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 311,673 G→A 10.2% L400L (CTC→CTT)  acrB ← multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE311,6730GA10.2% 341.4 / 19.2 117L400L (CTC→CTT) acrBmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base G (51/53);  new base A (3/9);  total (54/63)
Fisher's exact test for biased strand distribution p-value = 1.37e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 119 total aligned reads displayed.

TCTTCCGCCATAACACGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCC  >  minE/311605‑311741
                                                                    |                                                                    
tcttcCGCCATAACACGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAg                                                                    >  1:3077261/1‑71 (MQ=255)
tcttcCGCCATAACACGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAg                                                                    >  1:109510/1‑71 (MQ=255)
 cttcCGCCATAACACGCTCAACGTTTTCTACCATAACGATGGCGTCATCCACCAACAGGCCGATGGCGAg                                                                    >  1:5422651/1‑70 (MQ=255)
 cttcCGCCATAACACGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGat                                                                    <  1:463952/70‑2 (MQ=255)
 cttcCGCCATAACACGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAg                                                                    <  1:1815962/70‑1 (MQ=255)
   tcCGCCATAACACGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCg                                                                      <  1:19042/66‑1 (MQ=255)
     cGCCATAACACGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCTATGGCGAGCACCa                                                               <  1:538705/71‑1 (MQ=255)
      gCCATAACACGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCAt                                                              <  1:1433740/71‑1 (MQ=255)
       ccATAACACGCTCAACGTTATCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAg                                                                    <  1:3258236/64‑1 (MQ=255)
         aTAACATGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATccc                                                           >  1:1056061/1‑71 (MQ=255)
         aTAACACGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATccc                                                           >  1:4990330/1‑71 (MQ=255)
         aTAACACGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATccc                                                           >  1:1644918/1‑71 (MQ=255)
          tAACACGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCg                                                          <  1:4198635/71‑1 (MQ=255)
           aaCACGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCg                                                          >  1:3579065/1‑70 (MQ=255)
           aaCACGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCg                                                          >  1:3062090/1‑70 (MQ=255)
            acacGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGaa                                                        <  1:252856/71‑1 (MQ=255)
              acGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACa                                                      >  1:2951861/1‑71 (MQ=255)
              acGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACa                                                      >  1:4959289/1‑71 (MQ=255)
              acGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACa                                                      >  1:3007397/1‑71 (MQ=255)
                gCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACAtt                                                    >  1:4596310/1‑71 (MQ=255)
                  tCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAg                                                                    <  1:2701007/53‑1 (MQ=255)
                  tCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGt                                                  >  1:4315453/1‑71 (MQ=255)
                  tCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGt                                                  >  1:5357395/1‑71 (MQ=255)
                  tCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGt                                                  >  1:4643062/1‑71 (MQ=255)
                      cGTTTTCTACCACAACGATGGCGTCATCCCCCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGc                                              >  1:2161141/1‑71 (MQ=255)
                          ttCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCgtgt                                          >  1:1397721/1‑71 (MQ=255)
                          ttCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCgtgt                                          >  1:5433983/1‑71 (MQ=255)
                          ttCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCgtg                                           <  1:4225786/70‑1 (MQ=255)
                           tCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCgtgt                                          <  1:3700339/70‑1 (MQ=255)
                            cTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACAt                                                     <  1:1941279/58‑1 (MQ=255)
                             caccaccACTATCGCATCATCGACGAGCAGCCCGATGGCAAGCACCATCCCGAACATCGTTAGTGTGttga                                       >  1:4149736/2‑69 (MQ=9)
                             caccaccACTATCGCATCATCGACGAGCAGCCCGATGGCAAGCACCATCCCGAACATCGTTAGTGTGttg                                        <  1:4994313/69‑2 (MQ=9)
                               ccaccaCTATCGCATCATCGACGAGCAGCCCGATGGCAAGCACCATCCCGAACATCGTTAGTGTGTTGAtg                                     <  1:477367/71‑2 (MQ=2)
                               ccACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATc                                     >  1:1276196/1‑71 (MQ=255)
                                caccacTATCGCATCATCGACGAGCAGCCCGATGGCAAGCACCATCCCGaa                                                        >  1:3822069/1‑51 (MQ=2)
                                caccacTATCGCATCATCGACGAGCAGCCCGATGGCAAGCACCATCCCGAACATCGTTAGTGTGTTGAtg                                     <  1:5562986/70‑2 (MQ=2)
                                 acaACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCga                                   <  1:2423164/71‑1 (MQ=255)
                                  caACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCa                                                                  >  1:2347169/1‑39 (MQ=255)
                                        tGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCa                            <  1:1071670/71‑1 (MQ=255)
                                          gcatCATCGACGAGCAGCCCGATGGCAAGCACCATCCCGAACATCGTTAGTGTGTTGATGGAGTAACCaa                           >  1:1607906/4‑70 (MQ=9)
                                          gCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCa                            >  1:3622721/1‑69 (MQ=255)
                                            gTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAgg                        >  1:5049028/1‑71 (MQ=255)
                                             tCATCGACGAGCAGCCCGATGGCAAGCACCATCCCGAACATCGt                                                  <  1:1496414/44‑1 (MQ=9)
                                             tCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAggc                       <  1:4854868/71‑1 (MQ=255)
                                             tCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAggc                       <  1:1420939/71‑1 (MQ=255)
                                               aTCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAggcgg                     >  1:539611/1‑71 (MQ=255)
                                                tCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCaa                           <  1:2642586/64‑1 (MQ=255)
                                                tCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCaa                           <  1:5550556/64‑1 (MQ=255)
                                                tCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAggcgg                     >  1:4525407/1‑70 (MQ=255)
                                                tCCACCAACAGGCAGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCaa                           <  1:4851666/64‑1 (MQ=255)
