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 F57 I0 R1 18 37.5 860368 95.0% 817349 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_ALE2,532,2980AT100.0% 113.3 / ‑6.5 38T15T (ACA→ACT) femA_3Aminoacyltransferase FemA
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base T (8/29);  total (8/30)
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.

GTATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACA  >  USA300TCH1516_ALE/2532164‑2532427
                                                                                                                                      |                                                                                                                                 
gtATTAGTAATCAATTTTAAATAAAAAAAAAAAATAGCATTATAAAAAAATACAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAg                                                                                                                             <  2:30599/141‑1 (MQ=255)
               ttttGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTac                                                                                                              <  2:148259/141‑1 (MQ=255)
                 ttGATAAAATGAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTacac                                                                                                            <  2:310278/141‑1 (MQ=255)
                   aaaaaaataaaaAAATAGCAGTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGTTAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTacacac                                                                                                          <  2:373420/138‑1 (MQ=255)
                       aaataaaaAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATc                                                                                                      <  1:192161/141‑1 (MQ=255)
                        aataaaaAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCCGTGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCa                                                                                                     <  2:164518/141‑1 (MQ=255)
                        aataaaaAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGTACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCa                                                                                                     <  1:230206/141‑1 (MQ=255)
                        aataaaaAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCa                                                                                                     <  1:333232/141‑1 (MQ=255)
                           aaaaaaaTAGCATTATTAATAAAATCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCt                                                                                                  <  1:139432/141‑1 (MQ=255)
                               aaaTAGCATGATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTc                                                                                              <  1:222758/141‑1 (MQ=255)
                                  aagtagtattaATAAATTCAAAAAGTATAGTTCAATTCAGAGAGGGATAGGATAAAATTAACTTTGTAACGTTGACTTCTGATGAGTTCAATTCGTGTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCAtt                                                                                           <  2:77093/135‑1 (MQ=255)
                                         attaATAAATTCAAGAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCa                                                                                    <  1:253898/141‑1 (MQ=255)
                                            aataaATTCAAAACTTATAGTTCAATTCAGAGAGAGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCATTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATaa                                                                                 >  2:265252/1‑140 (MQ=255)
                                                 aTTTAAGAATTATAGTTCAATTCATGGAGGGATGGTATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTAACAACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTg                                                                            <  2:213821/141‑1 (MQ=255)
                                                     aaaaaTTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGCTGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGAttt                                                                        <  1:163855/141‑1 (MQ=255)
                                                      aaaaTTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTa                                                                       >  1:186763/1‑141 (MQ=255)
                                                      aaaaTTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTAATAAAAAGATGGGTTCTCAATACACACAATCAGCTATTCATTACAATCATAGAGGTGATTTa                                                                       >  1:185247/1‑141 (MQ=255)
                                                        aactataGTGCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTaaa                                                                     <  1:175668/138‑1 (MQ=255)
                                                              tgTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATTGTGTTGATTTAAAAGGCGa                                                               <  2:74473/140‑1 (MQ=255)
                                                                    atgcAGAGAGTGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCCCCTTACACACTATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCa                                                         <  2:325701/138‑1 (MQ=255)
                                                                      tCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATc                                                       <  1:129983/141‑1 (MQ=255)
                                                                               gatgggatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAgggg                                              <  1:373507/141‑1 (MQ=255)
                                                                                atgggatAAAATGAACTTTGTAACGTTGACGTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGt                                             <  2:234309/141‑1 (MQ=255)
                                                                                 tgggatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGtt                                            >  2:281929/1‑141 (MQ=255)
                                                                                     atAAAATGAACTTTGTAACGTTGAGTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAg                                        <  2:267541/141‑1 (MQ=255)
                                                                                          aTGAAATTTGTAACGTTGACTTCGGATAAGTTAAATGCGTTTACTAAAAAGCATTTTTCACAGTACACACAATCAGCTATTCATTACAATCATAGATTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGAc                                   <  2:202823/141‑1 (MQ=255)
                                                                                                tttGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATCGTGCAGAATTGGCGATGCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGt                             <  1:426032/141‑1 (MQ=255)
                                                                                                  tGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCa                           <  2:408689/141‑1 (MQ=255)
                                                                                                  tGTAACGTTGACTTCGGATGAGTTCAATGCGCTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCa                           <  1:65096/141‑1 (MQ=255)
                                                                                                        gTTGACTTCGGATGAGTTCAATGCGTTTACTACAATGCATTTTTCACATTACACACAATGAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGAt                     <  2:287558/141‑1 (MQ=255)
                                                                                                         ttGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGAtt                    <  1:138131/141‑1 (MQ=255)
                                                                                                           gACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGc                  <  1:252577/141‑1 (MQ=255)
                                                                                                            aCTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCa                 <  2:250610/141‑1 (MQ=255)
                                                                                                            aCTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCa                 <  2:407937/141‑1 (MQ=255)
                                                                                                                       gTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTGAtt      >  1:254164/1‑141 (MQ=255)
                                                                                                                          cAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGCAGGGGTTAAAGATGACAATGGTCAACTGAATGCAGAATGCATATTGaa   >  1:169132/1‑140 (MQ=255)
                                                                                                                           aaTGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGCGTTGATTTAAACGCCGATGTGCATCTTGTATGACTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACa  >  2:132152/1‑141 (MQ=255)
                                                                                                                           aaTGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACa  >  1:50677/1‑141 (MQ=255)
                                                                                                                                      |                                                                                                                                 
GTATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACA  >  USA300TCH1516_ALE/2532164‑2532427

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