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
A4 F1 I1 R1 765 39.6 1867486 94.4% 1762906 108.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 932,340 (A)8→7 intergenic (‑290/‑255) trxB ← / → lrp thioredoxin reductase, FAD/NAD(P)‑binding/leucine‑responsive global transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913932,3330A.100.0% 164.7 / NA 38intergenic (‑283/‑262)trxB/lrpthioredoxin reductase, FAD/NAD(P)‑binding/leucine‑responsive global transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (19/19);  total (19/19)

CTACTTAAATTTCCCGCTTTATAAGCCGATTAAATGATGAATAAACGCCCCTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAGAAAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTAAATACCATGTTTACCGTGCTAGTGAAATCTACGTATGGCGTGGACAGACGCCATTCGTGATGTCGATAGCTGCCACAAGGCAACGGTCTT  >  NC_000913/932196‑932463
                                                                                                                                         |                                                                                                                                  
cTACTTAAATTTCCCGCTTTATAAGCCGATTAAATGATGAATAAACGCCCCTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGgaagaa                                                                                                                                   <  1:476114/139‑1 (MQ=255)
     tAAATTTCCCGCTTTATAAGCCGATTAAATGATGAATAAACGCCCCTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAGaaaaaaa                                                                                                                              <  1:83124/139‑1 (MQ=255)
         tttCCCGCTTTATAAGCCGATTAAATGATGAATAAACGCCCCTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAGaaaaaaacagt                                                                                                                          <  1:55639/139‑5 (MQ=255)
         tttCCCGCTTTATAAGCCGATTAAATGATGAATAAACGCCCCTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAGaaaaaaacagt                                                                                                                          <  2:324339/139‑5 (MQ=255)
          ttCCCGCTTTATAAGCCGATTAAATGATGAATAAACGCCCCTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTa                                                                                                                        <  1:324473/139‑1 (MQ=255)
                   tataAGCCGATTAAATGATGAATAAACGCCCCTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTatat                                                                                                               >  1:898725/1‑139 (MQ=255)
                      aaGCCGATTAAATGATGAATAAACGCCCCTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATgcg                                                                                                            <  1:798102/139‑1 (MQ=255)
                           gATTAAATGATGAATAAACGCCCCTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAATACAGTATTCTTATATGCGCATaa                                                                                                       >  2:134929/1‑139 (MQ=255)
                             ttAAATGATGAATAAACGCCCCTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTtat                                                                                                                 >  1:14498/1‑127 (MQ=255)
                             ttAAATGATGAATAAACGCCCCTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTtat                                                                                                                 <  2:14498/127‑1 (MQ=255)
                             ttAAATGATGAATAAACGCCCCTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAAcc                                                                                                     <  2:354450/139‑1 (MQ=255)
                                aaTGATGAATAAACGCCCCTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACcatg                                                                                                  <  1:731629/139‑1 (MQ=255)
                                aaTGATGAATAAACGCCCCTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACcatg                                                                                                  <  1:134929/139‑1 (MQ=255)
                                       aaTAAACGCCCCTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTaa                                                                                           >  2:411913/1‑139 (MQ=255)
                                           aaCGCCCCTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTAAATAc                                                                                       <  2:700797/139‑1 (MQ=255)
                                             cGCCCCTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAGaaaaaaa                                                                                                                              <  2:63990/99‑1 (MQ=255)
                                             cGCCCCTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAGaaaaaaa                                                                                                                              >  1:63990/1‑99 (MQ=255)
                                               ccccTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTAAATACCATg                                                                                   >  1:704096/1‑139 (MQ=255)
                                                 ccTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAGaaaaaaa                                                                                                                              >  1:786124/1‑95 (MQ=255)
                                                 ccTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAGaaaaaaa                                                                                                                              <  2:786124/95‑1 (MQ=255)
                                                  cTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAGaaaa                                                                                                                                 <  1:906814/91‑1 (MQ=255)
                                                  cTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAGaaaa                                                                                                                                 >  2:906814/1‑91 (MQ=255)
                                                   tGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAGaaaaaaa                                                                                                                              >  2:900861/1‑93 (MQ=255)
                                                   tGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAGaaaaaaa                                                                                                                              <  1:900861/93‑1 (MQ=255)
                                                             tatCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACcatg                                                                                                  <  1:415404/110‑1 (MQ=255)
                                                             tatCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACcatg                                                                                                  >  2:415404/1‑110 (MQ=255)
                                                             tatCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTAAATACCATGTGTACCGTGCTAGt                                                                     >  2:555515/1‑139 (MQ=255)
                                                               tCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTAAATACCATGTTTACCGTGCTAGt                                                                     >  1:918/1‑137 (MQ=255)
