Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,559,578	A→G	E437E (GAA→GAG)	rtcR →	DNA‑binding transcriptional activator RtcR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,559,578	0	A	G	100.0%	168.3 / NA	48	E437E (GAA→GAG)	rtcR	DNA‑binding transcriptional activator RtcR
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (21/27);  total (21/27)

AAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAAGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGGCGCAGAGGCAGAAAACATCGATCTCTTCGACCGTATGCAACTGGAACACGTTATCGCTATCTGCCGCC  >  NC_000913/3559442‑3559714                                                                                                                                         |                                                                                                                                         aaGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGAt                                                                                                                                       >  2:651074/1‑140 (MQ=255) aaGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGAt                                                                                                                                       <  1:257213/140‑1 (MQ=255) aaGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGAt                                                                                                                                       <  1:651074/140‑1 (MQ=255) aaGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTACCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGAt                                                                                                                                       >  2:317697/1‑140 (MQ=255)   gcgcggcgcgCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATga                                                                                                                                     <  2:401538/140‑1 (MQ=255)           cgcCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAAcc                                                                                                                             <  1:1057179/140‑1 (MQ=255)           cgcCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAAcc                                                                                                                             >  2:456417/1‑140 (MQ=255)             ccTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGt                                                                                                                           <  1:563090/140‑1 (MQ=255)             ccTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGt                                                                                                                           <  1:505234/140‑1 (MQ=255)              cTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTc                                                                                                                          <  1:398779/140‑1 (MQ=255)                 gTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTgc                                                                                                                       >  1:934106/1‑140 (MQ=255)                     gCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCta                                                                                                                   <  1:456417/140‑1 (MQ=255)                     gCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCta                                                                                                                   <  2:920107/140‑1 (MQ=255)                           gCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTg                                                                                                                        <  1:547953/129‑1 (MQ=255)                           gCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTg                                                                                                                        >  2:547953/1‑129 (MQ=255)                                  ctcCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGgag                                                                                                      >  1:494611/1‑140 (MQ=255)                                     cccAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAgc                                                                                                   >  2:217398/1‑140 (MQ=255)                                               aTGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCcg                                                                                         <  1:255827/140‑1 (MQ=255)                                               aTGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCcg                                                                                         >  2:365922/1‑140 (MQ=255)                                                   cgcgGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCt                                                                                     <  2:75274/140‑1 (MQ=255)                                                   cgcgGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCt                                                                                     >  1:426727/1‑140 (MQ=255)                                                      ggTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTAc                                                                                  >  2:838364/1‑140 (MQ=255)                                                               cgcgAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCt                                                                         <  1:317697/140‑1 (MQ=255)                                                                gcgAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTg                                                                        >  1:822473/1‑140 (MQ=255)                                                                    aCTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGgcg                                                                    <  2:1036080/140‑1 (MQ=255)                                                                      tttCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGGCGCa                                                                  >  2:23487/1‑140 (MQ=255)                                                                                      gcgGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGGCGCAGAGGCAGAAAACATCg                                                  <  2:822473/140‑1 (MQ=255)                                                                                      gcgGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGGCGCAGAGGCAGAAAACATCg                                                  <  1:85166/140‑1 (MQ=255)                                                                                         gATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGGCGCAGAGGCAGAAAACATCGAtc                                               >  1:732699/1‑140 (MQ=255)                                                                                                aCCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGGCGCAGAGGCAGAAAACATCGATCTCTTCGa                                        <  1:103251/140‑1 (MQ=255)                                                                                                aCCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGGCGCAGAGGCAGAAAACATCGATCTCTTCGa                                        <  2:426727/140‑1 (MQ=255)                                                                                                 ccTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGGCGCAGAGGCAGAAAACATCGATCTCTTCGAc                                       <  2:494611/140‑1 (MQ=255)                                                                                                     tGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGGCGCAGAGGCAGAAAACATCGATCTCTTCGa                                        <  2:436653/135‑1 (MQ=255)                                                                                                     tGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGGCGCAGAGGCAGAAAACATCGATCTCTTCGa                                        >  1:436653/1‑135 (MQ=255)                                                                                                     tGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGGCGCAGAGGCAGAAAACATCGATCTCTTCGACCGTa                                   <  1:850292/140‑1 (MQ=255)                                                                                                     tGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGGCGCAGAGGCAGAAAACATCGATCTCTTCGACCGTa                                   <  2:732699/140‑1 (MQ=255)                                                                                                      gCCACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGGCGCAGAGGCAGAAAACATCGATCTCTTCGACCGTAt                                  <  1:47668/140‑1 (MQ=255)                                                                                                        cACTAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGGCGCAGAGGCAGAAAACATCGATCTCTTCGACCGTATGc                                <  1:601569/140‑1 (MQ=255)                                                                                                           tAGCGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGGCGCAGAGGCAGAAAACATCGATCTCTTCGACCGTATGCAAc                             <  1:217398/140‑1 (MQ=255)                                                                                                              cGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGGCGCAGAGGCAGAAAACATCGATCTCTTCGACCGTATGCAAc                             >  2:587191/1‑137 (MQ=255)                                                                                                              cGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGGCGCAGAGGCAGAAAACATCGATCTCTTCGACCGTATGCAAc                             <  1:587191/137‑1 (MQ=255)                                                                                                              cGGACGCATCACTCTGGACGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGGCGCAGAGGCAGAAAACATCGATCTCTTCGACCGTATGCAACTgg                          >  2:962670/1‑140 (MQ=255)                                                                                                                               aCGTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGGCGCAGAGGCAGAAAACATCGATCTCTTCGACCGTATGCAACTGGAACACGTTATCGCTATc         >  2:217559/1‑140 (MQ=255)                                                                                                                                 gTGGTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGGCGCAGAGGCAGAAAACATCGATCTCTTCGACCGTATGCAACTGGAACACGTTATCGCTATCTg       >  2:417341/1‑140 (MQ=255)                                                                                                                                   ggTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGGCGCAGAGGCAGAAAACATCGATCTCTTCGACCGTATGCAACTGGAACACGTTATCGCTATCTgcc     >  1:954372/1‑140 (MQ=255)                                                                                                                                    gTTGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGTTGGGCGCAGAGGCAGAAAACATCGATCTCTTCGACCGTATGCAACTGGAACACGTTATCGCTATCTgccg    >  1:667849/1‑140 (MQ=255)                                                                                                                                    gTTGAGGATGAGATAAACCGTCTGCGCCATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGGCGCAGAGGCAGAAAACATCGATCTCTTCGACCGTATGCAACTGGAACACGTTATCGCTATCTgccg    >  1:1077088/1‑140 (MQ=255)                                                                                                                                      tGAGGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGTTGGGCGCAGAGGCAGAAAACATCGATCTCTTCGACCGTATGCAACTGGAACACGTTATCGCTATCTgccgcc  <  2:667849/140‑1 (MQ=255)                                                                                                                                         |                                                                                                                                         AAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGGACGTGGTTGAAGATGAGATAAACCGTCTGCGCTATAACTGGCAGGAGAGCCGCCCCTCCGCGCTTACGGCGTTGCTGGGCGCAGAGGCAGAAAACATCGATCTCTTCGACCGTATGCAACTGGAACACGTTATCGCTATCTGCCGCC  >  NC_000913/3559442‑3559714

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