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
A19 F166 I0 R1	50	63.8	1389156	94.9%	1318309	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,027,751	C→G	100%	V66L (GTA→CTA)	vraS ←	sensor histidine kinase VraS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,027,751	0	C	G	100.0%	217.4 / NA	62	V66L (GTA→CTA)	vraS	sensor histidine kinase VraS
Reads supporting (aligned to +/- strand): ref base C (0/0); new base G (36/26); total (36/26)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATG  >  CP000730/2027620‑2027885

ttGGTATAAATCTAACGTTTCACTATCTTTGTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACcaac                                                                                                                               <  2:534338/140‑1 (MQ=255)

agagcataAATCTAACCTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGATCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACcaac                                                                                                                               <  2:189865/136‑1 (MQ=255)

          tCTAACGTTTCACTATATATTTCTATATTTTGATCATTCATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATacac                                                                                                                     >  2:318833/1‑141 (MQ=255)

           cTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATAcaca                                                                                                                    >  2:500849/1‑141 (MQ=255)

           cTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCACCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATAcaca                                                                                                                    <  1:364016/141‑1 (MQ=255)

             aaCGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACaat                                                                                                                  >  1:556447/1‑141 (MQ=255)

             aaCGTTTCACTATATATTTCGATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGCGTAGCGAACCAACAATAATACACaaa                                                                                                                  >  1:421431/1‑140 (MQ=255)

                      cTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTACGTCTTAATCCAATCATTTTGCTGATGGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATatgatg                                                                                                         >  1:288548/1‑141 (MQ=255)

                       tatataTTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATATATATTATTatgatgg                                                                                                        >  1:50956/1‑140 (MQ=255)

                          atatTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATAtgatgatga                                                                                                     <  2:384538/141‑1 (MQ=255)

                            atTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATgaga                                                                                                   <  1:76133/141‑1 (MQ=255)

                              ttCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGAtt                                                                                                 >  1:382237/1‑141 (MQ=255)

                                   tatTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaa                                                                                            >  1:519995/1‑141 (MQ=255)

                                    atTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaaa                                                                                           <  1:370804/141‑1 (MQ=255)

                                    atTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaaa                                                                                           <  1:242511/141‑1 (MQ=255)

                                    atTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAAGAATACACAATAATATGAGGATGAGATTtaaaaa                                                                                           >  1:12080/1‑141 (MQ=255)

                                     ttttGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaaat                                                                                          >  1:133789/1‑141 (MQ=255)

                                           tCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaaa                                                                                           <  2:500456/134‑1 (MQ=255)

                                           tCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaaa                                                                                           >  1:500456/1‑134 (MQ=255)

                                              ttAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGTTTTAAAAATAAAAAAACt                                                                                 >  2:267903/1‑141 (MQ=255)

                                              ttAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAcc                                                                                 >  2:32253/1‑140 (MQ=255)

                                              ttAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGAGGATGAGATTTACAAATAAAAAAACt                                                                                 >  2:373937/1‑141 (MQ=255)

                                                aaTGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAAGCCAATCATTTTGCTGATTGATTTTGTGAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTgg                                                                               <  1:332854/141‑1 (MQ=255)

                                                  tGCCAACTGTTTCGCCTTCCCTTGGTTGTACAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAAAAAAAAAACTGGTa                                                                             >  2:320775/1‑141 (MQ=255)

                                                  tGCCAACTGTTTCGCCTTCCATTGTACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTGAAAAATAAAAAAACTGGTa                                                                             >  1:442969/1‑141 (MQ=255)

                                                  tGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAACGGTa                                                                             >  2:566333/1‑141 (MQ=255)

                                                    ccAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTAtt                                                                           >  1:591954/1‑141 (MQ=255)

                                                       aCTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTcca                                                                        >  1:373966/1‑140 (MQ=255)

                                                       aCTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATAGGATGATGAGATTTAAAAATAAACAAACTGGTATTACg                                                                        >  1:451600/1‑141 (MQ=255)

