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
A5 F8 I0 R1 43 62.4 4721813 98.4% 4646263 62.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,809,581 G→A 50.4% 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.gb2,809,5810GA50.4% ‑1.0 / 200.9 123G52G (GGG→GGA) mprADNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (27/34);  new base A (34/28);  total (61/62)
Fisher's exact test for biased strand distribution p-value = 2.81e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.77e-01

Only 100 of 130 total aligned reads displayed.

ACTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCTG  >  W3110S.gb/2809513‑2809651
                                                                    |                                                                      
aCTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAt                                                                      >  1:3639524/1‑71 (MQ=255)
  tCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                     >  1:4499594/1‑70 (MQ=255)
    gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                  >  1:4689717/1‑71 (MQ=255)
    gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTaa                                                                   <  1:734192/70‑1 (MQ=255)
    gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                  >  1:3739455/1‑71 (MQ=255)
     tCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                  >  1:2226893/1‑70 (MQ=255)
       tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                  >  1:575587/1‑68 (MQ=255)
         tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACgag                                                               <  1:2089741/69‑1 (MQ=255)
            atgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACg                                                                 <  1:2075290/64‑1 (MQ=255)
             tgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttg                                                         >  1:3105450/1‑71 (MQ=255)
             tgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttg                                                         <  1:2001133/71‑1 (MQ=255)
              gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgt                                                        >  1:3909850/1‑71 (MQ=255)
              gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgt                                                        >  1:4102879/1‑71 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       <  1:784529/71‑1 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       <  1:2828294/71‑1 (MQ=255)
                acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       >  1:1561748/1‑70 (MQ=255)
                 catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTaa                                                                   >  1:4534449/1‑57 (MQ=255)
                 catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgag                                                               >  1:1300218/1‑61 (MQ=255)
                 catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgag                                                               >  1:919190/1‑61 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                       <  1:3158272/68‑1 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttg                                                         >  1:2145222/1‑66 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTa                                                     >  1:3159682/1‑70 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                    >  1:3743230/1‑71 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGATCAGGGGAtt                                                                     >  1:2517251/1‑54 (MQ=255)
                   tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                  <  1:2260514/56‑1 (MQ=255)
                   tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                                   >  1:3268865/1‑71 (MQ=255)
                    gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                  <  1:119244/55‑1 (MQ=255)
                     caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                                >  1:3951478/1‑56 (MQ=255)
                        agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                              >  1:598602/1‑71 (MQ=255)
                        agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                              <  1:48167/71‑1 (MQ=255)
                        agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                  <  1:4407965/51‑1 (MQ=255)
                         gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                              <  1:4425562/70‑1 (MQ=255)
                           aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:1246514/71‑1 (MQ=255)
                            agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                            >  1:3519778/1‑69 (MQ=255)
                             gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTa                                         <  1:186626/71‑1 (MQ=255)
                              ctgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTAc                                        <  1:2422008/71‑1 (MQ=255)
                               tgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:4146749/67‑1 (MQ=255)
                               tgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                         <  1:3583348/69‑1 (MQ=255)
                                gctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                    <  1:4180579/57‑1 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:4156531/65‑1 (MQ=255)
                                  tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                              <  1:652454/61‑1 (MQ=255)
                                   ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    >  1:2818413/1‑70 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAtt                                          <  1:2155858/63‑1 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:1263081/69‑1 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:844899/69‑1 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:1779476/69‑1 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:334512/69‑1 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:2505830/69‑1 (MQ=255)
                                      gaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                     >  1:4678214/1‑50 (MQ=255)
                                      gaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                     >  1:1164351/1‑50 (MQ=255)
                                       aaCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATg                                                   <  1:4047526/51‑1 (MQ=255)
                                       aaCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTT‑ATTACGCTGGAGtct                              <  1:210441/71‑1 (MQ=255)
                                          cGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACcttgtt                                                       <  1:1747408/44‑1 (MQ=255)
                                          cGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                              <  1:1630016/69‑1 (MQ=255)
                                           gCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGc                                                 <  1:223454/49‑1 (MQ=255)
                                           gCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                                   >  1:1822129/1‑47 (MQ=255)
                                            cAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                              <  1:4337109/51‑1 (MQ=255)
                                            cAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                              <  1:1148268/51‑1 (MQ=255)
                                            cAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAgg                          <  1:3804218/71‑1 (MQ=255)
                                            cAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                           >  1:2384045/1‑70 (MQ=255)
                                            cAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACg                                                            <  1:935786/37‑1 (MQ=255)
                                            cAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                           >  1:363579/1‑70 (MQ=255)
                                             aaTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                              <  1:2996416/50‑1 (MQ=255)
                                             aaTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAgg                          >  1:2851522/1‑70 (MQ=255)
                                              aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACgtt                                                          >  1:2386591/1‑37 (MQ=255)
                                              aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACgtt                                                          >  1:3941756/1‑37 (MQ=255)
                                              aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                              <  1:117745/49‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                    <  1:778767/42‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                        >  1:1087592/1‑70 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                        >  1:3281995/1‑70 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                              >  1:1891966/1‑46 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                              >  1:1111915/1‑46 (MQ=255)
                                                 aaaTGATGAAGGCTCAGGGAATTAACGAGAAGTTGTTTATGGAGt                                               >  1:1106377/1‑45 (MQ=255)
                                                  aaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTAAGCTGGAGTCTCAGGAAAAc                     <  1:4123730/70‑1 (MQ=255)
                                                   aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCa                            >  1:197220/1‑62 (MQ=255)
                                                   aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCa                            >  1:4259790/1‑62 (MQ=255)
                                                   aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                   >  1:1792698/1‑71 (MQ=255)
                                                    tGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                   >  1:4012365/1‑70 (MQ=255)
                                                     gCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                   >  1:4024749/1‑69 (MQ=255)
                                                     gCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                   >  1:1795652/1‑69 (MQ=255)
                                                     gCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                   >  1:4444392/1‑69 (MQ=255)
                                                      cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcaca                 <  1:3872485/70‑1 (MQ=255)
                                                      cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcaca                 <  1:788134/70‑1 (MQ=255)
                                                      cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcaca                 <  1:3077892/70‑1 (MQ=255)
                                                       tGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACg                                       <  1:2441743/47‑1 (MQ=255)
                                                         aaGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGc                                      <  1:1727112/46‑1 (MQ=255)
                                                          aGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                  >  1:3746198/1‑49 (MQ=255)
                                                          aGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt            <  1:222223/71‑1 (MQ=255)
                                                          aGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt            <  1:3381863/71‑1 (MQ=255)
                                                          aGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt            <  1:2559660/71‑1 (MQ=255)
                                                               cAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    >  1:613456/1‑42 (MQ=255)
                                                               cAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    >  1:3868660/1‑42 (MQ=255)
                                                               cAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGcc       >  1:269105/1‑71 (MQ=255)
                                                                aGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGa                         >  1:2809418/1‑52 (MQ=255)
                                                                aGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg                >  1:2163558/1‑61 (MQ=255)
                                                                aGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGcc       <  1:3085074/70‑1 (MQ=255)
                                                                 ggggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                      >  1:615335/1‑54 (MQ=255)
                                                                   ggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCt   >  1:1957152/1‑71 (MQ=255)
                                                                   ggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCt   >  1:588534/1‑71 (MQ=255)
                                                                    gATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCTg  <  1:1993446/71‑1 (MQ=255)
                                                                    |                                                                      
ACTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCTG  >  W3110S.gb/2809513‑2809651

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