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
A1 F8 I0 R1 311 50.1 4085234 95.9% 3917739 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,809,581 G→A 87.4% 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.gb2,809,5810GA87.4% 1284.6 / 149.8 485G52G (GGG→GGA) mprADNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (24/37);  new base A (176/248);  total (200/285)
Fisher's exact test for biased strand distribution p-value = 7.82e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 497 total aligned reads displayed.

CTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCTG  >  W3110S.gb/2809514‑2809651
                                                                   |                                                                      
cTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAtt                                                                     <  1:690293/71‑1 (MQ=255)
cTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAt                                                                      >  1:2081711/1‑70 (MQ=255)
cTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAt                                                                      >  1:2901244/1‑70 (MQ=255)
  cGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                                    >  1:3155093/1‑70 (MQ=255)
   gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                  >  1:3261438/1‑71 (MQ=255)
    tCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                  <  1:2118685/70‑1 (MQ=255)
      tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                  >  1:1021217/1‑68 (MQ=255)
      tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                  >  1:1059936/1‑68 (MQ=255)
      tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                  >  1:875762/1‑68 (MQ=255)
        tgcatgcaCATTCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgag                                                               <  1:598107/69‑1 (MQ=255)
        tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgag                                                               <  1:2021877/69‑1 (MQ=255)
        tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgag                                                               <  1:3506703/69‑1 (MQ=255)
        tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                                <  1:3384423/68‑1 (MQ=255)
        tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                                <  1:1331389/68‑1 (MQ=255)
        tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGAc                                                             >  1:1085393/1‑71 (MQ=255)
          catgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgt                                                           <  1:2058441/71‑1 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       <  1:1733853/71‑1 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       >  1:1296229/1‑71 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       <  1:2140667/71‑1 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       <  1:2395517/71‑1 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       >  1:2618379/1‑71 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       <  1:3625798/71‑1 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       >  1:2943306/1‑71 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       <  1:3348032/71‑1 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgt                                                        <  1:3491101/70‑1 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgt                                                        <  1:3011819/70‑1 (MQ=255)
              cacaagcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       <  1:1510142/71‑1 (MQ=255)
                catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTa                                                     <  1:2783581/71‑1 (MQ=255)
                  tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                  <  1:4033067/56‑1 (MQ=255)
                    caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                                              >  1:449668/1‑58 (MQ=255)
                    caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                     >  1:1261766/1‑67 (MQ=255)
                    caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                                 >  1:2627574/1‑71 (MQ=255)
                    caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                                 >  1:3394656/1‑71 (MQ=255)
                    caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                                 <  1:802825/71‑1 (MQ=255)
                       agcaagcTGCTGGAGAACCGCATTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                              <  1:2877329/71‑1 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGTCGTTGTTTATGGCGtt                                              <  1:321062/71‑1 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                              <  1:2269456/71‑1 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                              <  1:271083/71‑1 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                              <  1:2698172/71‑1 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                              <  1:829544/71‑1 (MQ=255)
                        gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                              <  1:3294774/70‑1 (MQ=255)
                        gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTg                                             <  1:546405/71‑1 (MQ=255)
                        gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTg                                             <  1:1920151/71‑1 (MQ=255)
                         caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgtt                                                          <  1:3861401/57‑1 (MQ=255)
                          aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:1225820/71‑1 (MQ=255)
                          aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:3040025/71‑1 (MQ=255)
                           agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgt                                                        <  1:1887129/57‑1 (MQ=255)
                            gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                         <  1:1314090/71‑1 (MQ=255)
                             ctgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                     <  1:1005854/42‑1 (MQ=255)
                                ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCt                                     <  1:3746319/71‑1 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:3413044/69‑1 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:2583597/69‑1 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:377371/69‑1 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                  <  1:2240420/71‑1 (MQ=255)
                                     gaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGt                                >  1:2755098/1‑71 (MQ=255)
                                        ccGCAATAAAATTCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTa                                                     <  1:2379783/47‑1 (MQ=255)
                                          gCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                         <  1:161365/57‑1 (MQ=255)
                                          gCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                         >  1:390715/1‑57 (MQ=255)
                                          gCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                           >  1:3551937/1‑71 (MQ=255)
                                            aaTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:1431450/53‑1 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                       <  1:923910/40‑1 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                  <  1:3319427/61‑1 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTCATGGCGTTGATTACGCTGGa                                  <  1:972773/61‑1 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       <  1:1367695/40‑1 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                        <  1:1942376/71‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGTAATTAACGAGACgttgtt                                                       <  1:196787/39‑1 (MQ=37)
                                              tAAAATGCTGAAGGCTCAGGTAATTAACGAGACGTTGTTTAt                                                    <  1:665582/42‑1 (MQ=38)
                                              tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaa                       <  1:3723310/71‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                    <  1:1152342/42‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                    <  1:777103/42‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                    <  1:410798/42‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                              <  1:3071354/48‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                              <  1:851046/48‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:3650636/51‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:3983186/51‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                         >  1:2543658/1‑53 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtc                               <  1:2656454/63‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                        <  1:3360926/70‑1 (MQ=255)
                                               aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                    >  1:2182823/1‑41 (MQ=255)
                                               aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                      >  1:1744985/1‑71 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                            >  1:1799330/1‑48 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGttt                                                      >  1:738173/1‑38 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                              <  1:3948658/46‑1 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                            >  1:1643166/1‑48 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc                     >  1:1452968/1‑71 (MQ=255)
                                                   tGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                    <  1:1685798/37‑1 (MQ=255)
                                                   tGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcac                  <  1:2486162/71‑1 (MQ=255)
                                                   tGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                   <  1:4049145/70‑1 (MQ=255)
                                                     cTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg                <  1:510093/71‑1 (MQ=255)
                                                     cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATgg                                                  >  1:2761036/1‑37 (MQ=255)
                                                     cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg                <  1:2219605/71‑1 (MQ=255)
                                                        aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt             <  1:1387459/71‑1 (MQ=255)
                                                        aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt             <  1:1718315/71‑1 (MQ=255)
                                                          ggCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACGACAGTAtt            >  1:560585/1‑70 (MQ=255)
                                                          ggCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa              >  1:1868361/1‑68 (MQ=255)
                                                           gCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCa          <  1:232155/71‑1 (MQ=255)
                                                             tCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAg         <  1:2995458/70‑1 (MQ=255)
                                                             tCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGc        >  1:2447669/1‑71 (MQ=255)
                                                                ggggATTAACGAGACGTTTTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg                <  1:3526818/60‑1 (MQ=255)
                                                                  ggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa              >  1:2832675/1‑60 (MQ=255)
                                                                   |                                                                      
CTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCTG  >  W3110S.gb/2809514‑2809651

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