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
A2 F1 I2 R1	764	42.0	2018750	95.5%	1927906	109.2

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%	126.3 / 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)

TAGCAACCGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAACTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCATATTGTGC  >  NC_000913/3265998‑3266255

tAGCAACCGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAAtaattaa                                                                                                                               >  2:836246/1‑133 (MQ=255)

tAGCAACCGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAAtaattaa                                                                                                                               <  1:836246/133‑1 (MQ=255)

                     tAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTa                                                                                                    <  2:893524/139‑1 (MQ=255)

                           gCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCtt                                                                                                          >  1:145438/1‑127 (MQ=255)

                           gCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCtt                                                                                                          <  2:145438/127‑1 (MQ=255)

                            cATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCAt                                                                                             >  2:381422/1‑139 (MQ=255)

                               tataAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATtat                                                                                          >  2:953335/1‑139 (MQ=255)

                               tataAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATtat                                                                                          <  2:619865/139‑1 (MQ=255)

                                         ctTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAAtaattaa                                                                                                                               <  2:748876/92‑1 (MQ=255)

                                         ctTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAAtaattaa                                                                                                                               >  1:748876/1‑92 (MQ=255)

                                         ctTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACAcc                                                                                                >  1:563343/1‑123 (MQ=255)

                                         ctTCGCCTCAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACAcc                                                                                                <  2:563343/123‑1 (MQ=255)

                                           tCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAAcc                                                                                                                             <  2:421550/92‑1 (MQ=255)

                                           tCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAAcc                                                                                                                             <  1:903956/92‑1 (MQ=255)

                                           tCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAAcc                                                                                                                             >  1:421550/1‑92 (MQ=255)

                                           tCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAAcc                                                                                                                             >  2:903956/1‑92 (MQ=255)

                                            cGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAAc                                                                                                                          >  1:625015/1‑94 (MQ=255)

                                            cGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAAc                                                                                                                          <  2:625015/94‑1 (MQ=255)

                                                  aaTTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTc                                                                                                                       <  1:54648/91‑1 (MQ=255)

                                                  aaTTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTc                                                                                                                       >  2:54648/1‑91 (MQ=255)

                                                            gTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAAcc                                                                                                                             <  2:1003984/75‑1 (MQ=255)

                                                            gTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAAcc                                                                                                                             >  1:1003984/1‑75 (MQ=255)

                                                            gTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCt                                                                                                                      >  1:452123/1‑82 (MQ=255)

                                                            gTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCt                                                                                                                      <  2:452123/82‑1 (MQ=255)

                                                            gTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTccacc                                                             >  1:507640/1‑139 (MQ=255)

                                                               ggTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTCTTAATTGcc                                                                                                            >  1:610804/1‑89 (MQ=255)

                                                               ggTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGcc                                                                                                            <  2:610804/89‑1 (MQ=255)

                                                                   accgtaaccgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAAt                                                                                 >  2:112514/1‑112 (MQ=255)

                                                                   accgtaaccgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAAt                                                                                 <  1:112514/112‑1 (MQ=255)

                                                                     cgtaaccgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATaa                                                                                        <  1:756918/103‑1 (MQ=255)

                                                                     cgtaaccgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATaa                                                                                        >  2:756918/1‑103 (MQ=255)

                                                                                 cTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGcc                                                                                                            <  2:364359/71‑1 (MQ=255)

                                                                                 cTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGcc                                                                                                            >  1:364359/1‑71 (MQ=255)

                                                                                     aaGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTTCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGAtg                                                   >  2:570152/1‑124 (MQ=255)

                                                                                     aaGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGAtg                                                   <  1:570152/124‑1 (MQ=255)

                                                                                            acagGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGcc                                                                                                            >  2:572684/1‑60 (MQ=255)

                                                                                            acagGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGcc                                                                                                            <  1:572684/60‑1 (MQ=255)

                                                                                                          tatGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATa                                     >  1:789341/1‑117 (MQ=255)

                                                                                                          tatGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATa                                     <  2:789341/117‑1 (MQ=255)

                                                                                                          tatGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATAcc                >  2:257710/1‑138 (MQ=255)

                                                                                                          tatGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATAcc                <  1:257710/138‑1 (MQ=255)

                                                                                                              tttAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCa                    <  2:106635/130‑1 (MQ=255)

                                                                                                              tttAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCa                    >  1:106635/1‑130 (MQ=255)

                                                                                                                       aaaCAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCATATTGTGc  <  2:507640/139‑1 (MQ=255)

TAGCAACCGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAACTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCATATTGTGC  >  NC_000913/3265998‑3266255

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A