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 I1 R1	773	79.9	4112934	92.2%	3792125	104.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,521,593	C→T	295 (TAG→TAA)	xapR ←	transcriptional activator of xapAB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,521,593	0	C	T	100.0%	207.4 / NA	63	295 (TAG→TAA)	xapR	transcriptional activator of xapAB
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (35/28); total (35/28)

CCCACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACCTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGCCAGTTCATTTGTGCGTA  >  NC_000913/2521478‑2521727

cccACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAg                                                                                                                 >  2:1000699/1‑139 (MQ=255)

cccACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAg                                                                                                                 >  1:1224575/1‑139 (MQ=255)

cccACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAg                                                                                                                 >  2:2021929/1‑139 (MQ=255)

                  cgcCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGt                                                                                               <  1:1000699/139‑1 (MQ=255)

                  cgcCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGt                                                                                               >  1:1058586/1‑139 (MQ=255)

                               cTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATcg                                                                                                      >  1:1735859/1‑119 (MQ=255)

                               cTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATcg                                                                                                      <  2:1735859/119‑1 (MQ=255)

                                      gCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATaaa                                                                           <  2:1029154/139‑1 (MQ=255)

                                         aTCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACaa                                                                        >  2:487177/1‑139 (MQ=255)

                                            tGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCa                                                                                                                         <  1:1100455/87‑1 (MQ=255)

                                            tGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCa                                                                                                                         >  2:1100455/1‑87 (MQ=255)

                                            tGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCa                                                                                                                     >  1:30228/1‑91 (MQ=255)

                                            tGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCa                                                                                                                     <  2:30228/91‑1 (MQ=255)

                                            tGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACa                                                                         >  2:114998/1‑135 (MQ=255)

                                            tGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACa                                                                         <  1:114998/135‑1 (MQ=255)

                                            tGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAatat                                                                     >  2:297621/1‑139 (MQ=255)

                                            tGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAatat                                                                     >  2:712860/1‑139 (MQ=255)

                                            tGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAatat                                                                     >  1:853696/1‑139 (MQ=255)

                                                aTTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATaa                                                                 <  1:1084809/139‑1 (MQ=255)

                                                    gCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAc                                                                                                                                     >  2:1026241/1‑67 (MQ=255)

                                                    gCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTAc                                                                                                                                     <  1:1026241/67‑1 (MQ=255)

                                                        aaTTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAg                                                         >  1:396138/1‑139 (MQ=255)

                                                           tGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGa                                                      <  1:2021929/139‑1 (MQ=255)

                                                             ccTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAAc                                                                                                                   >  1:1299486/1‑76 (MQ=255)

                                                             ccTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAAc                                                                                                                   <  2:1299486/76‑1 (MQ=255)

                                                             ccTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCtgt                                                                                     <  1:909851/106‑1 (MQ=255)

                                                             ccTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCtgt                                                                                     >  2:909851/1‑106 (MQ=255)

                                                             ccTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATg                                                    <  2:853696/139‑1 (MQ=255)

                                                                      cTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCtgt                                                                                     >  2:199218/1‑97 (MQ=255)

                                                                      cTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCtgt                                                                                     <  1:199218/97‑1 (MQ=255)

                                                                       ttCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCtgt                                                                                     >  1:1581588/1‑96 (MQ=255)

                                                                       ttCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCtgt                                                                                     <  2:1581588/96‑1 (MQ=255)

                                                                            ttAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGTAGCCAACAGCTTAACCATcg                                                                                                      >  2:1046384/1‑74 (MQ=255)

                                                                            ttAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGTAGCCAACAGCTTAACCATcg                                                                                                      <  1:1046384/74‑1 (MQ=255)

                                                                                 aGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCAc                                                                                            <  2:1797545/79‑1 (MQ=255)

                                                                                 aGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCAc                                                                                            >  1:1797545/1‑79 (MQ=255)

                                                                                   actactATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGcc                                                                                                                      >  2:1984294/1‑51 (MQ=255)

                                                                                   actactATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGcc                                                                                                                      <  1:1984294/51‑1 (MQ=255)

                                                                                   actactATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATcg                                                                                                      >  2:2010662/1‑67 (MQ=255)

                                                                                   actactATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATcg                                                                                                      <  1:2010662/67‑1 (MQ=255)

                                                                                   actactATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGtttatgaaa                                                                           >  2:449619/1‑88 (MQ=255)

                                                                                   actactATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGtttatgaaa                                                                           <  1:449619/94‑7 (MQ=255)

                                                                                   actactATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGaaaa                              >  2:1979469/1‑139 (MQ=255)

                                                                                   actactATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGaaaa                              >  2:674645/1‑139 (MQ=255)

                                                                                    ctactaTTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATaa                                                                 <  1:6854/103‑1 (MQ=255)

                                                                                    ctactaTTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATaa                                                                 >  2:6854/1‑103 (MQ=255)

                                                                                    ctactaTTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAAt                             <  2:1058586/139‑1 (MQ=255)

                                                                                    ctactaTTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAAt                             <  1:297621/139‑1 (MQ=255)

                                                                                    ctactaTTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAAt                             <  1:487177/139‑1 (MQ=255)

                                                                                      actaTTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGa                           >  1:378105/1‑139 (MQ=255)

                                                                                        taTTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATgcg                                                  <  2:1295259/114‑1 (MQ=255)

                                                                                        taTTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATgcg                                                  >  1:1295259/1‑114 (MQ=255)

                                                                                             ccGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATcg                                                                                                      <  2:817086/57‑1 (MQ=255)

                                                                                             ccGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATcg                                                                                                      >  1:817086/1‑57 (MQ=255)

                                                                                               ggCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACa                                                                         >  2:996178/1‑84 (MQ=255)

                                                                                               ggCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACa                                                                         <  1:996178/84‑1 (MQ=255)

                                                                                                 cAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGCCAg                >  2:1098049/1‑139 (MQ=255)

                                                                                                    ttCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATaa                                                                 >  1:1430978/1‑87 (MQ=255)

                                                                                                    ttCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATaa                                                                 <  2:1430978/87‑1 (MQ=255)

                                                                                                           ctcctcACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGCCAGTTCATTtgtg      >  2:1481061/1‑139 (MQ=255)

                                                                                                               tcACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAAt                                                               >  2:2015349/1‑78 (MQ=255)

                                                                                                               tcACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAAt                                                               <  1:2015349/78‑1 (MQ=255)

                                                                                                               tcACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTCAGCGGACGGAAAATGACACCTGGCCAGTTCATTTGTGCGTa  >  1:1231904/1‑139 (MQ=255)

CCCACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACCTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGCCAGTTCATTTGTGCGTA  >  NC_000913/2521478‑2521727

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 34 ≤` `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