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
A2 F8 I0 R2 296 77.6 4260404 88.1% 3753415 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,986,542 A→G 33.1% L19L (TTG→CTG)  arcA ← DNA‑binding response regulator in two‑component regulatory system with ArcB or CpxA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,986,5420AG33.1% 157.5 / 132.3 133L19L (TTG→CTG) arcADNA‑binding response regulator in two‑component regulatory system with ArcB or CpxA
Reads supporting (aligned to +/- strand):  ref base A (53/36);  new base G (25/19);  total (78/55)
Fisher's exact test for biased strand distribution p-value = 8.52e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.35e-01

Only 100 of 136 total aligned reads displayed.

ATGCATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTAAA  >  minE/2986477‑2986610
                                                                 |                                                                    
aTGCATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACgt                                                                   <  1:1260509/69‑1 (MQ=255)
   cATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGc                                                              <  1:1012706/71‑1 (MQ=255)
   cATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGc                                                              <  1:2889002/71‑1 (MQ=255)
   cATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGc                                                              >  1:2414027/1‑71 (MQ=255)
   cATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGc                                                              >  1:1254960/1‑71 (MQ=255)
     tttCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCgt                                                            <  1:2506291/71‑1 (MQ=255)
      ttCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCgtg                                                           >  1:4146511/1‑71 (MQ=255)
       tCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCgtgt                                                          >  1:2003125/1‑71 (MQ=255)
       tCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCgtgt                                                          >  1:1508527/1‑71 (MQ=255)
       tCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCgtgt                                                          >  1:2912607/1‑71 (MQ=255)
       tCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCgtgt                                                          >  1:535069/1‑71 (MQ=255)
       tCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCgtgt                                                          >  1:4257997/1‑71 (MQ=255)
       tCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCgtgt                                                          >  1:4222865/1‑71 (MQ=255)
           cgcCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTAcc                                                      <  1:2728025/71‑1 (MQ=255)
           cgcCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTAcc                                                      <  1:4038738/71‑1 (MQ=255)
              cATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAAc                                                   <  1:1252419/71‑1 (MQ=255)
                 cTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCg                                                >  1:3896217/1‑71 (MQ=255)
                 cTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCg                                                >  1:1879309/1‑71 (MQ=255)
                 cTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCg                                                >  1:385168/1‑71 (MQ=255)
                 cTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCg                                                >  1:1761605/1‑71 (MQ=255)
                 cTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCg                                                >  1:362214/1‑71 (MQ=255)
                  tGTCGCTTCGAAAAGATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTc                                                 >  1:3573879/1‑69 (MQ=255)
                   gTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACgt                                                                   <  1:802745/50‑1 (MQ=255)
                    tCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCa                                                     <  1:2174283/63‑1 (MQ=255)
                    tCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACgt                                                                   <  1:1411516/49‑1 (MQ=255)
                    tCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTc                                                 <  1:1082136/67‑1 (MQ=255)
                    tCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTc                                                 <  1:1556739/67‑1 (MQ=255)
                      gCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTTTTGCGTGTTACCAAc                                                   >  1:3927043/1‑63 (MQ=255)
                      gCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAAc                                                   >  1:4012571/1‑63 (MQ=255)
                      gCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTc                                           <  1:2431931/71‑1 (MQ=255)
                      gCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTc                                           <  1:2747800/71‑1 (MQ=255)
                      gCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTc                                           <  1:4137939/71‑1 (MQ=255)
                        ttCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTAcc                                                      <  1:3508607/58‑1 (MQ=255)
                        ttCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTAcc                                                      <  1:1416960/58‑1 (MQ=255)
                        ttCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTAcc                                                      <  1:3126116/58‑1 (MQ=255)
                        ttCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCaa                                         >  1:1776439/1‑71 (MQ=255)
                        ttCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCaa                                         >  1:1798502/1‑71 (MQ=255)
                         tCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAAc                                        >  1:2609941/1‑71 (MQ=255)
                         tCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAAc                                        >  1:3049154/1‑71 (MQ=255)
                         tCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAAc                                        >  1:3978835/1‑71 (MQ=255)
                         tCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGAGTGTTACCAACTCGTCTTCAAc                                        >  1:3687572/1‑71 (MQ=255)
                          cGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTAcaa                                                     >  1:3367846/1‑55 (MQ=255)
                          cGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCaa                                                    >  1:3514148/1‑58 (MQ=255)
                          cGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCaa                                                    >  1:2580208/1‑58 (MQ=255)
                          cGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCaa                                                    >  1:3736527/1‑58 (MQ=255)
                          cGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCaa                                                    >  1:2084470/1‑58 (MQ=255)
                          cGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTc                                              >  1:2244158/1‑64 (MQ=255)
                          cGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTc                                              >  1:3323799/1‑64 (MQ=255)
                          cGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAAc                                        >  1:2143720/1‑70 (MQ=255)
