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
A1 F1 I2 R1	765	46.1	2269152	93.8%	2128464	105.7

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%	99.8 / NA	32	313 (TAG→TAA)	tdcA	tdc operon transcriptional activator
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (17/15); total (17/15)

CAACCGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAACTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCATATTGTGCCA  >  NC_000913/3266001‑3266257

cAACCGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCt                                                                                                                        >  1:863533/1‑139 (MQ=255)

   ccGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACAAACTTCTAtt                                                                                                                     >  2:778091/1‑139 (MQ=255)

          aTCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGcc                                                                                                              <  2:918490/139‑1 (MQ=255)

           tCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACTCCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTGACCAACTTCTATTAATTGCCt                                                                                                             <  2:1002049/139‑1 (MQ=255)

                     tatGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCaa                                                                                                                             <  2:796665/113‑1 (MQ=255)

                     tatGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCaa                                                                                                                             >  1:796665/1‑113 (MQ=255)

                      atGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACAcc                                                                                                  <  1:860336/139‑1 (MQ=255)

                       tGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                   <  2:962895/137‑1 (MQ=255)

                       tGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                   >  1:962895/1‑137 (MQ=255)

                            tataAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATtat                                                                                            >  2:618353/1‑139 (MQ=255)

                               aaaaCCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATtat                                                                                            <  1:564756/136‑1 (MQ=255)

                               aaaaCCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATtat                                                                                            >  2:564756/1‑136 (MQ=255)

                               aaaaCCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAg                                                                                         <  2:903536/139‑1 (MQ=255)

                                      ctTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATa                                                                                  >  1:155547/1‑139 (MQ=255)

                                        tCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATAct                                                                                >  2:644976/1‑139 (MQ=255)

                                                         gTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTa                                                                                                      <  1:765018/100‑1 (MQ=255)

                                                         gTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTa                                                                                                      >  2:765018/1‑100 (MQ=255)

                                                         gTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTccacc                                                               >  1:1053018/1‑139 (MQ=255)

                                                         gTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTccacc                                                               >  2:566179/1‑139 (MQ=255)

                                                                accgtaaccgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTaa                                                                                                                   >  2:335550/1‑80 (MQ=255)

                                                                accgtaaccgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTaa                                                                                                                   <  1:335550/80‑1 (MQ=255)

                                                                  cgtaaccgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTATACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGAt                                                      >  2:699438/1‑139 (MQ=255)

                                                                      accgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGAtgctg                                                  <  2:863533/139‑1 (MQ=255)

                                                                                        gacagGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATa                                       >  2:531052/1‑132 (MQ=255)

                                                                                        gacagGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATa                                       <  1:531052/132‑1 (MQ=255)

                                                                                                     tttatGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATtat                                                                                            >  1:900498/1‑66 (MQ=255)

                                                                                                     tttatGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATtat                                                                                            <  2:900498/66‑1 (MQ=255)

                                                                                                          gTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCgg              >  1:705250/1‑139 (MQ=255)

                                                                                                           tttAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGc             <  2:705250/139‑1 (MQ=255)

                                                                                                            ttAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCa            <  2:155547/139‑1 (MQ=255)

                                                                                                             taaataaaAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCat           >  2:108629/1‑139 (MQ=255)

                                                                                                                      aCAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCATATTGTGCca  <  1:644976/139‑1 (MQ=255)

CAACCGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAACTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCATATTGTGCCA  >  NC_000913/3266001‑3266257

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A