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 F55 I0 R1 26 48.4 1146576 93.4% 1070901 139.9

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_ALE2,532,2980AT99.2% 156.0 / ‑6.3 53T15T (ACA→ACT) femA_3Aminoacyltransferase FemA
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base T (13/38);  minor base G (0/1);  total (14/39)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.73e-01
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.

ATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGAC  >  USA300TCH1516_ALE/2532166‑2532426
                                                                                                                                    |                                                                                                                                
aTTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGc                                                                                                                           <  1:471958/140‑1 (MQ=255)
 tttGTAATCAAGATTTGATAAAATACAAAAAGAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCa                                                                                                                          <  1:563888/140‑1 (MQ=255)
   tGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAtt                                                                                                                        <  1:223590/140‑1 (MQ=255)
         cAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTcac                                                                                                                  >  2:131039/1‑140 (MQ=255)
               ttGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTaca                                                                                                            <  1:246322/140‑1 (MQ=255)
                 gaaaaaataaaaAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTacaca                                                                                                          <  2:351418/137‑1 (MQ=255)
                 gATAAAAGAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACATTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTacaca                                                                                                          <  2:215186/140‑1 (MQ=255)
                  ataaaataaaAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTacacac                                                                                                         >  1:386098/1‑140 (MQ=255)
                  ataaaataaaAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTacacac                                                                                                         <  1:421367/140‑1 (MQ=255)
                   taaaataaaaAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTAcacaca                                                                                                        <  1:365453/140‑1 (MQ=255)
                    aaaataaaaAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGAGGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACaa                                                                                                       <  2:540361/140‑1 (MQ=255)
                      aataaaaAAATAGCATTATTAATAAATTCGAAACTTATAGTTGCATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATc                                                                                                     <  1:340800/140‑1 (MQ=255)
                       ataaaaAAATAGCCTTATTAATAAAGTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCa                                                                                                    <  2:31152/140‑1 (MQ=255)
                         aaaaacaTAGCATTATTAATACATTCAAAAATTATAGTGCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGc                                                                                                  <  1:48658/140‑1 (MQ=255)
                          aaaaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCt                                                                                                 >  2:469493/1‑140 (MQ=255)
                           aaaaaTAGCATTATTAATAAATTCAAAAATTATAGTACAATTCAGAGAGGGATGAGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTAAAAAGCATTTTTCACAATACACACAATCAGCTa                                                                                                >  2:566293/1‑140 (MQ=255)
                            aaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTAt                                                                                               <  1:489232/140‑1 (MQ=255)
                            aaaaTAGAATTATTAATAAATTCAAACATTATAGTTCAATTCAGCGAGGGATGGGATAAAATGAACTTTGTAACGTTGACATCGGATGAGTTCGATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTAt                                                                                               <  1:81464/140‑1 (MQ=255)
                              aagaGCATTATTAATAAACTCAATAACTATAGTTCCATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTGCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTc                                                                                             <  1:437862/137‑1 (MQ=255)
                                  gCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAAAGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACCACAAAGCAGTTTTCACATTACACACAATCAGCTATTCATTa                                                                                         >  2:118746/1‑140 (MQ=255)
                                         taataaATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCAt                                                                                  >  2:282050/1‑140 (MQ=255)
                                                    gaaaTTATAGTGCAATTGAGGTAGGGATGGGAGAAAAGGGGCTTTGTAACGTTGGCTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGAttt                                                                       <  2:494373/139‑1 (MQ=255)
                                                        ttATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTaaaa                                                                   <  1:46621/140‑1 (MQ=255)
                                                            aGTGCAATGCGGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCg                                                               <  2:568958/140‑1 (MQ=255)
                                                                  atgcAGAGGGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGc                                                         <  2:241542/137‑1 (MQ=255)
                                                                    tCATAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCAt                                                       <  2:298550/140‑1 (MQ=255)
                                                                    tCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCAt                                                       <  1:458642/140‑1 (MQ=255)
