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
A23 F171 I0 R2	49	45.2	1012374	92.5%	936445	139.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,027,805	C→A	100%	V48F (GTT→TTT)	vraS ←	sensor histidine kinase VraS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,027,805	0	C	A	100.0%	181.4 / NA	50	V48F (GTT→TTT)	vraS	sensor histidine kinase VraS
Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (25/25); total (25/25)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGTTCTAATGTAGT  >  CP000730/2027672‑2027939

ccAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTAtt                                                                                                                                 >  2:209865/1‑141 (MQ=255)

 cAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTc                                                                                                                                <  1:354725/141‑1 (MQ=255)

 cAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATGTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTc                                                                                                                                <  1:346975/141‑1 (MQ=255)

 cAACTGTTTAGCCTTCCAATGAAAAATAAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATAAGAAAAAAAAAAAAAAAAAATGGTATTc                                                                                                                                <  2:289329/141‑1 (MQ=255)

 aaaCTGTTTCGCATTACAAAAAACAATCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATCATGATGAGAAAAAAAAAAAAAAAAAATGGTATTc                                                                                                                                <  2:450559/140‑1 (MQ=255)

       tttCGCCTTCCATTAAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAAAACACAATAATATGATGATAAGATTTAAAAATAAAAAAAATGGTATTCCGAata                                                                                                                          <  1:354341/141‑1 (MQ=255)

         tCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATAtt                                                                                                                        >  1:120729/1‑141 (MQ=255)

           gCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGAGTTTGTAAGCAGGTACCTAACCAACAATAATACACAGTAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTtg                                                                                                                      >  2:353581/1‑141 (MQ=255)

             cTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAAAATTtgtg                                                                                                                    >  1:455712/1‑141 (MQ=255)

               tCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGta                                                                                                                  <  1:443101/141‑1 (MQ=255)

                         gCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATAc                                                                                                        >  1:2845/1‑141 (MQ=255)

                            taagttatgTCTTAATCAAATTTTTTTGCTTATTTATTTTGTAAGCTAATACCGAACCAACAATAATACATAATAATATGATGATAATATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCtt                                                                                                     <  1:126164/133‑1 (MQ=255)

                              aTTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGa                                                                                                   >  1:182623/1‑141 (MQ=255)

                               tttGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGaa                                                                                                  <  1:90152/141‑1 (MQ=255)

                                  gCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAAt                                                                                               >  2:221780/1‑141 (MQ=255)

                                  gCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAAt                                                                                               >  2:419242/1‑141 (MQ=255)

                                    gTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAg                                                                                             >  2:442093/1‑141 (MQ=255)

                                                 cATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACaa                                                                                <  1:206870/141‑1 (MQ=255)

                                                  aTTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACaaa                                                                               <  1:389174/141‑1 (MQ=255)

                                                  aTTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACaaa                                                                               >  2:386119/1‑141 (MQ=255)

                                                   gcaaaatgattgatTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACaaaa                                                                              >  1:43869/7‑141 (MQ=255)

                                                    tttGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACaaaaa                                                                             >  2:161481/1‑141 (MQ=255)

                                                    tttGCT‑ATTGATTTGGTAAGCAAGTACCGAACCAACAATAATACACAATAATATGATTATGAGATAAAAAAAAAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAAc                                                                            <  2:200102/141‑1 (MQ=255)

                                                     ttGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAAc                                                                            <  2:370477/141‑1 (MQ=255)

                                                     ttGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAAc                                                                            <  2:442143/141‑1 (MQ=255)

                                                       gCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACtt                                                                          <  2:300792/141‑1 (MQ=255)

                                                       gCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTAAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACtt                                                                          <  2:300802/141‑1 (MQ=255)

                                                          gattgattTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTAt                                                                       <  1:342858/141‑1 (MQ=255)

                                                                        gCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAAt                                                         >  1:40274/1‑141 (MQ=255)

                                                                         cGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATg                                                        >  2:188898/1‑141 (MQ=255)

                                                                          gAGTAAAGAACCAACAATAATACATAATAATATGATGATGAAATATAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGc                                                       <  2:103195/141‑1 (MQ=255)

                                                                                cGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATAAACAGAAATGCAGCTAg                                                 >  1:407055/1‑141 (MQ=255)

                                                                                  aaCCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCa                                               <  1:459472/141‑1 (MQ=255)

                                                                                         aataatACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCtata                                        >  1:125618/1‑141 (MQ=255)

                                                                                         aataatACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCtata                                        >  2:400576/1‑141 (MQ=255)

                                                                                         aataatACACAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCtata                                        >  1:370759/1‑141 (MQ=255)

                                                                                               acacAATAATATGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTaa                                  >  2:449121/1‑141 (MQ=255)

                                                                                                   aataatATGATGATGAGATGTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATg                              <  2:303656/141‑1 (MQ=255)

                                                                                                       atatGATGATGAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCa                          >  1:323120/1‑141 (MQ=255)

                                                                                                         atgatgatgAGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCAtt                        <  1:414775/141‑1 (MQ=255)

                                                                                                          tgatgatgaGATTTAAAAATAAAAAAAATGGTATTACGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTg                       >  1:240647/1‑141 (MQ=255)

                                                                                                            atgatgaGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAATTAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGaa                     <  1:194259/141‑1 (MQ=255)

                                                                                                            atgatgaGATTTAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGaa                     >  1:217535/1‑141 (MQ=255)

                                                                                                             tgatgaGATTTAAAAATAAAAAAAATGGTATCCCGAATATTTGTGTATAAAACATACCTTGAAAATAGACAATAAAAACAAAAACTTTATCGATGACCAGACATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAAc                    <  1:453291/141‑1 (MQ=255)

                                                                                                                     tttAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGtt            <  1:442093/141‑1 (MQ=255)

                                                                                                                      ttAAAAATAAAAAAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGTTc           <  1:454946/141‑1 (MQ=255)

                                                                                                                       taaaaataaaaaAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGTTCt          <  1:386119/141‑1 (MQ=255)

                                                                                                                           aataaaaaAAATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGTTCTAATg      >  1:276729/1‑141 (MQ=255)

                                                                                                                              aaaaaaaaTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGTTCTAATGTAg   >  1:199512/1‑141 (MQ=255)

                                                                                                                              aaaaaaaaTGGTATACCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGTTCTAATGTAg   <  2:485019/141‑1 (MQ=255)

                                                                                                                               aaaaaaATGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGTTCTAATGTAGt  >  1:497861/1‑141 (MQ=255)

                                                                                                                               aaaaaaATGGTATTCCGAATATTTGTGTAAAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATACTATATACTAAGATGAGCATTGAACTAATTGTTCTAATGTAGt  >  2:345994/1‑141 (MQ=255)

CCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAACATACCTTGAAAATAGATGATATTTACAAAAACTTTATCGATGAACAGAAATGCAGCTAGCATGCTATATACTAAGATGAGCATTGAACCAATTGTTCTAATGTAGT  >  CP000730/2027672‑2027939

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A