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
A122 F1 I1 R1 27 151.2 10056804 92.4% 9292486 76.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA REL606 3,911,991 (T)5→4 intergenic (‑192/‑131) yifB ← / → ilvL predicted bifunctional enzyme and transcriptional regulator/ilvG operon leader peptide

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*REL6063,911,9870T.92.1% 590.6 / 49.6 141intergenic (‑188/‑135)yifB/ilvLpredicted bifunctional enzyme and transcriptional regulator/ilvG operon leader peptide
Reads supporting (aligned to +/- strand):  ref base T (4/7);  new base . (55/74);  total (60/81)
Fisher's exact test for biased strand distribution p-value = 7.60e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.42e-01

Only 100 of 159 total aligned reads displayed.

GCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCGGCCAAAAAATATCTTGTAC  >  REL606/3911913‑3912058
                                                                           |                                                                       
  ggACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTattttatttt                                                                      <  2:1919241/76‑1 (MQ=255)
  ggACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTattttatttt                                                                      <  2:2043838/76‑1 (MQ=255)
    aCAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTattttattttaa                                                                    >  1:45372/1‑74 (MQ=255)
    aCAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTATTTTTa                                                                    >  1:1554215/1‑76 (MQ=255)
     cAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTATTTTaaa                                                                   <  1:785639/76‑1 (MQ=255)
     cAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTATTTTaaa                                                                   <  2:489922/76‑1 (MQ=255)
     cAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTATTTTaaa                                                                   >  2:4384669/1‑76 (MQ=255)
      aaaGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTATTTTaaaa                                                                  <  1:4372996/76‑1 (MQ=255)
      aaaGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTATTTTaaaa                                                                  <  2:1606090/76‑1 (MQ=255)
       aaGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTATTTTAaaaa                                                                 <  1:778258/76‑1 (MQ=255)
         ggATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTATTTTaaaaaac                                                               >  2:832949/1‑75 (MQ=255)
          gATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAaaca                                                             >  1:893067/1‑76 (MQ=255)
           aTGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAaacaa                                                            >  1:3600658/1‑76 (MQ=255)
           aTGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAaacaa                                                            <  2:4415330/76‑1 (MQ=255)
            tGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAaacaac                                                           <  1:3720377/76‑1 (MQ=255)
            tGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAaacaac                                                           <  2:975898/76‑1 (MQ=255)
            tGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAaacaac                                                           <  2:1095947/76‑1 (MQ=255)
            tGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAaacaac                                                           <  1:4224367/76‑1 (MQ=255)
             gAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAacaaca                                                          <  2:2505458/76‑1 (MQ=255)
             gAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAacaaca                                                          <  1:4681748/76‑1 (MQ=255)
             gAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAacaaca                                                          <  1:2587245/76‑1 (MQ=255)
              aaCTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAAcaacaa                                                         <  2:2443296/76‑1 (MQ=255)
              aaCTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAAcaacaa                                                         >  2:4162846/1‑76 (MQ=255)
              aaCTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAAcaacaa                                                         <  2:1006895/76‑1 (MQ=255)
               aCTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAAt                                                        <  1:2536743/76‑1 (MQ=255)
               aCTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAAt                                                        <  2:3599427/76‑1 (MQ=255)
               aCTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAAt                                                        <  1:1009925/76‑1 (MQ=255)
                cTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAAtt                                                       >  1:4945285/1‑76 (MQ=255)
                cTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAAtt                                                       <  1:4582933/76‑1 (MQ=255)
                 tACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAAttt                                                      <  2:1576295/76‑1 (MQ=255)
                    gAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTtata                                                   <  1:3044186/76‑1 (MQ=255)
                    gAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTtata                                                   <  2:2190721/76‑1 (MQ=255)
                    gAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTtata                                                   >  2:252561/1‑76 (MQ=255)
                     aGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTatat                                                  >  2:4822228/1‑76 (MQ=255)
                      ggAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATAtt                                                 <  1:1587717/76‑1 (MQ=255)
                        aaGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGa                                               <  1:1033898/76‑1 (MQ=255)
                         aGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGaa                                              <  2:1990145/76‑1 (MQ=255)
                         aGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGaa                                              >  2:1834501/1‑76 (MQ=255)
                             aacaacATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAatta                                          >  2:4007473/1‑76 (MQ=255)
                                aacaTTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAAttatta                                       <  2:4472456/76‑1 (MQ=255)
                                aacaTTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAAttatta                                       >  1:3671680/1‑76 (MQ=255)
                                aacaTTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAAttatta                                       <  1:2937191/76‑1 (MQ=255)
                                aacaTTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAAttatta                                       >  1:561530/1‑76 (MQ=255)
                                  caTTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTaaa                                     <  2:1775003/76‑1 (MQ=255)
                                  caTTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTaaa                                     >  2:456896/1‑76 (MQ=255)
                                  caTTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTaaa                                     <  2:2711779/76‑1 (MQ=255)
                                  caTTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTaaa                                     <  1:4169787/76‑1 (MQ=255)
                                   aTTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAAc                                    >  2:2809802/1‑76 (MQ=255)
                                    ttCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACg                                   <  1:4484331/76‑1 (MQ=255)
