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 2,065,013 A→G 6.0% K418K (AAA→AAG)  rpoD → RNA polymerase, sigma 70 (sigma D) factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,065,0130AG 6.0% 404.9 / 13.1 133K418K (AAA→AAG) rpoDRNA polymerase, sigma 70 (sigma D) factor
Reads supporting (aligned to +/- strand):  ref base A (67/58);  new base G (3/5);  total (70/63)
Fisher's exact test for biased strand distribution p-value = 4.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

Only 100 of 145 total aligned reads displayed.

CCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGC  >  minE/2064943‑2065082
                                                                      |                                                                     
ccAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaaa                                                                       <  1:1062831/71‑1 (MQ=255)
 cAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAAt                                                                      >  1:659923/1‑71 (MQ=255)
    ccGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                                   <  1:1357052/71‑1 (MQ=255)
    ccGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                                   <  1:627763/71‑1 (MQ=255)
         gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaaa                                                                       >  1:1098499/1‑62 (MQ=255)
         gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATa                                                               <  1:928443/70‑1 (MQ=255)
         gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATa                                                               <  1:4265932/70‑1 (MQ=255)
         gCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATa                                                               <  1:3531724/70‑1 (MQ=255)
             gCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAccgcc                                                          >  1:1719058/1‑71 (MQ=255)
             gCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAccgcc                                                          >  1:486590/1‑71 (MQ=255)
             gCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAccgc                                                           >  1:3328902/1‑70 (MQ=255)
              caattCCTCGACCTGATCCAGGAAGGCAATATCGGCCTGATGAAGGCGGTGGACAAGTTCGAATAccgtcg                                                         >  1:181924/4‑71 (MQ=16)
              caattCCTCGACCTGATCCAGGAAGGCAATATCGGCCTGATGAAGGCGGTGGACAAGTTCGAATAccgtcg                                                         >  1:593885/4‑71 (MQ=16)
              caattCCTCGACCTGATCCAGGAAGGCAATATCGGCCTGATGAAGGCGGTGGACAAGTTCGAATAccgtcg                                                         >  1:1226268/4‑71 (MQ=16)
              cAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAccgccg                                                         <  1:1642067/71‑1 (MQ=255)
                gTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTg                                                       >  1:2339213/1‑71 (MQ=255)
                 ttCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTgg                                                      >  1:2477734/1‑71 (MQ=255)
                   ccTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATaaa                                                                       >  1:3703360/1‑52 (MQ=255)
                    cTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGaa                                                                 <  1:2885371/57‑1 (MQ=255)
                    cTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGaa                                                                 <  1:5786319/57‑1 (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)
                       gACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTgg                                                      >  1:296902/1‑65 (MQ=255)
                       gACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTg                                                       >  1:849608/1‑64 (MQ=255)
                         ccTGATCCAGGAAGGCAATATCGGCCTGATGAAGGCGGTGGACAAGTTCGAATACCGTCGCGGCTATaaat                                              <  1:2275039/71‑3 (MQ=12)
                         ccTGATCCAGGAAGGCAATATCGGCCTGATGAAGGCGGTGGACAAGTTCGAATACCGTCGCGGCTATaaat                                              <  1:5919113/71‑3 (MQ=12)
                          cTGATCCAGGAAGGCAATATCGGCCTGATGAAGGCGGTGGACAAGTTCGAATACCGTCGCGGCTATaaat                                              <  1:6131862/70‑3 (MQ=12)
                            gATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTtct                                           >  1:4451688/1‑71 (MQ=255)
                            gATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTtc                                            >  1:5464138/1‑70 (MQ=255)
                            gATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATAACGCCGTGGTTACAAGTtct                                           >  1:3737742/1‑71 (MQ=255)
                             aTTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                                   <  1:3876586/46‑1 (MQ=255)
                             aTTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                                   <  1:1921343/46‑1 (MQ=255)
                             aTTCAGGAAGGCAACATCGGTCTGATGAAAGCGGCTGATAAATTCg                                                                   <  1:4995951/46‑1 (MQ=255)
                               tCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCa                                        >  1:986200/1‑71 (MQ=255)
                               ccAGGAAGGCAATATCGGCCTGCTCAAGGCCGTGGATAAATTCGAATACCGTCGCGGTTATAAATtctcg                                         >  1:2251713/2‑69 (MQ=255)
                                  ggAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCt                                     <  1:5725593/71‑1 (MQ=255)
                                  ggAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCt                                     <  1:1301026/71‑1 (MQ=255)
                                  ggAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCt                                     <  1:4786549/71‑1 (MQ=255)
                                  ggAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCt                                     <  1:6186843/71‑1 (MQ=255)
                                  ggAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCt                                     <  1:4123415/71‑1 (MQ=255)
                                   gAAGGCAATATCGGCCTGATGAAGGCGGTGGACAAGTTCGAATACCGTCGCGGCTATAAATTCTCGACCTa                                    <  1:5372516/71‑1 (MQ=255)
                                   gAAGGCAATATCGGCCTGATGAAGGCGGTGGACAAGTTCGAATACCGTCGCGGCTATAAATTCTCGACCTa                                    <  1:2127993/71‑1 (MQ=255)
                                      ggCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                                   <  1:555968/37‑1 (MQ=255)
                                      ggCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                                   <  1:6151418/37‑1 (MQ=255)
                                      ggCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                                   <  1:470093/37‑1 (MQ=255)
                                      ggCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                                   <  1:452616/37‑1 (MQ=255)
