Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A14 F1 I2 R1	774	49.2	2112398	96.9%	2046913	118.5

Breseq alignment

BRESEQ :: Evidence

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%	211.7 / NA	65	313 (TAG→TAA)	tdcA	tdc operon transcriptional activator
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (35/30); total (35/30)

ATCAATAGCAACCGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAACTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCATATTGTGCCAC  >  NC_000913/3265993‑3266258

atcaATAGCAACCGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAAtaattaac                                                                                                                                 >  2:105527/1‑139 (MQ=255)

        cAACCGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCt                                                                                                                         <  1:105527/139‑1 (MQ=255)

          aCCGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTAt                                                                                                                       >  2:918013/1‑139 (MQ=255)

           ccGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTAtt                                                                                                                      >  2:176746/1‑139 (MQ=255)

               agattCGAATGTAATAGGAATAAT‑AAACCTCCTTGCCTTAAATAAAAATTTTGGTTACCCGAACCCAACACC‑GGAAGGCAGGCCAGTTGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTg                                                                                                                 <  1:890544/135‑1 (MQ=255)

                   tCGTATCTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCt                                                                                                              <  2:595151/139‑1 (MQ=255)

                    cGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCtt                                                                                                             <  1:176746/139‑1 (MQ=255)

                    cGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCtt                                                                                                             <  1:745111/139‑1 (MQ=255)

                     gTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTaa                                                                                                                    <  2:336250/131‑1 (MQ=255)

                     gTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTaa                                                                                                                    >  1:336250/1‑131 (MQ=255)

                       aTGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGt                                                                                                          >  1:291051/1‑139 (MQ=255)

                        tGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTc                                                                                                         <  1:41632/139‑1 (MQ=255)

                            atatGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTaca                                                                                                     >  2:752590/1‑139 (MQ=255)

                            atatGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTaca                                                                                                     <  2:291051/139‑1 (MQ=255)

                             tatGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                    <  2:997340/139‑1 (MQ=255)

                             tatGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                    <  1:927931/139‑1 (MQ=255)

                               tGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTa                                                                                                       <  2:470122/134‑1 (MQ=255)

                               tGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTa                                                                                                       >  1:470122/1‑134 (MQ=255)

                                 cATTATAAAACCTCTTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                    >  1:596120/1‑135 (MQ=255)

                                 cATTATAAAACCTCTTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                    <  2:596120/135‑1 (MQ=255)

                                         aaCCTCTTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGAt                                                                                        >  2:631241/1‑139 (MQ=255)

                                            ctctTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGaa                                                                                     <  1:752590/139‑1 (MQ=255)

                                              ctTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGcc                                                                                                               >  2:810936/1‑111 (MQ=255)

                                              ctTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGcc                                                                                                               <  1:810936/111‑1 (MQ=255)

                                              ctTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                    >  2:89454/1‑122 (MQ=255)

                                              ctTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                    <  1:89454/122‑1 (MQ=255)

                                              ctTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATa                                                                                   >  1:26698/1‑139 (MQ=255)

                                              ctTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATa                                                                                   >  2:828853/1‑139 (MQ=255)

                                              ctTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATa                                                                                   >  2:340208/1‑139 (MQ=255)

                                              ctTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATa                                                                                   >  1:445189/1‑139 (MQ=255)

                                              ctTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATa                                                                                   >  1:643701/1‑139 (MQ=255)

                                                tCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATAct                                                                                 >  2:438739/1‑139 (MQ=255)

                                                                 gTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                    <  1:628080/103‑1 (MQ=255)

                                                                 gTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                    >  2:628080/1‑103 (MQ=255)

                                                                 gTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTccacc                                                                >  1:656493/1‑139 (MQ=255)

                                                                 gTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTccacc                                                                >  2:539082/1‑139 (MQ=255)

                                                                   aGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAAAAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCaa                                                              >  2:412887/1‑139 (MQ=255)

                                                                        aaccgtaaccgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAAcc                                                          >  1:914345/1‑139 (MQ=255)

                                                                           cgtaaccgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGAt                                                       <  1:631241/139‑1 (MQ=255)

                                                                           cgtaaccgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGAt                                                       >  1:674199/1‑139 (MQ=255)

                                                                           cgtaaccgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGAt                                                       >  1:264009/1‑139 (MQ=255)

                                                                             taaccgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGAtgc                                                     <  1:340208/139‑1 (MQ=255)

                                                                                ccgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGAtgctgc                                                  >  1:1012595/1‑139 (MQ=255)

                                                                                     acCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGcc                                                                                                               <  1:564321/73‑1 (MQ=255)

                                                                                     acCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGcc                                                                                                               >  2:564321/1‑73 (MQ=255)

                                                                                     acCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                    <  1:423019/84‑1 (MQ=255)

                                                                                     acCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                    >  2:423019/1‑84 (MQ=255)

                                                                                     acCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCttttt                                             >  1:964333/1‑139 (MQ=255)

                                                                                     acCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCttttt                                             >  1:252481/1‑139 (MQ=255)

                                                                                      ccTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCtttttt                                            <  1:828853/139‑1 (MQ=255)

                                                                                       cTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATtat                                                                                             >  1:412360/1‑89 (MQ=255)

                                                                                       cTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATtat                                                                                             <  2:412360/89‑1 (MQ=255)

                                                                                                 gacagGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAAt                                 >  1:179582/1‑139 (MQ=255)

                                                                                                   cagGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAAttt                               <  1:918013/139‑1 (MQ=255)

                                                                                                         gATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGAc                         >  2:808529/1‑139 (MQ=255)

                                                                                                              tttatGTTGAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTGTTCGACCATAc                    >  1:686011/1‑139 (MQ=255)

                                                                                                                tatGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAGAACCGAtgctg                                                   >  1:939179/1‑106 (MQ=255)

                                                                                                                tatGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAGAACCGAtgctg                                                   <  2:939179/106‑1 (MQ=255)

                                                                                                                  tGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACcgcg                <  2:252481/139‑1 (MQ=255)

                                                                                                                   gTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCgg               >  1:187148/1‑139 (MQ=255)

                                                                                                                        aataaaAACAAATAATTAACCAACTTCTATTAATTACCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGAtgctg                                                   <  2:795081/98‑1 (MQ=255)

                                                                                                                        aataaaAACAAATAATTAACCAACTTCTATTAATTACCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGAtgctg                                                   >  1:795081/1‑98 (MQ=255)

                                                                                                                         ataaaAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCATAtt         <  2:674199/139‑1 (MQ=255)

                                                                                                                               aCAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCATATTGTGCca   <  2:264009/139‑1 (MQ=255)

                                                                                                                               aCAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCATATTGTGCca   <  2:26698/139‑1 (MQ=255)

                                                                                                                                cAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCATATTGTGCcac  <  2:914345/139‑1 (MQ=255)

ATCAATAGCAACCGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGG‑TAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAACTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCATATTGTGCCAC  >  NC_000913/3265993‑3266258

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A