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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,130,596 G→A 33.6% T103T (ACC→ACT)  mtr ← tryptophan transporter of high affinity

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,130,5960GA33.6% 140.2 / 96.6 116T103T (ACC→ACT) mtrtryptophan transporter of high affinity
Reads supporting (aligned to +/- strand):  ref base G (37/40);  new base A (20/19);  total (57/59)
Fisher's exact test for biased strand distribution p-value = 8.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.28e-01

Only 100 of 127 total aligned reads displayed.

CCGGGACGTTTAGTGACATCTCTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCT  >  minE/2130526‑2130665
                                                                      |                                                                     
ccGGGACGTTTAGTGACATCTCTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAg                                                                       >  1:1114316/1‑71 (MQ=255)
     aCGTTTAGTGACATCTCTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAg                                                                  >  1:1720400/1‑71 (MQ=255)
          tAGTGACATCTCTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAg                                                                       >  1:4870407/1‑61 (MQ=255)
          tAGTGACATCTCTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAg                                                                       >  1:3415538/1‑61 (MQ=255)
            gTGACATCTCTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATag                                                           <  1:4904743/71‑1 (MQ=255)
               aCATCTCTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATagag                                                         <  1:4527283/70‑1 (MQ=255)
               aCATCTCTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATaga                                                          >  1:309727/1‑69 (MQ=255)
                  tctcTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGat                                                               <  1:2468780/61‑1 (MQ=255)
                    tctGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAgg                                                                      >  1:1716750/1‑52 (MQ=255)
                    tctGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAgg                                                                      >  1:2008580/1‑52 (MQ=255)
                    tctGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGatat                                                             >  1:1395357/1‑61 (MQ=255)
                    tctGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGatat                                                             >  1:1895592/1‑61 (MQ=255)
                    tctGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGatat                                                             >  1:4725327/1‑61 (MQ=255)
                    tctGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGat                                                               <  1:4985590/59‑1 (MQ=255)
                    tctGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGcaca                                                     >  1:4181047/1‑69 (MQ=255)
                    tctGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGcaca                                                     >  1:5024971/1‑69 (MQ=255)
                      tGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGcaca                                                     <  1:900020/67‑1 (MQ=255)
                      tGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACaa                                                    <  1:3376644/68‑1 (MQ=255)
                          aaGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAAt                                             <  1:1850097/71‑1 (MQ=255)
                            ggTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATgg                                           <  1:2725584/71‑1 (MQ=255)
                            ggTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATgg                                           <  1:635539/71‑1 (MQ=255)
                             gtgtGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGt                                                                     <  1:3140290/44‑1 (MQ=255)
                             gtgtGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGa                                          <  1:1183978/71‑1 (MQ=255)
                              tgtgATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAg                                                                  <  1:4441807/46‑1 (MQ=255)
                                  aTGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAAt                                             >  1:838448/1‑63 (MQ=255)
                                     cAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATgg                                           <  1:3606152/62‑1 (MQ=255)
                                      aGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                 <  1:5352501/71‑1 (MQ=255)
                                      aGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                 <  1:4577236/71‑1 (MQ=255)
                                       tgaTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACgaa                                                   >  1:2113700/3‑52 (MQ=255)
                                       tgaTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACggt                                          <  1:4399599/59‑2 (MQ=255)
                                       tgaTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGtaa                                        <  1:2464514/61‑1 (MQ=255)
                                       gAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGa                                          <  1:814313/61‑1 (MQ=255)
                                       gAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGa                                          <  1:126007/61‑1 (MQ=255)
                                       gAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGa                                          <  1:2594640/61‑1 (MQ=255)
                                       gAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGtt                                 >  1:4628389/1‑70 (MQ=255)
                                        gaTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAg                                                  >  1:1433660/2‑52 (MQ=255)
                                         aTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATag                                                           <  1:545485/42‑1 (MQ=16)
                                         aTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGat                              <  1:1227092/71‑2 (MQ=255)
                                         aTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGat                              <  1:5186317/71‑2 (MQ=255)
                                         aTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGat                              <  1:1718479/71‑2 (MQ=255)
                                         aTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGat                              <  1:4250176/71‑2 (MQ=255)
                                         aTCGCACCATTAGCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGat                              <  1:4173012/71‑2 (MQ=255)
                                          tCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGaa                                         <  1:1585121/59‑1 (MQ=255)
                                          tCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGAc                              >  1:2605545/1‑70 (MQ=255)
                                          tCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGAc                              >  1:4458215/1‑70 (MQ=255)
                                          tCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGAc                              >  1:2932335/1‑70 (MQ=255)
                                           cGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGaaa                                        >  1:2291876/1‑59 (MQ=255)
                                           cGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGaaa                                        >  1:3640919/1‑59 (MQ=255)
                                            gAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCa                            >  1:1514809/1‑70 (MQ=255)
