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
A112 F1 I1 R1 17 249.1 16570612 93.0% 15410669 76.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA REL606 4,162,570 T→A I572N (ATC→AAC)  rpoB → DNA‑directed RNA polymerase subunit beta

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*REL6064,162,5700TA98.9% 1080.1 / 1.4 262I572N (ATC→AAC) rpoBDNA‑directed RNA polymerase subunit beta
Reads supporting (aligned to +/- strand):  ref base T (3/0);  new base A (128/131);  total (131/131)
Fisher's exact test for biased strand distribution p-value = 2.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.97e-01

Only 100 of 271 total aligned reads displayed.

CGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCGTATCGTAAAGTGACCGA  >  REL606/4162497‑4162642
                                                                         |                                                                        
cGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACa                                                                        <  2:5575536/76‑1 (MQ=255)
cGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACa                                                                        >  2:5306832/1‑76 (MQ=255)
   gaggTACGCCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAAct                                                                     <  1:1540007/73‑1 (MQ=255)
      gTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAActctc                                                                  >  1:3159857/1‑76 (MQ=255)
       tACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAActctct                                                                 >  1:130113/1‑76 (MQ=255)
       tACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAActctct                                                                 >  2:2521708/1‑76 (MQ=255)
        acacCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTg                                                                <  2:2275720/76‑1 (MQ=255)
        acacCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTg                                                                >  1:7167576/1‑76 (MQ=255)
        acacCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTg                                                                >  1:3572894/1‑76 (MQ=255)
        acacCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTg                                                                >  1:939377/1‑76 (MQ=255)
         cacCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGt                                                               >  2:6998197/1‑76 (MQ=255)
          acCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTc                                                              >  1:7729265/1‑76 (MQ=255)
            ccGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCg                                                            <  2:2081265/76‑1 (MQ=255)
            ccGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCg                                                            >  2:5473779/1‑76 (MQ=255)
            ccGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCg                                                            <  2:48304/76‑1 (MQ=255)
              gACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCgtg                                                          >  1:4217993/1‑76 (MQ=255)
              gACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCgtg                                                          >  1:5783497/1‑76 (MQ=255)
              gACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCgtg                                                          <  2:1842515/76‑1 (MQ=255)
              gACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCgtg                                                          >  2:2882741/1‑76 (MQ=255)
               gcTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCgtgt                                                         <  2:5956537/75‑1 (MQ=255)
               aCTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCgtgt                                                         >  1:7416946/1‑76 (MQ=255)
               aCTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCgtgt                                                         >  2:409960/1‑76 (MQ=255)
               aCTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCgtgt                                                         >  2:1069910/1‑76 (MQ=255)
                cTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTa                                                        >  1:6921925/1‑76 (MQ=255)
                    cTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGca                                                    <  1:5058330/76‑1 (MQ=255)
                    cTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGca                                                    <  1:823345/76‑1 (MQ=255)
                     tACGGTCGCGTATGCCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGcac                                                   <  1:5707565/76‑1 (MQ=255)
                      aCGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGcaca                                                  >  2:5791199/1‑76 (MQ=255)
                      aCGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGcaca                                                  <  1:6679773/76‑1 (MQ=255)
                       cGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAg                                                 <  2:6004415/76‑1 (MQ=255)
                        ggTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGa                                                >  1:5873377/1‑76 (MQ=255)
                         gTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGAc                                               >  1:544950/1‑76 (MQ=255)
                          tCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACt                                              >  2:6329214/1‑76 (MQ=255)
                          tCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACt                                              <  1:5609242/76‑1 (MQ=255)
                           cgcgTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTa                                             >  1:4454382/1‑76 (MQ=255)
                           cgcgTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTa                                             >  2:4429153/1‑76 (MQ=255)
                           cgcgTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTa                                             <  2:6845629/76‑1 (MQ=255)
                           cgcgTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTa                                             <  1:7911675/76‑1 (MQ=255)
                            gcgTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTaa                                            <  1:6299661/76‑1 (MQ=255)
                            gcgTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTaa                                            >  1:7958969/1‑76 (MQ=255)
                             cgTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTAAc                                           >  2:370743/1‑76 (MQ=255)
                              gTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACg                                          >  1:5369245/1‑76 (MQ=255)
                              gTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACg                                          <  2:5712500/76‑1 (MQ=255)
                              gTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACg                                          <  2:900987/76‑1 (MQ=255)
                              gTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACg                                          <  2:499907/76‑1 (MQ=255)
                              ctATGTCGAATCTAACACCTTGACGTTCCGAACAGCCGTCTAAACACTTCTCAGTCCGTGGACCCACAGACTAACg                                          <  2:499908/75‑1 (MQ=255)
                                aTGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGaa                                        <  2:6950066/76‑1 (MQ=255)
                                aTGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGaa                                        >  1:1847477/1‑76 (MQ=255)
                                 tGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAAt                                       <  1:6492485/76‑1 (MQ=255)
