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
A5 F178 I0 R1 41 49.4 1100758 95.6% 1052324 140.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 607,884 G→A 100% R209* (CGA→TGA)  dck ← Deoxyadenosine/deoxycytidine kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE607,8840GA100.0% 169.8 / ‑6.5 63R209* (CGA→TGA) dckDeoxyadenosine/deoxycytidine kinase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (29/33);  minor base C (0/1);  total (29/34)
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.

TGTGAATTAATGTATTCGATAGAATTGATAAAATAA‑TCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTTTC  >  USA300TCH1516_ALE/607751‑608017
                                                                                                                                      |                                                                                                                                     
tgtgAATTAATGTATTCGATAGAATTGATAAAATAA‑TCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAAt                                                                                                                                 <  2:197934/140‑1 (MQ=255)
   gAATTAATGTATGCCATAAAATTGATAAAATAA‑TCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTTTAGAGGTTTGAATAATTCAAGCAAtttt                                                                                                                              <  2:117757/140‑1 (MQ=255)
    aaTTAATGTATTCGATAGAATTGATAAAATAA‑TCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTg                                                                                                                             <  2:460055/140‑1 (MQ=255)
    aaTTAATGTATTCGATAGAATTGAAAAAATAA‑TCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTAAAGCAATTTTg                                                                                                                             >  2:49025/1‑140 (MQ=255)
       tAATGTATTCGATAGAATTGATAAAATAA‑TCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGGTATGTTTGAATAATTAAAGCAATTTTGttt                                                                                                                          >  2:347770/1‑140 (MQ=255)
        aaTGTATTCGATAGAATTGATAAAATAA‑TCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTa                                                                                                                         <  1:45781/140‑1 (MQ=255)
          tGTATTCGATAGAATGTATAAAATAATTCCTTAAGCTGT‑TGCATTTTACAGTGAATATAAACATATACGCTATGTCTTTAGACTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCCAGCAATTCTGTTTATc                                                                                                                       <  2:113942/140‑1 (MQ=255)
            tATTCGATAGGATTGATAAAATAA‑TTGATAATATCTATGGAATATACATTGAATATGAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCAt                                                                                                                     <  2:99548/140‑1 (MQ=255)
            tATTCGATAGAATTGATAAAATAA‑TCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCAt                                                                                                                     <  1:360755/140‑1 (MQ=255)
            tATTCGATAGAATTGATAAAATAA‑TCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATATACTTGTCGATATGTTTGAATAATTCAAACAAATTTGTTTATCAt                                                                                                                     >  2:472004/1‑140 (MQ=255)
              ttCGATAGAATTGATAAAATAA‑TCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAg                                                                                                                   >  1:321063/1‑140 (MQ=255)
                    aGAATTGATAAAATAA‑TCGATAATATTTATGGAATATACATTGAATATAAACATATATGCTATTTCTTTTGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTa                                                                                                             <  1:63372/140‑1 (MQ=255)
                    aGAATTGATAAAATAA‑TCGATAATATCTATGGAATATACATTGAATATAAACATATATGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTa                                                                                                             >  2:386880/1‑140 (MQ=255)
                    aGAATTGATAAAATAA‑TCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTa                                                                                                             >  2:165824/1‑140 (MQ=255)
                    aGAATTGATAAAATAA‑TCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTATCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTa                                                                                                             >  1:78903/1‑140 (MQ=255)
                        ttGATAAAATAA‑TCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGa                                                                                                         <  2:402280/140‑1 (MQ=255)
                          gATAAAATAA‑TCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGAtt                                                                                                       <  1:221815/140‑1 (MQ=255)
                          gATAAAATAA‑CCGAAAATATTTATGGAATATACAGTGACTATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGGAATTTTGTTTATCATAGGATTTAAAGAtt                                                                                                       <  2:119634/140‑1 (MQ=255)
                                     tCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCtt                                                                                             <  1:35361/140‑1 (MQ=255)
                                        ataataTCTATGGAATATACATTGAATATAAACATATACGCTATGTGTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATg                                                                                          >  2:334925/1‑140 (MQ=255)
                                           atatCCATAGAATATAAATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGat                                                                                       <  2:395643/140‑1 (MQ=255)
                                            tatCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGata                                                                                      >  1:117689/1‑140 (MQ=255)
                                             atCTATGGAATATCCATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTTTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGCatat                                                                                     <  1:393479/140‑1 (MQ=255)
                                                tATGGAATATACATTGAATATAAACATGTACGCTATGTCTTTAGTCTTTTACCGTGTATTTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCat                                                                                  >  1:15943/1‑140 (MQ=255)
                                                 aTGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGTAATTTTGTTTATCATAGGATTTAAAGAGTCGGGGTCCTTATGGATATCata                                                                                 <  1:414018/140‑1 (MQ=255)
                                                   ggAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATAtt                                                                               <  1:340252/140‑1 (MQ=255)
                                                   ggAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATAtt                                                                               <  1:49025/140‑1 (MQ=255)
                                                    gAATATACATTGAATATAATCATATAGGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTc                                                                              <  1:122137/140‑1 (MQ=255)
                                                     aaTATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCa                                                                             >  1:235657/1‑140 (MQ=255)
                                                      atatACATTGAATATAAACATATAGGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTAAAGCAATTTTGTTTATCATATGATTTAAAGATTCGGGGTTCTTATGGATATTttatttat                                                                            >  1:244370/1‑140 (MQ=255)
                                                      atatACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTCTCGTGTATCTACTTGTAGTTTTGTTTGGATATTTCAAGCATTTTTATATACGAAATTAATTATAGATTAGAGTTCCTTATGGATATCATATTCAt                                                                            >  1:259896/1‑140 (MQ=255)