                                                 ccaccaACAGGCCGATGGCGAGCACCATCCCGAACATTg                                                   <  1:1978624/39‑1 (MQ=255)
                                                  caccaACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTGTCGAGAAGCCAAAg                         >  1:4383075/1‑64 (MQ=255)
                                                  caccaACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTAt                                      >  1:2497605/1‑51 (MQ=255)
                                                  caccaACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCga                                   >  1:2975313/1‑54 (MQ=255)
                                                  caccaACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAggcggc                    >  1:65230/1‑69 (MQ=255)
                                                  caccaACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAg                         >  1:2174257/1‑64 (MQ=255)
                                                   accaACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAg                 <  1:3421285/71‑1 (MQ=255)
                                                   accaACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAg                 <  1:2964428/71‑1 (MQ=255)
                                                   accaACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAg                 <  1:3755918/71‑1 (MQ=255)
                                                    ccaACAGGCCGATGGCGAGCACCATCCCGAACATTg                                                   <  1:3126267/36‑1 (MQ=255)
                                                    ccaACAGGCCGATGGCGAGCACCATCCCGAACATTg                                                   <  1:3975930/36‑1 (MQ=255)
                                                    ccaACAGGCCGATGGCGAGCACCATCCCGAACATTg                                                   <  1:5381640/36‑1 (MQ=255)
                                                     gagcAGCCCGATGGCAAGCACCATCCCGAACATCGTTAGTGTGTTGATGGAGTAACCAAAagc                       <  1:600496/60‑1 (MQ=9)
                                                     caACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTAt                                      <  1:5616912/48‑1 (MQ=255)
                                                     caACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTAt                                      <  1:4071180/48‑1 (MQ=255)
                                                     caACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTAt                                      <  1:540908/48‑1 (MQ=255)
                                                     caACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCga                                   <  1:510460/51‑1 (MQ=255)
                                                     caACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGa               >  1:2970675/1‑71 (MQ=255)
                                                      aaCAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGc                              >  1:2718452/1‑55 (MQ=255)
                                                      aaCAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCaaa                          >  1:497563/1‑59 (MQ=255)
                                                      aaCAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCaaa                          >  1:793641/1‑59 (MQ=255)
                                                      aaCAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCaaa                          >  1:1893672/1‑59 (MQ=255)
                                                      aaCAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCa                            >  1:5318445/1‑57 (MQ=255)
                                                      aaCAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCa                            >  1:560383/1‑57 (MQ=255)
                                                      aaCAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGAc              >  1:469348/1‑71 (MQ=255)
                                                      aaCAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGAc              >  1:4240022/1‑71 (MQ=255)
                                                      aaCAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGAc              >  1:5483622/1‑71 (MQ=255)
                                                      aaCAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGAc              >  1:3244469/1‑71 (MQ=255)
                                                       gcAGCCCGATGGCAAGCACCATCCCGAACATCGTTAgtgt                                            <  1:161080/39‑1 (MQ=18)
                                                       aCAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAg                 <  1:5028315/67‑1 (MQ=255)
                                                         aGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGc           <  1:841289/71‑1 (MQ=255)
                                                          ggCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCa          <  1:4191323/71‑1 (MQ=255)
                                                          ggCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCa          <  1:572928/71‑1 (MQ=255)
                                                           cccGATGGCAAGCACCATCCCGAACATCGTTAGTGTGTTGATGGAGTAACCAAAAGCGGCGAGGATGGCaa         <  1:1437865/70‑1 (MQ=16)
                                                            ccGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAggcggc                    <  1:3557547/59‑1 (MQ=255)
                                                             cGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAg       <  1:1094316/71‑1 (MQ=255)
                                                              gATGGCTAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGcc                             <  1:3399714/48‑1 (MQ=255)
                                                              gATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGcc                             <  1:82209/48‑1 (MQ=255)
                                                              gATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGcc                             <  1:1626237/48‑1 (MQ=255)
                                                              gATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGcc                             <  1:5422774/48‑1 (MQ=255)
                                                               aTGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAggcggc                    <  1:4838550/56‑1 (MQ=255)
                                                               aTGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAggcggc                    <  1:219989/56‑1 (MQ=255)
                                                               aTGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAggcggc                    <  1:3707842/56‑1 (MQ=255)
                                                               aTGGCAAGCACCATCCCGAACATCGTTAGTGTGTTGATGGAGTAACCAAAAGCGGCGAGGATGGCAAACGt     <  1:1344227/71‑1 (MQ=12)
                                                                 ggCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCgaga                                 >  1:37014/1‑41 (MQ=255)
                                                                 ggCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCaaa        >  1:5263517/1‑66 (MQ=255)
                                                                  gCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTccc  <  1:1865527/71‑1 (MQ=255)
                                                                  gCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTccc  <  1:1676517/71‑1 (MQ=255)
                                                                  gCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTccc  <  1:3276581/71‑1 (MQ=255)
                                                                  gCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTccc  <  1:4340837/71‑1 (MQ=255)
                                                                    |                                                                    
TCTTCCGCCATAACACGCTCAACGTTTTCTACCACAACGATGGCGTCATCCACCAACAGGCCGATGGCGAGCACCATCCCGAACATTGTTAGCGTGTTTATCGAGAAGCCAAAGGCGGCAAGGACGGCAAAGGTCCC  >  minE/311605‑311741

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A