Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,266,127	C→T	*313* (TAG→TAA)	tdcA ←	tdc operon transcriptional activator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,266,127	0	C	T	100.0%	124.9 / NA	40	*313* (TAG→TAA)	tdcA	tdc operon transcriptional activator
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (20/20);  total (20/20)

ATAGCAACCGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAACTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCATATTGTGCCACAGGT  >  NC_000913/3265997‑3266262                                                                                                                                   |                                                                                                                                        aTAGCAACCGGCAGATCGTATGTAATATGCATTATAAAACCTTTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAAc                                                                                                                                 <  1:280327/139‑1 (MQ=255)                       tAATATGCATTATAAAGCCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCATGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTa                                                                                                           <  2:228267/139‑1 (MQ=255)                         atatGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTaca                                                                                                         <  1:352674/139‑1 (MQ=255)                          tatGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCtt                                                                                                                 >  1:866432/1‑130 (MQ=255)                          tatGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCtt                                                                                                                 <  2:866432/130‑1 (MQ=255)                          tatGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                        <  2:248200/139‑1 (MQ=255)                          tatGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                        >  1:492802/1‑139 (MQ=255)                          tatGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                        <  2:545518/139‑1 (MQ=255)                          tatGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacaa                                                                                                        >  1:810969/1‑138 (MQ=255)                            tGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACAccc                                                                                                      <  1:402512/139‑1 (MQ=255)                             gCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                        <  2:365844/136‑1 (MQ=255)                             gCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                        >  1:365844/1‑136 (MQ=255)                                ttATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTCCAAGACAGGCCGGTTGATTATTTATGTTCAAGTAAAAACTATTAATCAACCAACTACTATTAATTGCCTTAGTCTacaagcagta                                                                                                  >  2:159256/1‑132 (MQ=255)                                 tataAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATtat                                                                                                 <  1:836521/139‑1 (MQ=255)                                 tataAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATtat                                                                                                 >  1:112946/1‑139 (MQ=255)                                  ataAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCtt                                                                                                                 >  2:784840/1‑122 (MQ=255)                                  ataAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCtt                                                                                                                 <  1:784840/122‑1 (MQ=255)                                      aaCCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                        <  1:145480/127‑1 (MQ=255)                                      aaCCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                        >  2:145480/1‑127 (MQ=255)                                      aaCCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGAt                                                                                            >  2:300268/1‑139 (MQ=255)                                           ctTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTa                                                                                                           <  2:370058/119‑1 (MQ=255)                                           ctTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTa                                                                                                           >  1:370058/1‑119 (MQ=255)                                                      ttAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGcc                                                                                                                   >  2:96659/1‑100 (MQ=255)                                                      ttAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGcc                                                                                                                   <  1:96659/100‑1 (MQ=255)                                                              gTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCGACACCCATTATAAGATGAATACTCTTTGGCTAATTccacc                                                                    >  2:586862/1‑139 (MQ=255)                                                                      ccgtaaccgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAAcc                                                                                                                                    >  2:204531/1‑67 (MQ=255)                                                                      ccgtaaccgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAAcc                                                                                                                                    <  1:204531/67‑1 (MQ=255)                                                                       cgtaaccgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCa                                                                                                                                   <  2:169605/67‑1 (MQ=255)                                                                       cgtaaccgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCa                                                                                                                                   >  1:169605/1‑67 (MQ=255)                                                                         taaccgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGAtgc                                                         >  1:467777/1‑139 (MQ=255)                                                                           accgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATaa                                                                                               <  2:218693/99‑1 (MQ=255)                                                                           accgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATaa                                                                                               >  1:218693/1‑99 (MQ=255)                                                                                cacCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                        <  2:160676/85‑1 (MQ=255)                                                                                cacCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                        >  1:160676/1‑85 (MQ=255)                                                                                 acCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCttttt                                                 <  2:492802/139‑1 (MQ=255)                                                                                                            tatGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                        >  1:730204/1‑57 (MQ=255)                                                                                                            tatGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                        <  2:730204/57‑1 (MQ=255)                                                                                                            tatGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACcg                      >  2:739854/1‑139 (MQ=255)                                                                                                               gTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCgg                   >  2:438546/1‑139 (MQ=255)                                                                                                                 ttAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCa                 <  1:586862/139‑1 (MQ=255)                                                                                                                                taattaacCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCATATTGTGCCACAGGt  <  2:467777/139‑1 (MQ=255)                                                                                                                                   |                                                                                                                                        ATAGCAACCGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAACTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCATATTGTGCCACAGGT  >  NC_000913/3265997‑3266262

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