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 F3 I0 R2 88 130.8 6963722 93.6% 6518043 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,065,010 T→C 5.4% D417D (GAT→GAC)  rpoD → RNA polymerase, sigma 70 (sigma D) factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,065,0100TC 5.4% 456.0 / 12.5 149D417D (GAT→GAC) rpoDRNA polymerase, sigma 70 (sigma D) factor
Reads supporting (aligned to +/- strand):  ref base T (72/69);  new base C (3/5);  total (75/74)
Fisher's exact test for biased strand distribution p-value = 4.94e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-01

Only 100 of 157 total aligned reads displayed.

CACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACC  >  minE/2064941‑2065079
                                                                     |                                                                     
cacCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATa                                                                      <  1:1236955/71‑1 (MQ=255)
 acCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaa                                                                     <  1:1101925/71‑1 (MQ=255)
  ccAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAATGCAACATCGGTCTGATGAAAGCGGTTGATa                                                                      <  1:1029277/69‑1 (MQ=255)
  ccAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaaa                                                                    <  1:1062831/71‑1 (MQ=255)
  ccAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATa                                                                      <  1:2005012/69‑1 (MQ=255)
      ccGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                                <  1:627763/71‑1 (MQ=255)
      ccGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                                <  1:1357052/71‑1 (MQ=255)
         tGGCTTGGAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATa                                                                      <  1:365657/62‑1 (MQ=255)
         tGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATa                                                                      <  1:650810/62‑1 (MQ=255)
         tGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATa                                                                      <  1:6052850/62‑1 (MQ=255)
         tGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATa                                                                      <  1:3884138/62‑1 (MQ=255)
           gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaaa                                                                    >  1:1098499/1‑62 (MQ=255)
           gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATa                                                            <  1:4265932/70‑1 (MQ=255)
           gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATa                                                            <  1:5697636/70‑1 (MQ=255)
           gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATa                                                            <  1:3531724/70‑1 (MQ=255)
           gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATa                                                            <  1:1737267/70‑1 (MQ=255)
               gCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAccgcc                                                       >  1:486590/1‑71 (MQ=255)
               gCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAccgc                                                        >  1:3328902/1‑70 (MQ=255)
                caattCCTCGACCTGATCCAGGAAGGCAATATCGGCCTGATGAAGGCGGTGGACAAGTTCGAATAccgtcg                                                      >  1:181924/4‑71 (MQ=16)
                caattCCTCGACCTGATCCAGGAAGGCAATATCGGCCTGATGAAGGCGGTGGACAAGTTCGAATAccgtcg                                                      >  1:1226268/4‑71 (MQ=16)
                caattCCTCGACCTGATCCAGGAAGGCAATATCGGCCTGATGAAGGCGGTGGACAAGTTCGAATAccgtcg                                                      >  1:593885/4‑71 (MQ=16)
                cAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAccgccg                                                      <  1:1642067/71‑1 (MQ=255)
                 aGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATa                                                                      <  1:5513543/54‑1 (MQ=255)
                   ttCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTgg                                                   >  1:2477734/1‑71 (MQ=255)
                     ccTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaaa                                                                    >  1:1324349/1‑52 (MQ=255)
                      cTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGaa                                                              <  1:5786319/57‑1 (MQ=255)
                      cTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGaa                                                              <  1:2885371/57‑1 (MQ=255)
                      cTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGtt                                                 <  1:3299949/70‑1 (MQ=255)
                      cTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGtt                                                 <  1:4126821/70‑1 (MQ=255)
                       ttGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTa                                                >  1:5458637/1‑70 (MQ=255)
                        tGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTAc                                               >  1:298290/1‑70 (MQ=255)
                         gACCTGATTCAGGATGGCAACATCGGTCTGATGAAAGCGGTTGAt                                                                       >  1:6434216/1‑45 (MQ=255)
                         gACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGAt                                                                       >  1:476270/1‑45 (MQ=255)
                         gACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGAt                                                                       >  1:1304002/1‑45 (MQ=255)
                         gACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGAt                                                                       >  1:6305556/1‑45 (MQ=255)
                         gACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGAt                                                                       >  1:3934440/1‑45 (MQ=255)
                         gACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTgg                                                   >  1:4675642/1‑65 (MQ=255)
                         gACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTg                                                    >  1:849608/1‑64 (MQ=255)
                           ccTGATCCAGGAAGGCAATATCGGCCTGATGAAGGCGGTGGACAAGTTCGAATACCGTCGCGGCTATaaat                                           <  1:2275039/71‑3 (MQ=12)
                            cTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGt                                           <  1:3069935/70‑1 (MQ=255)
                            cTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGt                                           <  1:4970678/70‑1 (MQ=255)
                              gATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTtc                                         >  1:5464138/1‑70 (MQ=255)
                              gATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAACGCCGTGGTTACAAGTtct                                        >  1:3737742/1‑71 (MQ=255)
                               aTTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                                <  1:1921343/46‑1 (MQ=255)
                               aTTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTtc                                         <  1:1970486/69‑1 (MQ=255)
                               aTTCAGGAAGGCAACATCGGTCTGATGAAAGCGGCTGATAAATTCg                                                                <  1:4995951/46‑1 (MQ=255)
                                 tCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCa                                     >  1:986200/1‑71 (MQ=255)
                                 ccAGGAAGGCAATATCGGCCTGCTCAAGGCCGTGGATAAATTCGAATACCGTCGCGGTTATAAATtctcg                                      >  1:2251713/2‑69 (MQ=255)
