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
A13 F68 I0 R1	25	50.4	1217238	93.3%	1135683	133.9

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%	124.1 / NA	44	T15T (ACA→ACT)	femA_3	Aminoacyltransferase FemA
Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (19/25); total (19/25)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGAT  >  USA300TCH1516_ALE/2532168‑2532416

ttccaaTCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTactaca                                                                                                                     <  2:293407/130‑1 (MQ=255)

 tatAATCATTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTActacaa                                                                                                                    <  1:534293/132‑1 (MQ=255)

    aaTCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGc                                                                                                                 <  1:77521/134‑1 (MQ=255)

        aGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGCGTTCAATGCGTTTACTACAAAGCAttt                                                                                                             >  2:148175/1‑134 (MQ=255)

           ttttGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTAAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACATTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTc                                                                                                          >  2:140415/1‑134 (MQ=255)

             ttGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTcac                                                                                                        <  1:352801/134‑1 (MQ=255)

              tGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTcaca                                                                                                       >  2:385355/1‑134 (MQ=255)

               gATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGAATACTACAAAGCATTTTTCACAt                                                                                                      >  2:607348/1‑134 (MQ=255)

                ataaaataaaAAAATAGCATTATTAATAAATTCAAAAATTATAGTCCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACAtt                                                                                                     >  1:92515/1‑134 (MQ=255)

                     ataaaaAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCGATGCGTTTACTACAAAGCATTTTTTACAATacaca                                                                                                >  1:565137/1‑134 (MQ=255)

                         aaaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAAt                                                                                            <  1:229897/134‑1 (MQ=255)

                                 cATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTAtt                                                                                    >  1:485669/1‑134 (MQ=255)

                                   ttattaATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAAAGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCGCATTACACACAATCAGCTATTCa                                                                                  >  1:312585/1‑134 (MQ=255)

                                      ttaATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTa                                                                               <  2:43618/134‑1 (MQ=255)

                                          taaATTCAAAAATTGTAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGAGTTTACTACAAAGCATTTTTAACATTACACACAATCAGCTATTCATTACAAt                                                                           >  2:601048/1‑134 (MQ=255)

                                           aaaTTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATc                                                                          <  2:140042/134‑1 (MQ=255)

                                               tCAATAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCCCTGCGTCTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATag                                                                      <  2:458428/134‑1 (MQ=255)

                                                 aaataTTATAGTTCAATTCAGAGATGGATGGTATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAAGGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATagag                                                                    <  1:112633/134‑1 (MQ=255)

                                                  aaaaTTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGt                                                                   >  2:502190/1‑134 (MQ=255)

                                                     aTTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGa                                                                <  1:459840/134‑1 (MQ=255)

                                                      ttATGGTTCAATTCAGAGATGGATGGGATAAAATGATCTTTGTAACGTTGACTTCGGTTGAGTTCAATGCTTTTACTACAAATCATGTTTCACATTACACACAATCTGCTATTCATTACAATCATAGAGTTGAt                                                               <  2:65483/134‑1 (MQ=255)

                                                        ataGTTCAATTTATAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGAttt                                                             <  2:390376/134‑1 (MQ=255)

                                                          aGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAACCACAGAGTTGATTTaa                                                           >  2:231609/1‑134 (MQ=255)

                                                           gTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGCGTCCAATGCGCTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGATATGATTCaaa                                                          >  2:245104/1‑134 (MQ=255)

                                                            ttCAATTCAGAGAGGGATGGGATAATATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTaaaa                                                         <  1:405476/134‑1 (MQ=255)

                                                                    agagagGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCCGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGAtgt                                                 >  2:322133/1‑134 (MQ=255)

                                                                    agagagGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGAtgt                                                 >  1:587450/1‑134 (MQ=255)

                                                                         gagatgggatAAAATGAACTTTGTAACGGTGACTTCGGAAGAGTCAAAAGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATc                                            <  1:266586/132‑1 (MQ=255)

                                                                          ggatgggatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCt                                           <  2:533166/134‑1 (MQ=255)

                                                                             tgggatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGt                                        <  2:455828/134‑1 (MQ=255)

                                                                              ggcaaaaaaTGAACTTTGTAATGGGGACTTCGCATGGGTTCAATGCCTTTACTGCGAAGCATTTTTCACAATACACACAATCAGCTATTCATTACAATCATAGAGTTAATTTAAAAGTCGATGTGCATCTTGTa                                       <  2:604895/129‑1 (MQ=255)

                                                                                gatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATATTGTAgg                                     >  1:40083/1‑134 (MQ=255)

                                                                                        gAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATCGAGTTGATTTAAAAAGCGATGTGCATAATGTAGGGGTTAAAg                             >  1:213771/1‑134 (MQ=255)

                                                                                               gTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACaa                      <  1:385355/134‑1 (MQ=255)

                                                                                                  aCGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTTACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGCTGACAATgt                   >  2:459859/1‑133 (MQ=255)

                                                                                                  aCGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGCGTTGATTTAAAAGGCGATGTGCATCTAGTAGGGGTTAAAGATGACaaagg                   >  1:546869/1‑131 (MQ=255)

                                                                                                     ttGACCTCGCCTGAGTTCAATGCGTTTACTACACAGCATGCATCACAACACAGTGGCGCAGCTATTCAGTCCAAGCAGAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCa                <  1:196390/134‑1 (MQ=255)

                                                                                                         cTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAAGGGTCAAGTg            >  2:538061/1‑134 (MQ=255)

                                                                                                          ttCGGATTAGTTCAATGCGTTTACTACGAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGa           <  1:65326/134‑1 (MQ=255)

                                                                                                            cgaaTGAGTTCAATTCGTTTACTAAAAAGCATATTACACATAACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGAtt         <  1:329909/131‑1 (MQ=255)

                                                                                                               aTGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCa      <  2:240214/134‑1 (MQ=255)

                                                                                                               aTGAGTTCAATGCGTGTACTACAAAGCCTTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCa      <  2:110326/134‑1 (MQ=255)

                                                                                                                tGAGTTTAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAg     <  1:529200/134‑1 (MQ=255)

                                                                                                                 gattgcAATGCGTTTAATACAAAGCATGTTTCAGATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAgg    <  2:422794/129‑1 (MQ=255)

                                                                                                                 gAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCACCTTGGAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAgg    <  1:25024/134‑1 (MQ=255)

                                                                                                                   tttCAATGCGTTTACTACTAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGAt  <  2:60714/133‑1 (MQ=255)

TTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGAT  >  USA300TCH1516_ALE/2532168‑2532416

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A