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
A15 F17 I0 R1	21	55.4	1282596	94.8%	1215901	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,532,298	A→T	100%	T15T (ACA→ACT)	femA_3 →	Aminoacyltransferase FemA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,532,298	0	A	T	100.0%	157.9 / ‑6.5	50	T15T (ACA→ACT)	femA_3	Aminoacyltransferase FemA
Reads supporting (aligned to +/- strand): ref base A (0/0); major base T (17/32); minor base G (0/1); total (17/33)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGTGTATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACAGAAGCA  >  USA300TCH1516_ALE/2532161‑2532433

tgtgTATTTGTAATCAGTTTTTGATAACATAAAAAAATAGAATTCTTAATAAATTCAAAAATTACCGTGTGCGCCAGAAAGCGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCATTTactaca                                                                                                                                       >  2:161108/1‑141 (MQ=255)

       ttGTAATCAGTTTTTAATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAtt                                                                                                                                <  2:604494/141‑1 (MQ=255)

       ttGTAATCAGTTTATTATAAAATAAAAGAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATTAACTTTGTAACGTTGACTTCGGATGAGTTGAATGCGTTTACTACAAAGCAtt                                                                                                                                <  2:147288/141‑1 (MQ=255)

        tctAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAttt                                                                                                                               <  1:71897/139‑1 (MQ=255)

        tGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAttt                                                                                                                               <  1:13391/141‑1 (MQ=255)

        tGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAttt                                                                                                                               <  1:67101/141‑1 (MQ=255)

          tAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAttttt                                                                                                                             >  2:524467/1‑141 (MQ=255)

          tAATCAGTTTTAGCTCACATCCAATAATAGCATTAATAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAttttt                                                                                                                             <  1:239876/141‑1 (MQ=255)

           aaTCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAttcttc                                                                                                                            >  2:547396/1‑141 (MQ=255)

                 tttttGATAAAATAGAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGTGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTa                                                                                                                      <  2:603570/141‑1 (MQ=255)

                    ttGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTacac                                                                                                                   <  2:81047/141‑1 (MQ=255)

                      gATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATAAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCATTTACTACACATCATTTTTCACATTacccac                                                                                                                 >  2:18333/1‑141 (MQ=255)

                             aaaaaaaaTAGCATTATTAGTAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGc                                                                                                          <  1:357126/140‑1 (MQ=255)

                             aaaaaaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGc                                                                                                          <  1:611705/140‑1 (MQ=255)

                                aaaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGAATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTAt                                                                                                       >  2:466393/1‑141 (MQ=255)

                                 aaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTAtt                                                                                                      >  2:362741/1‑141 (MQ=255)

                                 aaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTAtt                                                                                                      <  2:340714/141‑1 (MQ=255)

                                       gCATTATTAATAATTGCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTAc                                                                                                <  1:53765/141‑1 (MQ=255)

                                            attaATAAATGTAAAAATTATAGTTCAATTCAGAGATGGATGGGATAGAATGAATGTTGTAACGACACCCTAGTAAGAGTTCAATGCGTTTACTACAAAGTATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑Ca                                                                                          <  2:161273/141‑1 (MQ=255)

                                                    aTTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTg                                                                                  <  2:16147/141‑1 (MQ=255)

                                                          aagttATAGTGCAATTCAGAGAGGGATGGGATAAAATGAACTTTTTAACGTTTACTTCGGAGAAGTTCAATGCATTTACTACAAAGAATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTaa                                                                            <  2:319056/138‑1 (MQ=255)

                                                             ttATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAg                                                                         <  1:47248/141‑1 (MQ=255)

                                                                taGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCg                                                                      <  1:598110/141‑1 (MQ=255)

                                                                taGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCg                                                                      <  2:426858/141‑1 (MQ=255)

                                                                taGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCg                                                                      <  1:192791/141‑1 (MQ=255)

                                                                    tCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCGAtgt                                                                  <  1:16253/141‑1 (MQ=255)