                                   aGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCAc                                    <  1:5898393/70‑1 (MQ=255)
                                    ggAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCt                                  <  1:3936255/71‑1 (MQ=255)
                                    ggAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCt                                  <  1:6186843/71‑1 (MQ=255)
                                    ggAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCt                                  <  1:4786549/71‑1 (MQ=255)
                                     gAAGGCAATATCGGCCTGATGAAGGCGGTGGACAAGTTCGAATACCGTCGCGGCTATAAATTCTCGACCTa                                 <  1:2127993/71‑1 (MQ=255)
                                     gAAGGCAATATCGGCCTGATGAAGGCGGTGGACAAGTTCGAATACCGTCGCGGCTATAAATTCTCGACCTa                                 <  1:5372516/71‑1 (MQ=255)
                                      aaGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTAc                                <  1:6587845/71‑1 (MQ=255)
                                        ggCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                                <  1:452616/37‑1 (MQ=255)
                                        ggCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                                <  1:6151418/37‑1 (MQ=255)
                                        ggCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                                <  1:555968/37‑1 (MQ=255)
                                        ggCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                                <  1:2959563/37‑1 (MQ=255)
                                         gCAACATCGTTCTGATGATAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCa                             <  1:377667/71‑1 (MQ=255)
                                         gCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCa                             <  1:5347566/71‑1 (MQ=255)
                                          cAACATCGGTCTAATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCaa                            <  1:3961382/71‑1 (MQ=255)
                                            aCATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTcc                                      <  1:4809046/59‑1 (MQ=255)
                                            aCATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTcc                                      <  1:1507474/59‑1 (MQ=255)
                                              aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCtg                        >  1:1432374/1‑71 (MQ=255)
                                                 ggTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCaa                            >  1:2589102/1‑64 (MQ=255)
                                                   tCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCtggtg                     >  1:663752/1‑69 (MQ=255)
                                                   tCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCtggtg                     >  1:6143565/1‑69 (MQ=255)
                                                    cTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCAcc                                   <  1:2851911/54‑1 (MQ=255)
                                                    cTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGAt                  >  1:3210071/1‑71 (MQ=255)
                                                    cTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGAt                  >  1:276128/1‑71 (MQ=255)
                                                      gatgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCt                                  <  1:4035737/53‑1 (MQ=255)
                                                       atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACaac                                            >  1:5141410/1‑41 (MQ=255)
                                                       atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCa                                     >  1:6260242/1‑49 (MQ=255)
                                                       atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAAc                           >  1:4415569/1‑59 (MQ=255)
                                                       atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCt                         <  1:6137594/61‑1 (MQ=255)
                                                        tgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGt              >  1:4890408/1‑71 (MQ=255)
                                                        tgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGt              <  1:4682136/71‑1 (MQ=255)
                                                         gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGt              >  1:3396338/1‑70 (MQ=255)
                                                          aaaGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTc             <  1:1568276/70‑1 (MQ=255)
                                                          aaaGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTc             <  1:2745295/70‑1 (MQ=255)
                                                          aaaGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTc             <  1:6107662/70‑1 (MQ=255)
                                                           aaGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAg           >  1:4452565/1‑71 (MQ=255)
                                                           aaGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAg           >  1:5084517/1‑71 (MQ=255)
                                                             gCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGc         >  1:6820629/1‑71 (MQ=255)
                                                              cGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCg        <  1:5050419/71‑1 (MQ=255)
                                                               ggTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGa       >  1:3643125/1‑71 (MQ=255)
                                                                gTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCt                         <  1:2329383/52‑1 (MQ=255)
                                                                gTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGa       >  1:6370412/1‑70 (MQ=255)
                                                                 ttGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGAt      >  1:767246/1‑70 (MQ=255)
                                                                 ttGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATc     <  1:5651283/71‑1 (MQ=255)
                                                                  tGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACg                               >  1:302082/1‑44 (MQ=255)
                                                                  tGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCa    >  1:6151798/1‑71 (MQ=255)
                                                                   gATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAAc                           >  1:3016382/1‑47 (MQ=255)
                                                                   gATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAAc                           >  1:5692588/1‑47 (MQ=255)
                                                                   gATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAAc                           >  1:6687419/1‑47 (MQ=255)
                                                                   gATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAAc                           >  1:4131421/1‑47 (MQ=255)
                                                                   gATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAAc                           >  1:1854702/1‑47 (MQ=255)
                                                                   gATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCAc   >  1:90264/1‑71 (MQ=255)
                                                                   gATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCAc   >  1:4425978/1‑71 (MQ=255)
                                                                     |                                                                     
CACCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACC  >  minE/2064941‑2065079

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A