                                                        ccgTTTCGCCTTCCATTGAACGCTCAATTTGCTTCTTAATCCAATCAGTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGa                                                                       <  1:527146/139‑1 (MQ=255)

                                                         tGTTTCGCCTTCCATTTAACGGTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTATAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGaa                                                                      <  2:259540/141‑1 (MQ=255)

                                                         tGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGaa                                                                      <  1:185944/141‑1 (MQ=255)

                                                               gCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTtg                                                                <  1:33120/141‑1 (MQ=255)

                                                                    ccATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGtat                                                           <  1:565838/141‑1 (MQ=255)

                                                                    ccATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATATTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGtat                                                           >  1:540377/1‑141 (MQ=255)

                                                                         gAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAAc                                                      <  2:519995/141‑1 (MQ=255)

                                                                            cGCTCAATTTGCGTCTTAATCCAATCATTTTGCGGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTAAAAAACATa                                                   >  2:491425/1‑141 (MQ=255)

                                                                              cTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAGAAAACTGGTATTCCGAATATTTGTGTATAAAACATAcc                                                 <  1:446965/141‑1 (MQ=255)

                                                                                 aaTTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTg                                              <  1:27297/141‑1 (MQ=255)

                                                                                       cGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATa                                        <  1:333791/141‑1 (MQ=255)

                                                                                            tAATCCAATCATCTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAGAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAATATACCTTGAAAATAgatga                                   <  2:389970/141‑1 (MQ=255)

                                                                                              aTCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGCAACTAGCTGata                                 >  2:542702/1‑141 (MQ=255)

                                                                                                ccAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATAtt                               <  2:382237/141‑1 (MQ=255)

                                                                                                ccAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATAtt                               <  2:43709/141‑1 (MQ=255)

                                                                                                acAATCATTTTGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACAAAATAATATGATGATGAGAAATAAAAAAAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATAtt                               <  2:571374/140‑1 (MQ=255)

                                                                                                 cAATCACTATGCTGATTGATTCTGTAAGCGAGCCGCGAACCAACAATAATACACAATCATACGACGATGAGAGTTAAAAATAAAAAAACACGCAAGCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATAttt                              >  2:336168/1‑141 (MQ=255)

                                                                                                       ttttGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACaaaa                        >  1:196640/1‑141 (MQ=255)

                                                                                                        tttGCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACaaaaa                       >  1:627757/1‑141 (MQ=255)

                                                                                                           gCTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGCCTCAAGAAAAATTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACtt                    >  1:302844/1‑141 (MQ=255)

                                                                                                            cTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACttt                   <  1:574807/141‑1 (MQ=255)

                                                                                                            cTGATTGATTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACttt                   <  1:46762/141‑1 (MQ=255)

                                                                                                             tgattgatTTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTa                  >  1:585987/1‑141 (MQ=255)

                                                                                                              gattgattTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACCAAAACTTTAt                 >  1:595764/1‑141 (MQ=255)

                                                                                                                ttgattTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTtctca               >  1:413774/1‑140 (MQ=255)

                                                                                                                ttgattTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTAtag               >  1:413839/1‑139 (MQ=255)

                                                                                                                   attTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATg            >  1:583777/1‑141 (MQ=255)

                                                                                                                   attTTGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGAGTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATg            >  1:462446/1‑141 (MQ=255)

                                                                                                                     tttGTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGaa          <  1:107884/141‑1 (MQ=255)

                                                                                                                        gTAAGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAg       >  2:212097/1‑141 (MQ=255)

                                                                                                                           aGCGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGaaa    >  1:650353/1‑141 (MQ=255)

                                                                                                                            gctaGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAAt   <  1:336168/138‑1 (MQ=255)

                                                                                                                             cGAGTAGCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATg  >  1:174380/1‑141 (MQ=255)

ATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATG  >  CP000730/2027620‑2027885

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A