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 I1 R1	748	32.0	1685426	92.6%	1560704	103.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,736,157	G→A	393 (TAG→TAA)	xylR →	xylose divergent operon transcriptional activator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,736,157	0	G	A	100.0%	218.9 / NA	67	393 (TAG→TAA)	xylR	xylose divergent operon transcriptional activator
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (34/33); total (34/33)

ATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAGCG‑ATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGT  >  NC_000913/3736035‑3736280

aTCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTg                                                                                                              >  2:693650/1‑139 (MQ=255)

  cAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTc                                                                                                            <  1:511245/139‑1 (MQ=255)

       agaTATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGt                                                                                                       >  1:263696/1‑139 (MQ=255)

             cGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATc                                                                                                 >  2:823779/1‑139 (MQ=255)

             cGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATc                                                                                                 >  1:717235/1‑139 (MQ=255)

                   tgtgCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTaa                                                                                           >  2:776465/1‑139 (MQ=255)

                   tgtgCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTaa                                                                                           >  2:227151/1‑139 (MQ=255)

                   tgtgCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTaa                                                                                           <  1:836599/139‑1 (MQ=255)

                        ggTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTaa                                                                                           >  1:276892/1‑134 (MQ=255)

                        ggTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTaa                                                                                           <  2:276892/134‑1 (MQ=255)

                        ggTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTg                                                                                      >  2:334983/1‑139 (MQ=255)

                          ttATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCg                                                                                    <  2:717235/139‑1 (MQ=255)

                          ttATCCATCGCTGCAATATTACTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAAAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGAGGGCGTCACATCAGGTATCGCTGCg                                                                                    <  1:511448/139‑1 (MQ=255)

                             tCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTgg                                                                                 <  1:59000/139‑1 (MQ=255)

                                     tGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGa                                                                         <  1:693650/139‑1 (MQ=255)

                                      gCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGAt                                                                        >  2:243001/1‑139 (MQ=255)

                                       cAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATg                                                                       >  2:330442/1‑139 (MQ=255)

                                       cAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATg                                                                       <  1:243001/139‑1 (MQ=255)

                                              tCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTg                                                                <  1:823779/139‑1 (MQ=255)

                                               cTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTcaca                                                                                                   <  2:573363/103‑1 (MQ=255)

                                               cTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTcaca                                                                                                   >  1:573363/1‑103 (MQ=255)

                                                    ctGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGt                                                                                                       >  1:751477/1‑94 (MQ=255)

                                                    ctGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGt                                                                                                       <  2:751477/94‑1 (MQ=255)

                                                      gTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGAt                                                                        <  2:417253/123‑1 (MQ=255)

                                                      gTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGAt                                                                        >  1:417253/1‑123 (MQ=255)

                                                           tAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCg                                                   <  2:587522/139‑1 (MQ=255)

                                                                aaGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTa                                              <  1:334983/139‑1 (MQ=255)

                                                                 aGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTAc                                             >  1:449589/1‑139 (MQ=255)

                                                                           acgacgCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCa                                   <  1:709697/139‑1 (MQ=255)

                                                                             gacgCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATg                                 >  2:574976/1‑139 (MQ=255)

                                                                             gacgCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATg                                 <  2:778079/139‑1 (MQ=255)

                                                                                gCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGaa                                                                                                                 >  1:442437/1‑56 (MQ=255)

                                                                                gCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGaa                                                                                                                 <  2:442437/56‑1 (MQ=255)

                                                                                  cAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATgcg                                                                     >  1:534266/1‑98 (MQ=255)

                                                                                  cAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATgcg                                                                     <  2:534266/98‑1 (MQ=255)

                                                                                  cAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATaaa                            >  1:625667/1‑139 (MQ=255)

                                                                                   aaaaGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATaaaa                           <  1:574976/139‑1 (MQ=255)

                                                                                    aaaGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAAc                          >  1:513688/1‑139 (MQ=255)

                                                                                          tATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTcaca                                                                                                   >  1:489755/1‑60 (MQ=255)

                                                                                          tATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTcaca                                                                                                   <  2:489755/60‑1 (MQ=255)

                                                                                          tATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACca                    >  2:796105/1‑139 (MQ=255)

                                                                                            tCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACcaac                  <  2:513688/139‑1 (MQ=255)

                                                                                               cgATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCaacaac               >  1:724193/1‑139 (MQ=255)

                                                                                                 aTGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTca                                                                                                     >  2:826350/1‑51 (MQ=255)

                                                                                                 aTGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTca                                                                                                     <  1:826350/51‑1 (MQ=255)

                                                                                                  tGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATaaaa                           <  1:652181/124‑1 (MQ=255)

                                                                                                  tGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATaaaa                           >  2:652181/1‑124 (MQ=255)

                                                                                                   gTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCtt           <  2:724193/139‑1 (MQ=255)

                                                                                                    tAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTa                                              >  2:792878/1‑103 (MQ=255)

                                                                                                    tAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTa                                              <  1:792878/103‑1 (MQ=255)

                                                                                                           cGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCg   >  2:134212/1‑139 (MQ=255)

                                                                                                            gAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCg                                                                                    >  1:656123/1‑57 (MQ=255)

                                                                                                            gAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCg                                                                                    <  2:656123/57‑1 (MQ=255)

                                                                                                            gAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCg                                                                                    >  2:725534/1‑57 (MQ=255)

                                                                                                            gAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCg                                                                                    <  1:725534/57‑1 (MQ=255)

                                                                                                            gAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGt  <  1:134212/139‑1 (MQ=255)

                                                                                                            gAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGt  >  1:822479/1‑139 (MQ=255)

                                                                                                              ggTCATGTTGTAACGAATGATGAGAATTGTCGGCg                                                                                                        >  1:185158/1‑35 (MQ=255)

                                                                                                              ggTCATGTTGTAACGAATGATGAGAATTGTCGGCg                                                                                                        <  2:185158/35‑1 (MQ=255)

                                                                                                              ggTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGc                                                           >  2:259070/1‑80 (MQ=39)

                                                                                                              ggTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGc                                                           <  1:259070/80‑1 (MQ=39)

                                                                                                              ggTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCt                                               <  1:681426/92‑1 (MQ=38)

                                                                                                              ggTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCt                                               >  2:681426/1‑92 (MQ=38)

                                                                                                                tCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACg                                                                                         >  1:450776/1‑48 (MQ=255)

                                                                                                                tCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACg                                                                                         <  2:450776/48‑1 (MQ=255)

                                                                                                                 cATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGtt                                                                               <  1:382133/57‑1 (MQ=255)

                                                                                                                 cATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGtt                                                                               >  2:382133/1‑57 (MQ=255)

ATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAGCG‑ATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGT  >  NC_000913/3736035‑3736280

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `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