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
A3 F3 I0 R1 42 47.0 3685080 97.5% 3592953 60.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,809,581 G→A 59.4% G52G (GGG→GGA)  mprA → DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,809,5810GA59.4% 128.1 / 260.7 204G52G (GGG→GGA) mprADNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (43/39);  new base A (56/65);  total (99/105)
Fisher's exact test for biased strand distribution p-value = 3.95e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01

Only 100 of 207 total aligned reads displayed.

CTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCT  >  W3110S.gb/2809514‑2809650
                                                                   |                                                                     
cTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAtt                                                                    <  1:3655639/71‑1 (MQ=255)
cTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAt                                                                     >  1:3254982/1‑70 (MQ=255)
   gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                 >  1:3570971/1‑71 (MQ=255)
      tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                 >  1:2246441/1‑68 (MQ=255)
      tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                 >  1:1318905/1‑68 (MQ=255)
        tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACgag                                                              <  1:2007488/69‑1 (MQ=255)
         gcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACg                                                           >  1:1753591/1‑71 (MQ=255)
          catgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                               <  1:1734361/66‑1 (MQ=255)
             gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgt                                                       >  1:3647019/1‑71 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTa                                                                   >  1:959451/1‑58 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                      <  1:814325/71‑1 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTaa                                                                  >  1:3137908/1‑59 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTaa                                                                  >  1:1772358/1‑59 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                      <  1:1011213/71‑1 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                      <  1:3201606/71‑1 (MQ=255)
                catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                               <  1:718861/60‑1 (MQ=255)
                catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                               <  1:2227208/60‑1 (MQ=255)
                 atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                   >  1:164586/1‑71 (MQ=255)
                 atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                   <  1:2776486/71‑1 (MQ=255)
                  tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACgaga                                                             >  1:2853103/1‑60 (MQ=255)
                   gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTa                                                    >  1:2784037/1‑68 (MQ=255)
                   gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATgg                                                 >  1:2180372/1‑71 (MQ=255)
                   gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgt                                                       >  1:879517/1‑65 (MQ=255)
                    caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGAc                                                            >  1:2309283/1‑59 (MQ=255)
                    caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                                >  1:2546382/1‑71 (MQ=255)
                      aagcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGttt                                                     <  1:3396876/64‑1 (MQ=255)
                       agcaagcTGCTTGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgt                                                       <  1:280728/61‑1 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTGGTGTATGGCGtt                                             >  1:152161/1‑71 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                             <  1:3002299/71‑1 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                             <  1:2626267/71‑1 (MQ=255)
                        gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                             <  1:3500358/70‑1 (MQ=255)
                        gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                             >  1:2065444/1‑70 (MQ=255)
                        gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                             <  1:2868952/70‑1 (MQ=255)
                         caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGt                                              >  1:2396971/1‑68 (MQ=255)
                         caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                           >  1:850849/1‑71 (MQ=255)
                          aagcTGCTGGAGAACTGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                          <  1:922335/71‑1 (MQ=255)
                           agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                          >  1:634476/1‑70 (MQ=255)
                            gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACga                                                               <  1:3110899/48‑1 (MQ=255)
                            gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                 <  1:900207/46‑1 (MQ=255)
                             ctgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTAc                                       <  1:664339/71‑1 (MQ=255)
                             ctgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTAc                                       <  1:732346/71‑1 (MQ=255)
                                ctgGAGAACCGCAATAAAATGCTGAATGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACg                                      <  1:2926866/69‑1 (MQ=255)
                                ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACg                                      <  1:3381995/69‑1 (MQ=255)
                                 tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACga                                                               <  1:2379932/43‑1 (MQ=255)
                                 tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                             <  1:276831/61‑1 (MQ=255)
                                 tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACg                                      <  1:3520681/68‑1 (MQ=255)
                                  ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                                  >  1:821009/1‑55 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTgg                                  <  1:3641892/70‑1 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                   >  1:1164887/1‑69 (MQ=255)
                                   gagaACCGCAATAAAATGCCGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                 <  1:3083172/71‑1 (MQ=255)
