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 F3 I0 R1 43 41.2 3165159 98.4% 3114516 61.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,809,581 G→A 44.9% 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.gb2,809,5810GA44.9% 32.1 / 122.2 89G52G (GGG→GGA) mprADNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (24/25);  new base A (19/21);  total (43/46)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.32e-01

CTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCTG  >  W3110S.gb/2809514‑2809651
                                                                   |                                                                      
cTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAtt                                                                     <  1:478009/71‑1 (MQ=255)
      tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                                >  1:1808588/1‑70 (MQ=255)
       ttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                                              >  1:914069/1‑71 (MQ=255)
       ttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                                              >  1:2009959/1‑71 (MQ=255)
        tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGAc                                                             >  1:1872370/1‑71 (MQ=255)
         gcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTaa                                                                   >  1:1570517/1‑64 (MQ=255)
         gcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACg                                                            >  1:395269/1‑71 (MQ=255)
          catgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACg                                                            <  1:2494605/70‑1 (MQ=255)
           atgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgtt                                                          <  1:3022713/71‑1 (MQ=255)
           atgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgtt                                                          <  1:2934390/71‑1 (MQ=255)
             gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgt                                                        >  1:2985557/1‑71 (MQ=255)
             gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgt                                                        >  1:926207/1‑71 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                       <  1:1920312/71‑1 (MQ=255)
               acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACgaga                                                              >  1:284716/1‑63 (MQ=255)
               acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGAc                                                             >  1:374754/1‑64 (MQ=255)
               acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGttt                                                      <  1:2545233/71‑1 (MQ=255)
                catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTa                                                     <  1:761475/71‑1 (MQ=255)
                catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                     <  1:1391240/71‑1 (MQ=255)
                 atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                    >  1:2384831/1‑71 (MQ=255)
                 atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                    <  1:2953733/71‑1 (MQ=255)
                  tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                                   >  1:2132706/1‑71 (MQ=255)
                   gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                                <  1:2509999/57‑1 (MQ=255)
                   gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                                <  1:3061625/57‑1 (MQ=255)
                   gcaAAGCAAGCTGCTCGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                                <  1:49745/57‑1 (MQ=255)
                    caAAGCAAGCTGCTGGAGAACCG‑AATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCg                                                >  1:2326361/1‑71 (MQ=255)
                     aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCg                                                <  1:1550611/71‑1 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                              <  1:2634924/71‑1 (MQ=255)
                        gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAtt                                                                     >  1:1333308/1‑47 (MQ=255)
                           agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAtt                                          <  1:132844/71‑1 (MQ=255)
                            gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTa                                         <  1:3046873/71‑1 (MQ=255)
                             ctgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                    >  1:1507483/1‑59 (MQ=255)
                              tgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTAc                                        >  1:2363081/1‑70 (MQ=255)
                                ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTaa                                                                   >  1:676592/1‑41 (MQ=255)
                                ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                           >  1:2599522/1‑65 (MQ=255)
                                ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                  <  1:3071864/42‑1 (MQ=255)
                                ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCt                                     <  1:847054/71‑1 (MQ=255)
                                  ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    >  1:2699455/1‑70 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgt                                                        >  1:49490/1‑49 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:2118893/69‑1 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:1243266/69‑1 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:2507822/69‑1 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:1984172/69‑1 (MQ=255)
                                     gaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTATATGGCGTTGAATACGCTGGAGt                                >  1:1369470/1‑71 (MQ=255)
                                     gaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATgg                                                  <  1:194321/53‑1 (MQ=255)
                                     gaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                            <  1:2191967/59‑1 (MQ=255)
                                      aaCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttg                                                         <  1:2090857/45‑1 (MQ=255)
                                      aaCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgt                                                           <  1:1240430/43‑1 (MQ=255)
                                      aaCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:1537328/59‑1 (MQ=255)
                                        ccGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttg                                                         >  1:1473265/1‑43 (MQ=255)
                                        ccGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                              >  1:274910/1‑70 (MQ=255)
                                         cGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:343328/63‑1 (MQ=255)
                                          gCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                           >  1:2883914/1‑71 (MQ=255)
                                           cAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttg                                                         <  1:2524161/40‑1 (MQ=255)
                                           cAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                                              >  1:809496/1‑35 (MQ=255)
                                           cAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAgg                          <  1:606273/71‑1 (MQ=255)
                                           cAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                           >  1:1489139/1‑70 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTg                                             <  1:2015007/50‑1 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:3159960/52‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaa                       <  1:56254/71‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTTGa                                  <  1:860833/60‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                        >  1:690665/1‑70 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                        >  1:271701/1‑70 (MQ=255)
                                               aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                      >  1:1064645/1‑71 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGt                                               >  1:211532/1‑45 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTa                                         >  1:2767830/1‑51 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                  >  1:2748330/1‑58 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                      <  1:896858/70‑1 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc                     >  1:2569138/1‑71 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                            >  1:58437/1‑48 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                            >  1:2530132/1‑48 (MQ=255)
                                                 aaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                            >  1:1013946/1‑47 (MQ=255)
                                                  aTGCTGAAGGCTCAGGGGATTAACGAGACGTCGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                   <  1:2099011/71‑1 (MQ=255)
                                                  aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                   <  1:1164096/71‑1 (MQ=255)
                                                   tGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                   >  1:179243/1‑70 (MQ=255)
                                                    gCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTa                                                     >  1:1470350/1‑35 (MQ=255)
                                                    gCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAgg                          >  1:1494942/1‑62 (MQ=255)
                                                     cTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTAGGCTGGAg                                 >  1:1278618/1‑54 (MQ=255)
                                                     cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcaca                 <  1:2958730/70‑1 (MQ=255)
                                                       gAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                        <  1:232726/61‑1 (MQ=255)
                                                        aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt             <  1:1706293/71‑1 (MQ=255)
                                                        aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt             >  1:2727696/1‑71 (MQ=255)
                                                         aGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt            <  1:526329/71‑1 (MQ=255)
                                                         aGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt            <  1:272969/71‑1 (MQ=255)
                                                          ggCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTc           <  1:1913540/71‑1 (MQ=255)
                                                          ggCTCAGGGAATTAACGAGACGTTGTTTATGGCGt                                               >  1:2671432/1‑35 (MQ=255)
                                                          ggCTCAGGGAATTAACGAGACGTTGTTTATGGCGt                                               >  1:2700392/1‑35 (MQ=255)
                                                            cTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAg         <  1:398037/71‑1 (MQ=255)
                                                             tCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCt                                     <  1:2726676/42‑1 (MQ=255)
                                                             tCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCt                                     <  1:2730318/42‑1 (MQ=255)
                                                                   gATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCa                            >  1:154588/1‑45 (MQ=255)
                                                                   gATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCTg  <  1:485979/71‑1 (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