                                                             ttGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTAGACGATATGTTTAAATAATTCAAGCAATTATGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATAtt                                                                     >  1:457858/1‑140 (MQ=255)
                                                                   ataAACATATACGCTATGTCTTTAGTCCTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTAAAAGATTCGGGGTCCTTATGGATATCATCTTCTTTAATTTTGATACg                                                               >  2:110008/1‑140 (MQ=255)
                                                                   ataAACATATACGCTATGGGGATATGCAGTGATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATGTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACg                                                               <  2:523196/140‑1 (MQ=255)
                                                                    ttaaCATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGt                                                              <  1:85420/138‑1 (MQ=255)
                                                                    taAACATATACGTTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGt                                                              <  2:112660/140‑1 (MQ=255)
                                                                     aaaCATATACGCTATTTCTTTAGTCTTTTATTGTGTATTTACTTGTCGATATTTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTa                                                             <  1:183828/140‑1 (MQ=255)
                                                                        cATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATTATAGGATTTTAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGTTACTTACaa                                                          >  1:261585/1‑140 (MQ=255)
                                                                           ataCGCTATGTCTTTAGTCTTTTATCGTGTATCTCCTTGCCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTg                                                       >  2:2669/1‑140 (MQ=255)
                                                                               gCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGCCa                                                   >  2:297372/1‑140 (MQ=255)
                                                                               gCTATGTCTTTAGACTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTAAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGACCTTATGGATATAATATTCATTAATATTGATACGTACAACTGGACa                                                   >  2:539051/1‑140 (MQ=255)
                                                                                  atgcttttAGTTTTTTATCGTGTATCTACTTGTTGATATGTTTGAATAATTTAAGTAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGc                                                <  1:341545/135‑1 (MQ=255)
                                                                                  aTGTCATTAGTCTTTTAACGTGTATCTACTTGGCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAACGATTCGGGGTCCTTATGGATAGCATATTCATTAATATTGATACGTACAACTGGACATGc                                                <  2:197466/140‑1 (MQ=255)
                                                                                   tGTATTGAGTCTTTTATCGTGTATCTACTTGTTGATATTGTTTAACAATTCAAGCAATTTCGTTTATCATAGGATTTAAAGATTCGGGGTCCTTAGGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCa                                               <  1:87898/140‑1 (MQ=255)
                                                                                     tCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCAtt                                             >  1:184335/1‑140 (MQ=255)
                                                                                         tAGTCTTTTATCGTTTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAg                                         <  2:117689/140‑1 (MQ=255)
                                                                                         tAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAg                                         <  1:509997/140‑1 (MQ=255)
                                                                                          aGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATACTTCACGCAATTTCGTTTATCATAGGCTTTGGAATTTCAGCTCCCTGGTGGAGAGCATATGCAGTAAGATTGATACTTACAACTGGACATGCATTAAAGc                                        >  2:264854/1‑140 (MQ=255)
                                                                                              ttttATTGGGTATTTACTTGTCGATATGTTTGAATAATTCAGGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTTCTTATGGATATCAGATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTAtt                                    <  2:480133/140‑1 (MQ=255)
                                                                                              ttttATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCTATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATACTGATTATTTCGTGTGGACATGCATTAAAGCGAtt                                    <  1:543892/140‑1 (MQ=255)
                                                                                                ttATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTaa                                  <  2:64624/140‑1 (MQ=255)
                                                                                                ttATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTaa                                  <  2:513280/140‑1 (MQ=255)
                                                                                                         aTCTACTTGTCGATATGTTTTAATAATTCAAGTAATTTTTTTTATTATAGGATTTAAATATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGt                         <  1:58486/140‑1 (MQ=255)
                                                                                                         aTCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTTATACGTACAACTGGAAATGCATTAAAGCTATTAATCCAATCGt                         >  1:195981/1‑140 (MQ=255)
                                                                                                         aTCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATAATATTCACATAAACTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGt                         >  1:426252/1‑140 (MQ=255)
                                                                                                                 gttgATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATTGTCATCGCGt                 <  2:120269/137‑1 (MQ=255)
                                                                                                                 gTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAACTCTTAATTCAATCGTCATAGCGt                 >  1:111117/1‑140 (MQ=255)
                                                                                                                  tCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATAAGTACAACTGGACATGCATTAAAGCTATTAATCCAATCATCATAGCGtt                >  1:329806/1‑140 (MQ=255)
                                                                                                                       atGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATTGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAACGCTCTTAATCCAATCGTCATACCGTTTAAAt           <  2:267080/140‑1 (MQ=255)
                                                                                                                              aataatTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCtttt    >  1:520271/1‑140 (MQ=255)
                                                                                                                              aataatTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCtttt    >  2:225922/1‑140 (MQ=255)
                                                                                                                              aataatTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCtttt    >  1:427346/1‑140 (MQ=255)
                                                                                                                                taatTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTTTc  >  1:96435/1‑140 (MQ=255)
                                                                                                                                      |                                                                                                                                     
TGTGAATTAATGTATTCGATAGAATTGATAAAATAA‑TCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTTTC  >  USA300TCH1516_ALE/607751‑608017

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