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
A9 F1 I2 R1	760	52.7	2744488	90.2%	2475528	105.0

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%	104.2 / NA	33	313 (TAG→TAA)	tdcA	tdc operon transcriptional activator
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (16/17); total (16/17)

TCATCAATAGCAACCGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAACTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCATATTGTGCCACAGG  >  NC_000913/3265991‑3266261

tcatcaATAGCAACCGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAAtaatta                                                                                                                                      >  1:202019/1‑139 (MQ=255)

   tcaATAGCAACCGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAAcc                                                                                                                                   >  1:1193545/1‑139 (MQ=255)

     aaTAGCAACCGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCaa                                                                                                                                 <  2:1193545/139‑1 (MQ=255)

               ggCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTaa                                                                                                                       <  1:1021367/139‑1 (MQ=255)

               ggCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTaa                                                                                                                       >  1:1220884/1‑139 (MQ=255)

                      cGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCtt                                                                                                                <  2:1220884/139‑1 (MQ=255)

                           gTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCt                                                                                                           <  2:202019/139‑1 (MQ=255)

                              atatGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTc                                                                                                                             >  1:19644/1‑118 (MQ=255)

                              atatGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTc                                                                                                                             <  2:19644/118‑1 (MQ=255)

                                 tGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACAccc                                                                                                     >  1:614247/1‑139 (MQ=255)

                                      tataAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAAt                                                                                                                      >  1:1050766/1‑117 (MQ=255)

                                      tataAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAAt                                                                                                                      <  2:1050766/117‑1 (MQ=255)

                                           aaCCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATCTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGAt                                                                                           <  1:931711/139‑1 (MQ=255)

                                             ccTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATGTGTGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCCTCTACACCCATTATAAGATGa                                                                                         >  1:797284/1‑139 (MQ=255)

                                                ctTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGcc                                                                                                                  >  1:1288658/1‑111 (MQ=255)

                                                ctTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGcc                                                                                                                  <  2:1288658/111‑1 (MQ=255)

                                                  tCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATAct                                                                                    >  2:335428/1‑139 (MQ=255)

                                                                   gTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCt                                                                                                                 <  2:74837/93‑1 (MQ=255)

                                                                   gTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCt                                                                                                                 >  1:74837/1‑93 (MQ=255)

                                                                    tAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATtat                                                                                                >  2:1042227/1‑109 (MQ=255)

                                                                    tAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATtat                                                                                                <  1:1042227/109‑1 (MQ=255)

                                                                                      acCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATtat                                                                                                >  1:352228/1‑91 (MQ=255)

                                                                                      acCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATtat                                                                                                <  2:352228/91‑1 (MQ=255)

                                                                                      acCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCttttt                                                >  2:1151962/1‑139 (MQ=255)

                                                                                                  gacagGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAAt                                    >  2:183745/1‑139 (MQ=255)

                                                                                                   acagGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACAcc                                                                                                      >  1:66341/1‑72 (MQ=255)

                                                                                                   acagGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACAcc                                                                                                      <  2:66341/72‑1 (MQ=255)

                                                                                                              atttatGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATa                        <  1:1151962/139‑1 (MQ=255)

                                                                                                                ttatGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATAcc                      <  1:183745/139‑1 (MQ=255)

                                                                                                                ttatGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATAcc                      <  2:614247/139‑1 (MQ=255)

                                                                                                                                aCAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCATATTGTGCca      <  1:335428/139‑1 (MQ=255)

                                                                                                                                    aTAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTccacc                                                                   >  1:234852/1‑74 (MQ=255)

                                                                                                                                    aTAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTccacc                                                                   <  2:234852/74‑1 (MQ=255)

                                                                                                                                    aTAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCATATTGTGCCACAgg  >  1:1252599/1‑139 (MQ=255)

TCATCAATAGCAACCGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAACTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCATATTGTGCCACAGG  >  NC_000913/3265991‑3266261

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A