1 (MQ=255)                                                                            ccGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAAc                                                          <  1:265937/140‑1 (MQ=255)                                                                              gACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAACCg                                                        <  2:43354/140‑1 (MQ=255)                                                                              gACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAACCg                                                        <  2:543219/140‑1 (MQ=255)                                                                               aCATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAACCGt                                                       >  1:265899/1‑140 (MQ=255)                                                                                 aTCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAACCGTAt                                                     <  1:463885/140‑1 (MQ=255)                                                                                  tCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAACCGTATc                                                    <  2:767255/140‑1 (MQ=255)                                                                                     ggTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAACCGTATCGGa                                                 <  2:73015/140‑1 (MQ=255)                                                                                     ggTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAACCGTATCGGa                                                 <  2:631468/140‑1 (MQ=255)                                                                                       tACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAACCGTATc                                                    <  1:524941/135‑1 (MQ=255)                                                                                       tACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAACCGTATc                                                    >  2:524941/1‑135 (MQ=255)                                                                                               tAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAAGGGAAAGGCGTGAAAAACGCGTCAACCGTATCGGAAGATACTGCg                                       >  1:568838/1‑140 (MQ=255)                                                                                                      aGGATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAACCGTATCGGAAGATACTGCGTCGAATc                                >  2:234321/1‑140 (MQ=255)                                                                                                        gATACCCCGTTTAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAACCGTATCGGAAGATACTGCGTCGAATCaa                              >  1:417722/1‑140 (MQ=255)                                                                                                                 tttAACCGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAACCGTATCGGAAGATACTGCGTCGAATCAAGAGCCGACg                     >  1:480229/1‑140 (MQ=255)                                                                                                                       cGTGTGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAACCGTATCGGAAGATACTGCGTCGAATCAAGAGCCGACGCTTCAt               >  2:515463/1‑140 (MQ=255)                                                                                                                        gtgtGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAACCGTATCGGAAGATACTGCGTCGAATCAAGAGCCGACGCTTCAt               <  2:183734/139‑1 (MQ=255)                                                                                                                        gtgtGGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAACCGTATCGGAAGATACTGCGTCGAATCAAGAGCCGACGCTTCAt               >  1:183734/1‑139 (MQ=255)                                                                                                                         tgtgGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAACCGTATCGGAAGATACTGCGTCGAATCAAGAGCCGACGCTTCATcg             >  2:132619/1‑140 (MQ=255)                                                                                                                           tgGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAACCGTATCGGAAGATACTGCGTCGAATCAAGAGCCGACGCTTCATcgcg           >  1:615353/1‑140 (MQ=255)                                                                                                                           tgGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAACCGTATCGGAAGATACTGCGTCGAATCAAGAGCCGACGCTTCATcgcg           >  1:370507/1‑140 (MQ=255)                                                                                                                           tgGATTGTGTCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAACCGTATCGGAAGATACTGCGTCGAATCAAGAGCCGACGCTTCATcgcg           <  1:128315/140‑1 (MQ=255)                                                                                                                                  tgtCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAACCGTATCGGAAGATACTGCGTCGAATCAAGAGCCGACGCTTCATCGCGGATTACa    <  2:370507/140‑1 (MQ=255)                                                                                                                                    tCTTACGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAACCGTATCGGAAGATACTGCGTCGAATCAAGAGCCGACGCTTCATCGCGGATTACATa  >  2:136703/1‑140 (MQ=255)                                                                                                                                        |                                                                                                                                        GATTGGCGGCATGATCACCGCACCTTTGCTGTCGCTGTTTATTATCCCGGCGGCGTATAAGCTGATGTGGCTGCACCGACATCGGGTACGGAAATAAAAGCAGGATACCCCGTTTAACCGTGTGGATTGTGTCTTGCGACGATGGGCACTAAATGTTAAAAGGTGCCCCTCAACAAAAAAGACACACAGGGGAAAGGCGTGAAAAACGCGTCAACCGTATCGGAAGATACTGCGTCGAATCAAGAGCCGACGCTTCATCGCGGATTACATA  >  NC_000913/601761‑602031

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