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 F17 I0 R2 159 90.8 4763082 92.7% 4415377 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,804,090 G→A 70.7% G52G (GGG→GGA)  mprA → DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,804,0900GA70.7% 382.9 / 211.8 249G52G (GGG→GGA) mprADNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (42/31);  new base A (76/100);  total (118/131)
Fisher's exact test for biased strand distribution p-value = 5.07e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 250 total aligned reads displayed.

ACTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCT  >  minE/1804022‑1804156
                                                                    |                                                                  
aCTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAt                                                                  <  1:218006/71‑1 (MQ=255)
 cTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAtt                                                                 <  1:2957384/71‑1 (MQ=255)
   cGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTaa                                                               >  1:514649/1‑71 (MQ=255)
    gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                                <  1:842973/69‑1 (MQ=255)
    gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                              >  1:4110507/1‑71 (MQ=255)
    gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                              >  1:4546334/1‑71 (MQ=255)
       tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGa                                                                   >  1:4035164/1‑63 (MQ=255)
       tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                              >  1:2559816/1‑68 (MQ=255)
         tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGAc                                                         >  1:3112857/1‑71 (MQ=255)
              gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGAc                                                         >  1:3819858/1‑66 (MQ=255)
              gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgt                                                    >  1:1969927/1‑71 (MQ=255)
              gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgt                                                    >  1:1307099/1‑71 (MQ=255)
              gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgt                                                    >  1:675660/1‑71 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   >  1:1023040/1‑71 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   >  1:3998843/1‑71 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   <  1:1567070/71‑1 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   >  1:2813290/1‑71 (MQ=255)
                acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTaa                                                               >  1:4506367/1‑58 (MQ=255)
                 catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgtt                                                      <  1:4277089/66‑1 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                              <  1:4708298/57‑1 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                              <  1:958639/57‑1 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                              <  1:494923/57‑1 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                >  1:3781655/1‑71 (MQ=255)
                   tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                <  1:3038940/70‑1 (MQ=255)
                   tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                >  1:3387093/1‑70 (MQ=255)
                   tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                >  1:3398165/1‑70 (MQ=255)
                        agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTGAGGGAATTAACGAGACGTTGTTTATGGCGtt                                          <  1:2236032/71‑1 (MQ=255)
                        agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                                <  1:651912/49‑1 (MQ=255)
                        agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                                <  1:697073/49‑1 (MQ=255)
                        agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                          <  1:1921204/71‑1 (MQ=255)
                         gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                          <  1:2008824/70‑1 (MQ=255)
                          caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACg                                                        >  1:598992/1‑55 (MQ=255)
                          caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                        <  1:2909340/71‑1 (MQ=255)
                             gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTa                                     <  1:2601884/71‑1 (MQ=255)
                             gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                     <  1:2735498/71‑1 (MQ=255)
                              ctgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTAc                                    >  1:3584107/1‑71 (MQ=255)
                              ctgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTAc                                    >  1:392370/1‑71 (MQ=255)
                               tgcttGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTg                                         <  1:1072491/65‑1 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGc                                  <  1:4720017/70‑1 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCt                                 >  1:1045598/1‑71 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                             <  1:3276554/59‑1 (MQ=255)
                                  tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgt                                                    >  1:1533113/1‑51 (MQ=255)
                                  tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                >  1:288681/1‑71 (MQ=255)
                                   ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGttt                                                  <  1:785560/52‑1 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACg                                                        >  1:2646133/1‑45 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACg                                                        >  1:3496293/1‑45 (MQ=255)
                                     agaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAg                             >  1:3604610/1‑71 (MQ=255)
                                     agaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAg                             <  1:3418118/71‑1 (MQ=255)
                                     agaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                        >  1:21429/1‑60 (MQ=255)
                                     agaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                        >  1:2083398/1‑60 (MQ=255)
                                     agaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAg                             <  1:1166708/71‑1 (MQ=255)
                                       aaCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                            <  1:1599124/38‑1 (MQ=255)
                                       aaCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGt                                           <  1:3691857/55‑1 (MQ=255)
                                       aaCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtc                           <  1:888804/71‑1 (MQ=255)
                                       aaCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtc                           <  1:3171703/71‑1 (MQ=255)
                                        aCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                                          >  1:3469784/1‑39 (MQ=255)
                                        aCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                                          >  1:1349630/1‑39 (MQ=255)
                                         ccGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                                          >  1:4457212/1‑38 (MQ=255)
                                         ccGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                   <  1:1447946/45‑1 (MQ=255)
                                         ccGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                          >  1:247086/1‑70 (MQ=255)
                                         ccGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                          >  1:4162582/1‑70 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                       <  1:1844990/51‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                       <  1:3736414/51‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                       <  1:1801144/51‑1 (MQ=255)
                                                aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                 >  1:2481076/1‑40 (MQ=255)
                                                aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                  >  1:3252280/1‑71 (MQ=255)
                                                aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGGTGATTACGCTGGAGTCTCAGGaaa                   <  1:98146/70‑1 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                              >  1:3566720/1‑58 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc                 >  1:3348317/1‑71 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                 >  1:431832/1‑39 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc                 >  1:1779654/1‑71 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc                 >  1:3309548/1‑71 (MQ=255)
                                                  aaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                  <  1:4019868/69‑1 (MQ=255)
                                                    tGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                          <  1:2322554/43‑1 (MQ=255)
                                                     gCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                <  1:4758706/52‑1 (MQ=255)
                                                     gCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                  >  1:1424544/1‑66 (MQ=255)
                                                      cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcaca             <  1:4213956/70‑1 (MQ=255)
                                                      cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg            >  1:3914145/1‑71 (MQ=255)
                                                      cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg            >  1:4117470/1‑71 (MQ=255)
                                                      cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg            <  1:2965529/71‑1 (MQ=255)
                                                       tGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTgg                               >  1:4596228/1‑51 (MQ=255)
                                                       tGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTgg                               >  1:307242/1‑51 (MQ=255)
                                                       tGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                              >  1:4282916/1‑52 (MQ=255)
                                                       tGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                              >  1:92054/1‑52 (MQ=255)
                                                       tGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                              >  1:737772/1‑52 (MQ=255)
                                                       tGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                              >  1:3217750/1‑52 (MQ=255)
                                                        gAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                <  1:3980347/49‑1 (MQ=255)
                                                         aaGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt         <  1:3021021/71‑1 (MQ=255)
                                                         aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGc                                  <  1:4140288/46‑1 (MQ=255)
                                                         aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGc                                  <  1:2904661/46‑1 (MQ=255)
                                                         aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa          <  1:1720345/70‑1 (MQ=255)
                                                         aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt         <  1:1517532/71‑1 (MQ=255)
                                                          aGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcac              >  1:4604554/1‑65 (MQ=255)
                                                          aGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt        <  1:266826/71‑1 (MQ=255)
                                                            gCTCAGTGAATTAACGAGACGTTGTTTATGGCGTTGAt                                       <  1:304804/38‑1 (MQ=38)
                                                            gCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTg                                         <  1:4685430/36‑1 (MQ=255)
                                                            gCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTg                                         <  1:2015228/36‑1 (MQ=255)
                                                            gCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTg                                         <  1:2299682/36‑1 (MQ=255)
                                                            gCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                       <  1:582107/38‑1 (MQ=255)
                                                                aGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt        >  1:4448832/1‑65 (MQ=255)
                                                                    |                                                                  
ACTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCT  >  minE/1804022‑1804156

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