                                 tGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAAt                                       >  1:6074360/1‑76 (MQ=255)
                                 tGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAAt                                       <  1:1200203/76‑1 (MQ=255)
                                 tGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAAt                                       <  1:2448327/76‑1 (MQ=255)
                                 attCCAATCGAAACCCCTGAAGGTCCGACCATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAAt                                       <  2:753301/74‑1 (MQ=255)
                                  gTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATa                                      <  2:8240877/76‑1 (MQ=255)
                                  gTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATa                                      <  2:6792162/76‑1 (MQ=255)
                                   tCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATAc                                     >  1:2997459/1‑76 (MQ=255)
                                   tCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATAc                                     >  1:1627318/1‑76 (MQ=255)
                                    ccAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACg                                    >  2:7671762/1‑76 (MQ=255)
                                    ccAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACg                                    >  2:392624/1‑76 (MQ=255)
                                     cAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACgg                                   >  2:7358257/1‑76 (MQ=255)
                                     cAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACgg                                   <  2:1238594/76‑1 (MQ=255)
                                     cAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACgg                                   >  2:2775406/1‑76 (MQ=255)
                                     cAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACACACTAACGAATACgg                                   >  2:796068/1‑76 (MQ=255)
                                       aTCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCt                                 <  1:7106411/76‑1 (MQ=255)
                                       aTCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCt                                 <  1:3968926/76‑1 (MQ=255)
                                        tCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCtt                                <  1:1074099/76‑1 (MQ=255)
                                        tCGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCtt                                <  1:7772756/76‑1 (MQ=255)
                                         cGAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTc                               >  1:2065588/1‑76 (MQ=255)
                                          gAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCtttc                              >  2:3460027/1‑74 (MQ=255)
                                          gAAACCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCtttc                              >  1:2713182/1‑74 (MQ=255)
                                            acccccGGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCtt                            <  2:2599198/74‑1 (MQ=255)
                                            aaCCCCTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCtt                            <  2:3376252/76‑1 (MQ=255)
                                               cccTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTgag                         <  1:7251637/76‑1 (MQ=255)
                                                 cTGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTTCTTTAGAc                       >  2:6648747/1‑76 (MQ=255)
                                                  tGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACt                      <  1:3717910/76‑1 (MQ=255)
                                                  tGAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACt                      <  2:4290615/76‑1 (MQ=255)
                                                  tGAAGGTCCAAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACt                      >  1:6158921/1‑76 (MQ=255)
                                                   gAAGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTTCTTTCGACTc                     >  2:7793930/1‑76 (MQ=255)
                                                    aaGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACttc                    >  2:7249803/1‑74 (MQ=255)
                                                     aGGTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCg                   <  2:3240418/76‑1 (MQ=255)
                                                      ggTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTccct                  >  1:1678527/1‑74 (MQ=255)
                                                      ggTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCGt                  <  1:3058636/76‑1 (MQ=255)
                                                      gatCCGAACATCGGTCTGAACACGTCGCTGTCCGTGTACGCACAGCCTAACGAATACGGCTTCCTTGAGACTCCGt                  <  2:1679463/74‑1 (MQ=255)
                                                       gTCCGAACATCGGTCTGAACAACTCTCTGTCTGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCGTa                 <  2:2250634/76‑1 (MQ=255)
                                                       gTCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCGTa                 >  1:1007379/1‑76 (MQ=255)
                                                        tCCGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCGTAt                <  2:1577635/76‑1 (MQ=255)
                                                         ccGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTTCTTGAGACTCCGTATc               >  1:4051143/1‑76 (MQ=255)
                                                         ccGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCGTATc               >  1:3466724/1‑76 (MQ=255)
                                                          cGAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCGTATCg              >  1:8100237/1‑76 (MQ=255)
                                                           gAACATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCGTATCGt             <  1:1485993/76‑1 (MQ=255)
                                                            aaCATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTTCTTGAGACTCCGTATCGTa            >  2:3018529/1‑76 (MQ=255)
                                                            aaCATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCGTATCGTa            <  2:1431140/76‑1 (MQ=255)
                                                              cATCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCGTATCGTaaa          <  2:6209279/76‑1 (MQ=255)
                                                               aTCGGTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTTAGGATCCGTATCGTaaaa         >  2:4634965/1‑75 (MQ=255)
                                                                  ggTCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCGTATCGTAAAGTGa      <  2:7102407/76‑1 (MQ=255)
                                                                    tCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTTCTTGAGACTCCGTATCGTAAAgagaac    >  2:3760832/1‑74 (MQ=255)
                                                                    tCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCGTATCGTAAAGTGAcc    <  1:4281859/76‑1 (MQ=255)
                                                                    tCTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCGTATCGTAAAGTGAcc    <  2:3579540/76‑1 (MQ=255)
                                                                     cTGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTTCTTTAGACTTCGTATCCTAAAATGACCg   >  2:4536983/1‑76 (MQ=255)
                                                                      tGAACAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCGTATCGTAAAGTGAccca  >  1:1597189/1‑74 (MQ=255)
                                                                         |                                                                        
CGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAACCCCTGAAGGTCCGAACATCGGTCTGATCAACTCTCTGTCCGTGTACGCACAGACTAACGAATACGGCTTCCTTGAGACTCCGTATCGTAAAGTGACCGA  >  REL606/4162497‑4162642

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A