                                     tCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGc                                  <  1:61345/76‑1 (MQ=255)
                                       aTACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGcat                                <  1:1475813/76‑1 (MQ=255)
                                        tACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGcatc                               >  1:2060092/1‑76 (MQ=255)
                                        tACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGcatc                               >  1:2498991/1‑76 (MQ=255)
                                        tACTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGcatc                               <  1:2787457/76‑1 (MQ=255)
                                         aCTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGcatca                              >  2:4278415/1‑76 (MQ=255)
                                         aCTGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGcatca                              <  1:1691410/76‑1 (MQ=255)
                                          cTGAAATTGAATTTTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGcatc                               <  1:1508911/76‑1 (MQ=255)
                                           tGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATa                            <  2:309910/76‑1 (MQ=255)
                                           tGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATa                            >  1:2684083/1‑76 (MQ=255)
                                           tGAAATTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATa                            <  2:4732293/76‑1 (MQ=255)
                                             aaaTTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATaaa                          <  1:3111458/76‑1 (MQ=255)
                                             aaaTTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATaaa                          <  2:2835829/76‑1 (MQ=255)
                                             aaaTTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATaaa                          <  1:3302525/76‑1 (MQ=255)
                                              aaTTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATaaaa                         <  2:1697685/76‑1 (MQ=255)
                                              aaTTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATaaaa                         <  2:2603004/76‑1 (MQ=255)
                                               aTTGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATaaaaa                        >  1:4680755/1‑76 (MQ=255)
                                               aTTGAA‑TTTGTTTCGCTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATaaaaa                        <  1:1239307/76‑1 (MQ=255)
                                                ttGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAAt                       >  2:1205952/1‑76 (MQ=255)
                                                ttGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAAt                       <  1:4498666/76‑1 (MQ=255)
                                                ttGAA‑TTTTTTTCACTCACTATTTT‑GTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAAt                       >  1:5004415/1‑76 (MQ=255)
                                                 tGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATc                      >  2:920909/1‑76 (MQ=255)
                                                 tGAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATc                      >  1:891672/1‑76 (MQ=255)
                                                  gAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCg                     >  1:3404391/1‑76 (MQ=255)
                                                  gAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCg                     >  1:4898908/1‑76 (MQ=255)
                                                  gAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCg                     >  1:1622107/1‑76 (MQ=255)
                                                  gAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCg                     <  2:3378945/76‑1 (MQ=255)
                                                  gAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCg                     >  2:4510438/1‑76 (MQ=255)
                                                  gAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCg                     >  1:185942/1‑76 (MQ=255)
                                                  gAA‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCg                     >  1:3223622/1‑76 (MQ=255)
                                                   aa‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCgg                    >  2:3303005/1‑76 (MQ=255)
                                                   aa‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCgg                    >  2:3886056/1‑76 (MQ=255)
                                                   aa‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCgg                    <  2:605818/76‑1 (MQ=255)
                                                    a‑TTTTTTTCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCGGc                   <  2:522990/76‑1 (MQ=255)
                                                       ttttttCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCGGCCa                 <  2:2722452/76‑1 (MQ=255)
                                                       ttttttCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCGGCCa                 >  1:3929752/1‑76 (MQ=255)
                                                       ttttttCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCGGCCa                 >  1:1349111/1‑76 (MQ=255)
                                                         ttttCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCGGCCaaa               <  1:961249/76‑1 (MQ=255)
                                                          tttCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCGGCCaaaa              >  2:3535052/1‑76 (MQ=255)
                                                          tttCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCGGCCaaaa              <  2:621883/76‑1 (MQ=255)
                                                           ttCACTCACTATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCGGCCaaaaa             <  1:669997/76‑1 (MQ=255)
                                                               ctcactATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCGGCCAAAAAatat         <  1:4105293/76‑1 (MQ=255)
                                                                 cactATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCGGCCAAAAAATATCt       >  1:2559957/1‑76 (MQ=255)
                                                                   ctATTTTA‑TTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCGGCCAAAAAATATCTTg     >  1:3376093/1‑76 (MQ=255)
                                                                    tatttta‑tttTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCGGCCAAAAAATATCTTGt    >  1:2238022/1‑76 (MQ=255)
                                                                    tatttta‑tttTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCGGCCAAAAAATATCTTGt    >  1:1152025/1‑76 (MQ=255)
                                                                     attttattttTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCGGCCAAAAAATATCTTGt    <  1:3247538/76‑1 (MQ=255)
                                                                     atttta‑ttttAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCGGCCAAAAAATATCTTGTa   >  1:1254620/1‑76 (MQ=255)
                                                                     atttta‑ttttAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCGGCCAAAAAATATCTTGTa   >  1:1072899/1‑76 (MQ=255)
                                                                      ttttattttTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCGGCCAAAAAATATCTTGTa   <  2:1021382/76‑1 (MQ=255)
                                                                      tttta‑ttttaAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCGGCCAAAAAATATCTTGTAc  >  1:1965544/1‑76 (MQ=255)
                                                                           |                                                                       
GCGGACAAAGGATGAACTACGAGGAAGGGAACAACATTCATACTGAAATTGAA‑TTTTTTTCACTCACTATTTTATTTTTAAAAAACAACAATTTATATTGAAATTATTAAACGCATCATAAAAATCGGCCAAAAAATATCTTGTAC  >  REL606/3911913‑3912058

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A