                          cGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAAc                                        >  1:3278879/1‑70 (MQ=255)
                              aaCATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGAt                                     >  1:4240352/1‑69 (MQ=255)
                               aCATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTc                                                 <  1:4108514/56‑1 (MQ=255)
                               aCATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTc                                                 <  1:609098/56‑1 (MQ=255)
                               aCATCATAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTc                                                 <  1:164319/56‑1 (MQ=255)
                               aCATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGAt                                     >  1:4065612/1‑68 (MQ=255)
                                catcatAGGCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATATGa                                 <  1:2970128/71‑1 (MQ=255)
                                catcatAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGa                                 <  1:954687/71‑1 (MQ=255)
                                catcatAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGa                                 <  1:3907199/71‑1 (MQ=255)
                                  tcatAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAAt                               <  1:525396/71‑1 (MQ=255)
                                   catAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAAtg                              >  1:3574332/1‑71 (MQ=255)
                                   catAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGa                                      >  1:3962559/1‑63 (MQ=255)
                                   catAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGa                                      >  1:771100/1‑63 (MQ=255)
                                   catAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAAtg                              >  1:3353330/1‑71 (MQ=255)
                                    atAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCaa                                                    >  1:3125807/1‑48 (MQ=255)
                                    atAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCaa                                                    >  1:2878593/1‑48 (MQ=255)
                                    atAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAAtgt                             >  1:3243923/1‑71 (MQ=255)
                                     tAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAAtgtg                            <  1:1001504/71‑1 (MQ=255)
                                     tAGCCTTCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAAtgtg                            <  1:2171697/71‑1 (MQ=255)
                                     tAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAAtg                              >  1:2137819/1‑69 (MQ=255)
                                          ttCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGa                                      <  1:647412/56‑1 (MQ=255)
                                          ttCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGa                                      <  1:3109167/56‑1 (MQ=255)
                                           tCCGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGc                           >  1:3487651/1‑66 (MQ=255)
                                            ccGCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGt                      <  1:4070094/70‑1 (MQ=255)
                                            ccGCTTCGAAAATACTTTTCAGAGTGTTGCGTGTTACCAACTCGCCTTCAACGATAAGAATGTGCGGGGt                      <  1:468796/70‑1 (MQ=255)
                                             cGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCg                          >  1:3019670/1‑65 (MQ=255)
                                             cGCTTCGAAAATACTTTACAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCg                          >  1:3453400/1‑65 (MQ=255)
                                              gCTTCGAAAATACTTTTCAGCGTGTTGCGTTTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTg                   <  1:2909852/71‑1 (MQ=255)
                                              gCTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTg                   <  1:3551337/71‑1 (MQ=255)
                                               cTTCGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGc                  <  1:1145716/71‑1 (MQ=255)
                                                 tCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCggg                        >  1:3924459/1‑63 (MQ=255)
                                                  cGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCaa                                         >  1:3214948/1‑45 (MQ=255)
                                                  cGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCaa                                         >  1:636486/1‑45 (MQ=255)
                                                  cGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCaa                                         >  1:2436740/1‑45 (MQ=255)
                                                  cGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCggg                        >  1:4031658/1‑62 (MQ=255)
                                                  cGAAAATACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCggg                        >  1:2533522/1‑62 (MQ=255)
                                                     aaaTACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGttt            <  1:2514143/71‑1 (MQ=255)
                                                       aTACTTTTCAGCGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTg                   <  1:1725185/62‑1 (MQ=255)
                                                        tACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGt              <  1:1832718/66‑1 (MQ=255)
                                                        tACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGt              <  1:3902776/66‑1 (MQ=255)
                                                        tACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGt              <  1:2754082/66‑1 (MQ=255)
                                                          cTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCgggg                       <  1:2599490/55‑1 (MQ=255)
                                                          cTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCgggg                       <  1:877584/55‑1 (MQ=255)
                                                          cTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCgggg                       <  1:2904358/55‑1 (MQ=255)
                                                          cTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGttt            >  1:3960444/1‑66 (MQ=255)
                                                          cTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGttt            >  1:7138/1‑66 (MQ=255)
                                                          cTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGAGCgggg                       <  1:10123/55‑1 (MQ=255)
                                                             ttCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCt     >  1:1168284/1‑70 (MQ=255)
                                                             ttCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCt     >  1:2144316/1‑70 (MQ=255)
                                                             ttCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCt     >  1:2679583/1‑70 (MQ=255)
                                                               cAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTaaa  >  1:2807042/1‑71 (MQ=255)
                                                                 |                                                                    
ATGCATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTTTTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCTAAA  >  minE/2986477‑2986610

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