                                                                       aTTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCGATGTGCa                                                               <  1:553914/141‑1 (MQ=255)

                                                                       aTTCAGAGAGGGAGGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCGATGTGCa                                                               <  1:128274/141‑1 (MQ=255)

                                                                          gagagagGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCGATGTGCATCt                                                            <  2:503538/140‑1 (MQ=255)

                                                                            gagagGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACCAAGCATTTTTCCCATCACACACCTTCATCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCGACGTTCATCTTg                                                          >  2:456241/1‑141 (MQ=255)

                                                                            gagagGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTAAACCTAATCAGCTATTCATT‑CAATACTTTTATGTTTTTTAAAAGGCGATGTGCATCTTg                                                          >  1:403614/1‑141 (MQ=255)

                                                                             agagGGATGGGATAAAATGAACTTTGTAACGAAGACCTCGAATGAGTTCAATGCGTTGAATACAAAGCATTTTTCACATAACACACAAGGAGCTATTCATTACACT‑CAGAGAGTAGATCTAAACGGCGACGCGCATCtcgg                                                         >  2:566421/1‑138 (MQ=255)

                                                                                gggatgggatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAGTGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAgg                                                      <  1:280491/141‑1 (MQ=255)

                                                                                gggatgggatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTGTCATGACACACAATCAGCTATTCAGTACAAT‑CATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAgg                                                      <  1:304435/141‑1 (MQ=255)

                                                                                        atAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAg                                              <  1:78394/141‑1 (MQ=255)

                                                                                              tGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACa                                        <  1:208618/141‑1 (MQ=255)

                                                                                              tGAACTTGTTAACGTTGACTTCAGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAG‑CATAGAGCTGATTTAAAAAGCGATGTGCATCTTGTAGGGGTTAAAGATGACa                                        <  2:293202/141‑1 (MQ=255)

                                                                                                 aCTTTGTACCGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTCGGGGATAAAGATGACAGTg                                     >  2:443805/1‑141 (MQ=255)

                                                                                                            ttGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCCAGTGAtt                          >  2:335056/1‑141 (MQ=255)

                                                                                                            ttGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCGATGTGCACCTTGTAGGGGCTAAAGATGACAATGGTCACGTGAtt                          >  2:155088/1‑141 (MQ=255)

                                                                                                               aCTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCa                       <  2:461389/141‑1 (MQ=255)

                                                                                                               aCTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCGATGTGCATATTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCa                       >  1:380646/1‑141 (MQ=255)

                                                                                                                      aTGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCt                <  1:588725/141‑1 (MQ=255)

                                                                                                                              aaTGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACa        <  1:362741/141‑1 (MQ=255)

                                                                                                                              aaTGCGTTTACTACAAAGCATTTCCCACATTAGACACAAGCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACa        >  1:442684/1‑141 (MQ=255)

                                                                                                                               aTGCGTTTACTACAAAGCATTTTTCACATTACAAACAATCAGATATTCAGTACAAT‑CATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACAg       <  1:602833/141‑1 (MQ=255)

                                                                                                                                gccGTTTATGACAAAGCGTTGTTCTGATTAGACAGAAGCAGCTATTCGTTGCAAT‑CATAGAGTTGATTTAAAAGGCGGTGTGCATCTTGGGGAGGTGAAAGATGAGAATGGACAAGTGACTGCAGGATGCTTATTGACAGa      <  2:129572/139‑1 (MQ=255)

                                                                                                                                   gTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACAGAAgc   >  1:455046/1‑141 (MQ=255)

                                                                                                                                   gTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCGATCTGCATAATTTAGGGGTGAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACAGAAgc   >  1:467649/1‑141 (MQ=255)

                                                                                                                                    tttACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACAGAAgca  >  2:443480/1‑141 (MQ=255)

                                                                                                                                    tttACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACAGAAgca  >  2:139466/1‑141 (MQ=255)

TGTGTATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAT‑CATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACAGAAGCA  >  USA300TCH1516_ALE/2532161‑2532433

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A