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 F166 I0 R1 47 63.0 1389156 95.7% 1329422 140.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,010,363 C→T 100% C146Y (TGT→TAT)  USA300HOU_RS10125 ← Putative multidrug export ATP‑binding/permease protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,010,3630CT100.0% 156.5 / ‑6.5 54C146Y (TGT→TAT) USA300HOU_RS10125Putative multidrug export ATP‑binding/permease protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (17/36);  minor base G (0/1);  total (17/37)
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.

GTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTGTAT  >  USA300TCH1516_ALE/2010232‑2010500
                                                                                                                                   |                                                                                                                                         
gtgtCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAAcc                                                                                                                                  >  2:523291/1‑141 (MQ=255)
gtgtCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAAcc                                                                                                                                  <  1:474985/141‑1 (MQ=255)
 tgtCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCa                                                                                                                                 <  2:182825/141‑1 (MQ=255)
   tCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCaaa                                                                                                                               >  2:553050/1‑141 (MQ=255)
    cAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTACAATGGACAGATAAGCAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAAGATGATGGATAGTGCAATAGTAATTTTTATATAATCTAACCAAat                                                                                                                              >  1:59611/1‑141 (MQ=255)
       ttttCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATAtt                                                                                                                           >  2:290354/1‑141 (MQ=255)
              aaTCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAACTTAACCAAATATTAATTAAc                                                                                                                    >  2:620198/1‑141 (MQ=255)
                tCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAAccc                                                                                                                  <  1:679120/141‑1 (MQ=255)
                   tCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTACAAAGAACATTATGGATAGTGCAATACTAATTGTTCTATATTGAAACCAAATATTCATTAAGCCGGt                                                                                                               <  1:511045/141‑1 (MQ=255)
                   tCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGt                                                                                                               <  1:600899/141‑1 (MQ=255)
                     cAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGACCATTATGGATAGTGCAATAATAATTGATCTATAATATAACCATATATTCCTTAACACAGTTa                                                                                                             >  2:160012/1‑141 (MQ=255)
                        aGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGGTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTaaaa                                                                                                          >  1:652918/1‑141 (MQ=255)
                          aaaaCGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATg                                                                                                        <  1:116696/141‑1 (MQ=255)
                            aaCGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGaa                                                                                                      >  1:267602/1‑141 (MQ=255)
                            aaCGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAATGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGaa                                                                                                      >  2:349191/1‑141 (MQ=255)
                                     cGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATCATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTtttgt                                                                                             <  2:454814/141‑1 (MQ=255)
                                        aaaaatgtaaaatgAGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTtttgtttg                                                                                          <  2:375873/140‑1 (MQ=255)
                                         aaaatgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTCTATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTttgtttgt                                                                                         <  1:465280/141‑1 (MQ=255)
                                         aaaatgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTttgtttgt                                                                                         <  2:271806/141‑1 (MQ=255)
                                          aaatgtaaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTtgtttgtt                                                                                        <  1:61701/141‑1 (MQ=255)
                                             tggaagatgAGAAGATAAGAAGTGCTGCTAAAGTCAATTTCACATTTAAAAAGAGCATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATAGTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCaa                                                                                     <  2:471828/135‑1 (MQ=255)
                                               taaaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAca                                                                                   <  1:523291/141‑1 (MQ=255)
                                                aaaatgGGAAGATAAACAGTTCTGCTAAAGTCAATTTCACATCTAAACAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAcat                                                                                  <  1:595867/141‑1 (MQ=255)
                                                 aaatgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAcatc                                                                                 <  1:288451/141‑1 (MQ=255)
                                                   atgGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAAcatcat                                                                               <  2:678774/141‑1 (MQ=255)
                                                     gggAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTa                                                                             >  1:411023/1‑141 (MQ=255)
                                                      gaaaGATAAACAGTACTGCTAAAGTCAATTTCCCAGTTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTaa                                                                            <  2:544655/139‑1 (MQ=255)
                                                        aaGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATc                                                                          <  1:483322/141‑1 (MQ=255)