                                     gaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                      >  1:3505658/1‑48 (MQ=255)
                                      aaCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                      >  1:1388440/1‑47 (MQ=255)
                                      aaCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgag                                                              <  1:484511/39‑1 (MQ=255)
                                      aaCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                    >  1:1875951/1‑49 (MQ=255)
                                      aaCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                    >  1:1428646/1‑49 (MQ=255)
                                      aaCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtc                              <  1:430007/71‑1 (MQ=255)
                                       aCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                   >  1:3068593/1‑49 (MQ=255)
                                         cGCAATAAAATGCTGAAGGCTCAGGGGATTAACgaga                                                             >  1:1911681/1‑37 (MQ=255)
                                         cGCAATAAAATGCTGAAGGCTCAGGGGATTAACgaga                                                             >  1:3613359/1‑37 (MQ=255)
                                         cGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGttt                                                     <  1:852906/45‑1 (MQ=255)
                                           cAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                          >  1:3320419/1‑70 (MQ=255)
                                            aaTAAAATGCTGAAGGCTCAGGGAATTAACGAGACgt                                                          >  1:1829374/1‑37 (MQ=255)
                                            aaTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                   <  1:1931245/60‑1 (MQ=255)
                                            aaTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAgg                         <  1:2360064/70‑1 (MQ=255)
                                            aaTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCCGGAGTCTCAgg                         >  1:226049/1‑70 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTAc                                       <  1:588846/55‑1 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                       <  1:1186215/71‑1 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGGATTAACGAGAAGTTGTTTATGGCGTTGa                                           >  1:2790857/1‑51 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgt                                                       >  1:2437364/1‑39 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttg                                                        <  1:2142334/37‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAgg                         <  1:1195271/68‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaa                      <  1:3342056/71‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                             <  1:2705419/48‑1 (MQ=255)
                                               aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                    >  1:227465/1‑40 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                           >  1:1060830/1‑48 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                           >  1:244933/1‑48 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                     >  1:3335031/1‑70 (MQ=255)
                                                 aaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAcc                   <  1:728379/71‑1 (MQ=255)
                                                 aaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAcc                   <  1:1895176/71‑1 (MQ=255)
                                                  aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                          <  1:1277546/47‑1 (MQ=255)
                                                  aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                        >  1:3445900/1‑49 (MQ=255)
                                                  aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                        >  1:3275370/1‑49 (MQ=255)
                                                   tGCTGAAGGCTCAGGGGATTAACGTGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                       <  1:1406785/65‑1 (MQ=255)
                                                   tGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAtt                                         >  1:1789739/1‑47 (MQ=255)
                                                   tGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                     >  1:2632883/1‑67 (MQ=255)
                                                   tGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcac                 <  1:3014442/71‑1 (MQ=255)
                                                     cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg               <  1:2752855/71‑1 (MQ=255)
                                                      tGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCg                                               <  1:964764/38‑1 (MQ=255)
                                                      tGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCg                                               <  1:1332958/38‑1 (MQ=255)
                                                        aaGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt            <  1:3044588/71‑1 (MQ=255)
                                                        aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                             <  1:6516/38‑1 (MQ=255)
                                                         aGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt            >  1:1821908/1‑70 (MQ=255)
                                                         aGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt           <  1:468674/71‑1 (MQ=255)
                                                          ggCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                 >  1:1187469/1‑48 (MQ=255)
                                                           gCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                   <  1:1487790/45‑1 (MQ=255)
                                                           gCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                 >  1:1665677/1‑47 (MQ=255)
                                                           gCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                 >  1:3535075/1‑47 (MQ=255)
                                                           gCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                       <  1:2072402/57‑1 (MQ=255)
                                                            cttaGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAg        <  1:1854038/68‑1 (MQ=255)
                                                             tCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt            >  1:1079046/1‑66 (MQ=255)
                                                                   |                                                                     
CTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCT  >  W3110S.gb/2809514‑2809650

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