                                                               tCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTAAATACCATGTTTACCGTGCTAGt                                                                     <  2:918/137‑1 (MQ=255)
                                                               tCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTAAATACCATGTTTACCGTGCTAGTGa                                                                   >  2:266402/1‑139 (MQ=255)
                                                                 tGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTAAATACCATGTTTACCGTGCTAGTGaaa                                                                 <  1:303323/139‑1 (MQ=255)
                                                                  ggCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAGaaaaaaaca                                                                                                                            <  2:102339/80‑3 (MQ=255)
                                                                  ggCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAGaaaaaaaca                                                                                                                            >  1:102339/1‑78 (MQ=255)
                                                                    cATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTAAATACCATGTTTACCGTGCTAGTGAAATCt                                                              >  2:121949/1‑139 (MQ=255)
                                                                        ttgtACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGAGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTAAATACCATGTTTACCGTGCTAGTGAAATCTACGt                                                          <  1:555515/139‑1 (MQ=255)
                                                                         tgtACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTAAATAc                                                                                       <  2:314877/109‑1 (MQ=255)
                                                                         tgtACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTAAATAc                                                                                       >  1:314877/1‑109 (MQ=255)
                                                                         tgtACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTAAATACCATGTTTACCGTGCTAGTGAAATCTACGTa                                                         >  1:334595/1‑139 (MQ=255)
                                                                             cTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAAcc                                                                                                     >  2:21793/1‑91 (MQ=255)
                                                                             cTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAAcc                                                                                                     <  1:21793/91‑1 (MQ=255)
                                                                                 aaaTCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTAAATACCATGTTTACCGTGCTAGTGAAATCTACGTATGGCGTgg                                                 >  2:292831/1‑139 (MQ=255)
                                                                                     cGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATaa                                                                                                       >  1:821348/1‑81 (MQ=255)
                                                                                     cGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATaa                                                                                                       <  2:821348/81‑1 (MQ=255)
                                                                                     cGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTAAATACCATGTTTAcc                                                                             <  1:392497/107‑1 (MQ=255)
                                                                                     cGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTAAATACCATGTTTAcc                                                                             >  2:392497/1‑107 (MQ=255)
                                                                                       aTGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAGaaaaaaaca                                                                                                                            >  2:425643/1‑57 (MQ=255)
                                                                                       aTGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAGaaaaaaaca                                                                                                                            <  1:425643/59‑3 (MQ=255)
                                                                                       aTGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTAAATACCATGTTTACCGTGCTAGTGAAATCTACGTATGGCGTGGACAGAc                                           >  1:1261/1‑139 (MQ=255)
                                                                                              gCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTAAATACCATGTTTACCGTGCTAGTGAAATCTACGTATGGCGTGGACAGACGCCATTc                                    <  2:334595/139‑1 (MQ=255)
                                                                                                    aCAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAGaaaaaaaca                                                                                                                            >  2:471570/1‑44 (MQ=255)
                                                                                                    aCAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAGaaaaaaaca                                                                                                                            <  1:471570/46‑3 (MQ=255)
                                                                                                                 gtTTTGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTAAATACCATGTTTACCGTGCTAGTGAAATCTACGTATGGCGTGGACAGACGCCATTCGTGATGTCGATAGCTGCca                 <  1:121949/139‑1 (MQ=255)
                                                                                                                  ttttGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTAAATACCATGTTTACCGTGCTAGTGAAATCTACGt                                                          >  2:586027/1‑97 (MQ=255)
                                                                                                                  ttttGCGAAAACATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTAAATACCATGTTTACCGTGCTAGTGAAATCTACGt                                                          <  1:586027/97‑1 (MQ=255)
                                                                                                                          aaaCATTCGAGGAAG‑AAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTAAATACCATGTTTACCGTGCTAGTGAAATCTACGTATGGCGTGGACAGACGCCATTCGTGATGTCGCTAGCTGCCACAAGGCAAc        <  2:515889/139‑1 (MQ=255)
                                                                                                                                tCGAGGAAG‑AAAAAAACAGTAATCTTATATGCGCATAACCATGCATGTAAATACCATGTTTACCGTGCTAGTGAAATCTACGTATGGCGTGGACAGACGCCATTCGTGATGTCGATAGCTGCCACAAGGCAACGGtctt  >  1:11108/1‑139 (MQ=255)
                                                                                                                                         |                                                                                                                                  
CTACTTAAATTTCCCGCTTTATAAGCCGATTAAATGATGAATAAACGCCCCTGTTAATGAATATCTGGCATGTTGTACTAAAAATCGATGTTTTGCTTTGACAATCCCCTGGTGTTTTGCGAAAACATTCGAGGAAGAAAAAAAACAGTATTCTTATATGCGCATAACCATGCATGTAAATACCATGTTTACCGTGCTAGTGAAATCTACGTATGGCGTGGACAGACGCCATTCGTGATGTCGATAGCTGCCACAAGGCAACGGTCTT  >  NC_000913/932196‑932463

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A