                                                            tAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCActc                                                                      <  1:171808/141‑1 (MQ=255)
                                                            aaaaCCGAGCTGCTAAAGTCAATTTCACATCTAAAAAACACATTATTGATCGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAGCCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCActc                                                                      <  2:543100/140‑1 (MQ=255)
                                                               aaaGTGCTGCTAAAGTCACTTTCACATCAAAAAAGAAAATTACGGAAGGTGCAACAATAAGAGTTAAATAATCAAACCAAATATTCATAAATACAGTTAAAATGAAATCTTTTGTTTGTTCAACATCATGAATCACTCTaa                                                                   >  2:251215/3‑140 (MQ=255)
                                                               aCAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAAGAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAg                                                                   >  2:77944/1‑141 (MQ=255)
                                                                       gctAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACACTAGATATTACt                                                           >  2:105439/1‑141 (MQ=255)
                                                                            aGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGAcc                                                      <  2:226507/141‑1 (MQ=255)
                                                                            aGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGAcc                                                      <  1:553050/141‑1 (MQ=255)
                                                                                    tCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGat                                              <  2:411349/141‑1 (MQ=255)
                                                                                      aaatatAAAAAGAATAATATGTATATTGCAATAACAATGGTTATATAATCGAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGatta                                            <  2:652918/136‑1 (MQ=255)
                                                                                           tAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGc                                       >  1:533112/1‑141 (MQ=255)
                                                                                            aaaaaGAACATTATGGCTAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCa                                      <  2:259961/141‑1 (MQ=255)
                                                                                            aaaaaGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCa                                      <  2:259967/141‑1 (MQ=255)
                                                                                             aaaaGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCAt                                     >  1:632402/1‑141 (MQ=255)
                                                                                               aaGAACATTATGGATAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACCCCACTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATaa                                   <  1:477478/141‑1 (MQ=255)
                                                                                                         tgtaTAGTGCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCAc                         <  2:649455/138‑1 (MQ=255)
                                                                                                         tcgATAGTGCAATAATAATTGTTATATAAGCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCAc                         <  1:594082/139‑1 (MQ=255)
                                                                                                                 gCAATAATAATTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCt                 <  2:84380/141‑1 (MQ=255)
                                                                                                                   aatataaatTGTTATAGAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTg               <  1:251151/135‑1 (MQ=255)
                                                                                                                   aataataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTg               <  1:643503/141‑1 (MQ=255)
                                                                                                                   aataataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTg               <  2:314194/141‑1 (MQ=255)
                                                                                                                   aataataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTg               <  1:399846/141‑1 (MQ=255)
                                                                                                                     taataatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTa             <  1:285418/141‑1 (MQ=255)
                                                                                                                      aataatTGTTATATAATCTTACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAACCCCTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTaa            <  1:251215/141‑1 (MQ=255)
                                                                                                                      aagaatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTaa            <  1:77944/138‑1 (MQ=255)
                                                                                                                        taatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTCCTTGATTATTAGCCTAAACTCTCGCACTTAAATCTTGAAAAt          >  1:105884/1‑141 (MQ=255)
                                                                                                                         aatTGTTATATAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTCATCACTCTAGATATTCCTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATg         >  1:264756/1‑141 (MQ=255)
                                                                                                                               tatataATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTGta   <  1:349191/141‑1 (MQ=255)
                                                                                                                               tatataATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTGta   <  2:267602/141‑1 (MQ=255)
                                                                                                                                atatAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTGtat  <  1:648603/141‑1 (MQ=255)
                                                                                                                                atatAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAAGCTTTTGTTTGTTGAACAGCAATAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTGtat  <  1:160012/141‑1 (MQ=255)
                                                                                                                                   |                                                                                                                                         
GTGTCAATTTTCTTAATCTTCCAAAGAAAACGTACACCGTTAAAATGTAAAATGGGAAGATAAACAGTGCTGCTAAAGTCAATTTCACATCTAAAAAGAACATTATGGATAGTGCAATAATAATTGTTATACAATCTAACCAAATATTCATTAACCCGGTTAAAATGAAATCTTTTGTTTGTTCAACATCATTAATCACTCTAGATATTACTTGACCTACTTGATTATTAGCATAAAATCTCGCACTTAAAGCTTGTAAATGGTTGTAT  >  USA300TCH1516_ALE/2010232‑2010500

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