                                      ggCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                                   <  1:799211/37‑1 (MQ=255)
                                      ggCAACATCGGTCTGATGAAAGCGGTTGATAAATTCg                                                                   <  1:2959563/37‑1 (MQ=255)
                                       gCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCa                                <  1:5347566/71‑1 (MQ=255)
                                        cAACATCGGTCTAATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCaa                               <  1:3961382/71‑1 (MQ=255)
                                          aCATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTcc                                         <  1:1507474/59‑1 (MQ=255)
                                          aCATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTcc                                         <  1:4809046/59‑1 (MQ=255)
                                          aCATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAAcc                             >  1:3930994/1‑71 (MQ=255)
                                          aCATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAAcc                             <  1:1828410/71‑1 (MQ=255)
                                            aTCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCtg                           >  1:1432374/1‑71 (MQ=255)
                                               ggTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCaa                               >  1:2589102/1‑64 (MQ=255)
                                               ggTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCtggtg                        >  1:6804802/1‑71 (MQ=255)
                                                 tCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTtct                                           >  1:416159/1‑50 (MQ=255)
                                                 tCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCtggtg                        >  1:3948830/1‑69 (MQ=255)
                                                 tCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCtggtg                        >  1:663752/1‑69 (MQ=255)
                                                 tCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCtggtg                        >  1:4958472/1‑69 (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)
                                                   tgatgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCa                                <  1:199756/59‑1 (MQ=255)
                                                     atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACaac                                               >  1:5141410/1‑41 (MQ=255)
                                                     atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCa                                        >  1:6260242/1‑49 (MQ=255)
                                                     atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCa                                        >  1:5670959/1‑49 (MQ=255)
                                                     atgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCt                            <  1:6137594/61‑1 (MQ=255)
                                                      tgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGc                                 >  1:4294136/1‑55 (MQ=255)
                                                      tgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGt                 >  1:4890408/1‑71 (MQ=255)
                                                      tgaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGt                 <  1:4682136/71‑1 (MQ=255)
                                                       gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCCCCTACGCAACCTGGTGGATCCGt                 >  1:5502235/1‑70 (MQ=255)
                                                       gaAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGt                 >  1:1069121/1‑70 (MQ=255)
                                                        aaaGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTc                <  1:2745295/70‑1 (MQ=255)
                                                        aaaGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTc                <  1:1568276/70‑1 (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)
                                                              gTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCtggt                         >  1:4670623/1‑55 (MQ=255)
                                                              gTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCt                            <  1:2329383/52‑1 (MQ=255)
                                                              gTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGa          >  1:6370412/1‑70 (MQ=255)
                                                              gTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGa          >  1:3019055/1‑70 (MQ=255)
                                                              gTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGAt         >  1:6370581/1‑71 (MQ=255)
                                                              gTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGAt         >  1:6570201/1‑71 (MQ=255)
                                                              gTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCGACGCAACCTGGTGGATCCCTCAGGCGAt         >  1:1377658/1‑71 (MQ=255)
                                                                tGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACg                                  >  1:302082/1‑44 (MQ=255)
                                                                tGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCa       >  1:6151798/1‑71 (MQ=255)
                                                                tGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCa       >  1:3380070/1‑71 (MQ=255)
                                                                 gATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAAc                              >  1:5692588/1‑47 (MQ=255)
                                                                 gATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCAc      >  1:4425978/1‑71 (MQ=255)
                                                                 gATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCAc      >  1:1917868/1‑71 (MQ=255)
                                                                     aaTTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCg   >  1:5630505/1‑70 (MQ=255)
                                                                     aaTTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGc  <  1:2652340/71‑1 (MQ=255)
                                                                     aaTTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGc  >  1:6185318/1‑71 (MQ=255)
                                                                     aaTTCGAATACCACCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGc  >  1:3464263/1‑71 (MQ=255)
                                                                      |                                                                     
CCAACCGTGGCTTGCAGTTCCTTGACCTGATTCAGGAAGGCAACATCGGTCTGATGAAAGCGGTTGATAAATTCGAATACCGCCGTGGTTACAAGTTCTCCACCTACGCAACCTGGTGGATCCGTCAGGCGATCACCCGC  >  minE/2064943‑2065082

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