                                                                      agagagGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCACTGCGTTACGGTCAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCt                                                     <  1:417285/140‑1 (MQ=255)
                                                                      agagagGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCt                                                     <  2:208800/140‑1 (MQ=255)
                                                                      agagagGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCt                                                     <  2:279861/140‑1 (MQ=255)
                                                                          agGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTGCAATGCGTTTACTACAAAGCATTTTTCACAAAACAAACAATTAGATATTCATTACAATCATAGAGTTGATTTAAAAAGAGAAATGCATCTTGTa                                                 >  2:525608/1‑140 (MQ=255)
                                                                           gggatgggatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAg                                                <  1:347827/140‑1 (MQ=255)
                                                                            ggatgggatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAgg                                               >  1:300979/1‑140 (MQ=255)
                                                                             gatgggatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACGCACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAggg                                              <  2:333570/140‑1 (MQ=255)
                                                                                   atAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGCGTTGAGTTAAAAGTCGATGTGCATCTTGTAGGGGTTaaa                                        >  1:130161/1‑140 (MQ=255)
                                                                                          ggaCTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAGAGCATTTTTAACATTACACACAATCAGCTATTCAGTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACa                                 <  2:282866/138‑1 (MQ=255)
                                                                                           aaatttGTAACGTTGACTTCGGATGAGATCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCAATTCATTACAATCATAGAGGTGGTTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACaa                                >  1:39919/4‑140 (MQ=255)
                                                                                           aaCTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACaa                                <  1:377558/140‑1 (MQ=255)
                                                                                            aCTTTGTAACGTTGACTTCGGATGAGTGCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCAGTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAAt                               <  2:33544/140‑1 (MQ=255)
                                                                                                tggagcGTTGACTTCGGATGAGTTAAATGCGATTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTc                           <  2:389309/135‑1 (MQ=255)
                                                                                                tGTAACGTTGACTTCGGATGAGTTTTATGCGTTTAGTGTTAATGATTTTTCGCGTTTGCTACCATCGGCTATTCATTATCATCATAGAGTTGATTTACAAGGCGATGTGCATCCCGTAGGGGCCAAACATGACAATgcac                           >  2:408328/1‑137 (MQ=255)
                                                                                                       ttGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTCTTCATTACAATCATAGAGTTGATTTAAAACGCGATGTGCATCTTGCAGGGGTTGAAGATGACGATGGTCACGGGAt                    >  2:273918/1‑140 (MQ=255)
                                                                                                          ccTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTGGTAGGGGCGAAAGATGACAACGGTCACGTGATTGc                 >  2:548213/2‑140 (MQ=255)
                                                                                                           cTTCGGATGAGTTCAATGCGTTTACTACTAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTCATTGCa                <  2:481527/140‑1 (MQ=255)
                                                                                                           cTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAGCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCa                <  2:461438/140‑1 (MQ=255)
                                                                                                            ttCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTTCACACAATCAGCTATTCATTACAATCATAGAATTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAg               <  1:273472/140‑1 (MQ=255)
                                                                                                            atcagATGAGTTCAATGCGTTTACTACAAAGCTATTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAg               <  1:64766/136‑1 (MQ=255)
                                                                                                             tCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAgg              <  2:181513/140‑1 (MQ=255)
                                                                                                                     gTTCAATGCGTTTACTACAAAGCATTTTTCAACTTACCTACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTAt      <  1:18662/140‑1 (MQ=255)
                                                                                                                      aaaaaTGCGTTTACTACAAAGCATTTTTCACATTACAAACAATCAGCTATTCATAACAATCATAAAGTTGCTCTAAAAGGCGATGTGCATCTTGAAGCGGGTAAAGATGACAATGGTCAAGTGATTGCAGGATGGTTAtt     >  2:450618/4‑140 (MQ=255)
                                                                                                                        cAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGa   <  2:233291/140‑1 (MQ=255)
                                                                                                                        cAATGCGTTTACTACAAAGCATTTTTCACATTAAACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGa   <  2:56262/140‑1 (MQ=255)
                                                                                                                         ggtGCGTGTACTACAAAGCATTTGTCACGTTACACACAATCAGCTATGCATTACAATCATAGAGTGGATGTAAAAGGCGATGTGCATCTTGTAGGGGTGAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGAc  <  1:454705/138‑1 (MQ=255)
                                                                                                                                    |                                                                                                                                
ATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGAC  >  USA300TCH1516_ALE/2532166‑2532426

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