                                            gAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCAc                           >  1:1087905/1‑71 (MQ=255)
                                              aCCATTAGCAGAGATATAGGCATAAGTGATGATATAGAGAACGAAGGCAACggt                                          <  1:2002172/54‑2 (MQ=255)
                                               ccACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGtt                        <  1:648042/71‑1 (MQ=255)
                                                cACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTc                       <  1:4121138/71‑1 (MQ=255)
                                                  cTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCa                            >  1:1605069/1‑64 (MQ=255)
                                                  cTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGt                         <  1:1466945/67‑1 (MQ=255)
                                                  cTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGt                         <  1:2089049/67‑1 (MQ=255)
                                                  cTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTc                       >  1:2427702/1‑69 (MQ=255)
                                                    ggCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAgg                                                 >  1:4455261/1‑41 (MQ=255)
                                                    ggCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGc                   >  1:4870493/1‑71 (MQ=255)
                                                    agCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCaa                                              >  1:1574932/2‑44 (MQ=255)
                                                    agCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCaa                                              >  1:2620165/2‑44 (MQ=255)
                                                    agCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGa                               <  1:1761793/58‑1 (MQ=255)
                                                     gCAGAGATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTCCAgg                   >  1:3911616/1‑69 (MQ=255)
                                                     gCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGcc                  >  1:5184729/1‑71 (MQ=255)
                                                       agagATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGtaa                                        >  1:1194759/1‑47 (MQ=255)
                                                       agagATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGtaa                                        >  1:3960139/1‑47 (MQ=255)
                                                       agagATATAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGtaa                                        >  1:2682723/1‑47 (MQ=255)
                                                         agatatAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                      >  1:2351582/3‑63 (MQ=255)
                                                         agatatAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                      >  1:2501159/3‑63 (MQ=255)
                                                         agatatAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                      >  1:2284749/3‑63 (MQ=255)
                                                         agatatAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                      >  1:4209174/3‑63 (MQ=255)
                                                         agatatAGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                      >  1:5092420/3‑63 (MQ=255)
                                                           atatAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCa                     >  1:2791634/1‑62 (MQ=255)
                                                           atatAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCa                     >  1:1084562/1‑62 (MQ=255)
                                                           atatAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCa                     >  1:3938836/1‑62 (MQ=255)
                                                           atatAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGcc            >  1:1800618/1‑71 (MQ=255)
                                                           atatAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGcc            <  1:3590723/71‑1 (MQ=255)
                                                            tataGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGccc           <  1:2750719/71‑1 (MQ=255)
                                                             ataGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGccc           <  1:3340983/70‑1 (MQ=255)
                                                             ataGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGcc            <  1:5230412/69‑1 (MQ=255)
                                                              taGGCATAAGTGAGGATATAGAGAACGAAGGCAACggt                                          <  1:503752/38‑2 (MQ=16)
                                                              taGGCATAAGTGAGGATATAGAGAACGAAGGCAACggt                                          <  1:1024268/38‑2 (MQ=16)
                                                              taGGCATAAGTGAGGATATAGAGAACGAAGGCAACggt                                          <  1:3971318/38‑2 (MQ=16)
                                                              taGGCATAAGTGAGGATATAGAGAACGAAGGCAACggt                                          <  1:3792709/38‑2 (MQ=16)
                                                              taGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGat                              <  1:652054/50‑2 (MQ=255)
                                                              taGGCATAAGTGAGGATATAGAGAACGAAGGCAACGGTAATACCGCTGATAATGTTcc                      >  1:1468136/1‑58 (MQ=255)
                                                               aGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGc                                     >  1:3726080/1‑42 (MQ=255)
                                                                ggCATAAGTGAGGATATAGAGAACGAAGGCAACGGtaa                                        >  1:2596250/1‑38 (MQ=12)
                                                                ggCATAAGTGAGGATATAGAGAACGAAGGCAACGGtaa                                        >  1:1600465/1‑38 (MQ=12)
                                                                 gCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCa       >  1:3476297/1‑70 (MQ=255)
                                                                 gCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCa       >  1:2994315/1‑70 (MQ=255)
                                                                   aTAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAAt    <  1:5670630/71‑1 (MQ=255)
                                                                    tAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGt                         <  1:1523296/49‑1 (MQ=255)
                                                                    tAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGt                         <  1:2542552/49‑1 (MQ=255)
                                                                    tAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATc   >  1:389185/1‑71 (MQ=255)
                                                                     aGGTCAGGATATAGAGCACAAAGGCGATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCt  >  1:2905092/1‑71 (MQ=255)
                                                                      ggTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTc                       >  1:4955361/1‑49 (MQ=255)
                                                                      ggTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTc                       >  1:2629588/1‑49 (MQ=255)
                                                                      ggTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCttt               <  1:1562379/57‑1 (MQ=255)
                                                                      ggTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACAACGTTc                       >  1:5291231/1‑49 (MQ=255)
                                                                      |                                                                     
CCGGGACGTTTAGTGACATCTCTGCGAAGGTGTGATGCAGAATCGAACCACTGGCAGAAATATAGGCATAGGTCAGGATATAGAGCACAAAGGCAATGGAAATGCCGTTGACCACGTTCCAGCCTTTGCCCAGCAAATCT  >  minE/2130526‑2130665

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A