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 F1 I0 R2 47 59.8 4603576 97.9% 4506900 61.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,809,581 G→A 89.4% 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.gb2,809,5810GA89.4% 1788.3 / 163.5 663G52G (GGG→GGA) mprADNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (34/36);  new base A (294/298);  total (328/335)
Fisher's exact test for biased strand distribution p-value = 9.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 669 total aligned reads displayed.

ACTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCTG  >  W3110S.gb/2809513‑2809651
                                                                    |                                                                      
aCTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAt                                                                      >  1:2625274/1‑71 (MQ=255)
  tCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                     >  1:4598588/1‑70 (MQ=255)
    gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                     <  1:3845994/68‑1 (MQ=255)
    gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAt                                                                      <  1:4174142/67‑1 (MQ=255)
    gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTaa                                                                   <  1:3260909/70‑1 (MQ=255)
    gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                  >  1:3632616/1‑71 (MQ=255)
       tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                  >  1:596198/1‑68 (MQ=255)
       tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                  >  1:4571791/1‑68 (MQ=255)
         tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACga                                                                <  1:3388832/68‑1 (MQ=255)
         tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGAc                                                             >  1:228594/1‑71 (MQ=255)
         tgcatgcaCATGCAAAGCAAGCTGCTGGAAAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                                <  1:3570525/68‑1 (MQ=255)
          gcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACg                                                            >  1:2992581/1‑71 (MQ=255)
             tgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                     <  1:1408528/59‑1 (MQ=255)
             tgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttg                                                         >  1:1936866/1‑71 (MQ=255)
             tgcacatgcaAAGCAAACTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttg                                                         <  1:2064383/71‑1 (MQ=255)
              gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgt                                                        >  1:3821666/1‑71 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       <  1:1682704/71‑1 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       <  1:1440398/71‑1 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       >  1:564718/1‑71 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                    >  1:1619744/1‑71 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                    >  1:2092512/1‑71 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                    >  1:2386313/1‑71 (MQ=255)
                   tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTaa                                                                   >  1:4403787/1‑55 (MQ=255)
                    gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttg                                                         <  1:2877827/64‑1 (MQ=255)
                    gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATgg                                                  >  1:3496000/1‑71 (MQ=255)
                     caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTAAGGGAATTAACGAGACGTTGTTTa                                                     >  1:4320270/1‑67 (MQ=255)
                      aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGttt                                                      <  1:103359/65‑1 (MQ=255)
                      aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                                   >  1:1789926/1‑68 (MQ=255)
                      aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCg                                                <  1:4198323/71‑1 (MQ=255)
                       aagcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttg                                                         <  1:1359672/61‑1 (MQ=255)
                       aagcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGt                                               >  1:4075391/1‑71 (MQ=255)
                        agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                  >  1:2799188/1‑51 (MQ=255)
                        agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                              <  1:3526934/71‑1 (MQ=255)
                         gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGttt                                                      <  1:656691/62‑1 (MQ=255)
                         gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                              <  1:3119443/70‑1 (MQ=255)
                          caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                    >  1:1193567/1‑63 (MQ=255)
                           aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:3461246/71‑1 (MQ=255)
                           aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:69200/71‑1 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGc                                      <  1:3313466/70‑1 (MQ=255)
                                 ctgGAAAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                    >  1:1089302/1‑56 (MQ=255)
                                   ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgt                                                        >  1:3172162/1‑50 (MQ=255)
                                   ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    >  1:848973/1‑70 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                     >  1:1723031/1‑36 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                            >  1:2119342/1‑61 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:967479/69‑1 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:2847643/69‑1 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    >  1:1645776/1‑69 (MQ=255)
                                       aaCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                                 <  1:202881/53‑1 (MQ=255)
                                        aCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                              <  1:2741562/71‑1 (MQ=255)
                                        aCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                              <  1:4226197/71‑1 (MQ=255)
                                         ccGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:889923/57‑1 (MQ=255)
                                          cGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttg                                                         >  1:4461482/1‑42 (MQ=255)
                                          cGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       <  1:1012663/44‑1 (MQ=255)
                                          cGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTg                                             <  1:1335144/54‑1 (MQ=255)
                                           gCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                           >  1:2324841/1‑71 (MQ=255)
                                           ccAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                     <  1:2697210/44‑1 (MQ=39)
                                            cAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtctc                             >  1:4046651/1‑68 (MQ=255)
                                              aTAAAATGCTGAAGGGTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGa                         >  1:3616862/1‑70 (MQ=255)
                                              aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                              <  1:4015330/49‑1 (MQ=255)
                                              aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                        <  1:4374841/71‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaa                       <  1:175266/71‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGAATTAACGAGACgt                                                           >  1:2170272/1‑35 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGttt                                                      <  1:2410253/40‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCg                                                <  1:3660228/46‑1 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaa                       <  1:753507/71‑1 (MQ=255)
                                                aaaaTGCTTAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGc                                      <  1:3224885/55‑1 (MQ=255)
                                                aaaaTGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       <  1:734833/38‑1 (MQ=255)
                                                aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                     >  1:794696/1‑40 (MQ=255)
                                                aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                      >  1:1289037/1‑71 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCt                                     >  1:3926359/1‑55 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                            >  1:4507359/1‑48 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                  >  1:1122186/1‑58 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                  >  1:3431319/1‑58 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAg                                 >  1:544497/1‑59 (MQ=255)
                                                  aaTGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       <  1:2529055/36‑1 (MQ=255)
                                                   aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                   <  1:3344654/71‑1 (MQ=255)
                                                   aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                      >  1:1145127/1‑68 (MQ=255)
                                                   aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                      >  1:500246/1‑68 (MQ=255)
                                                   aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                        <  1:1485759/66‑1 (MQ=255)
                                                    tGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcac                  <  1:1589911/71‑1 (MQ=255)
                                                    tGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                   >  1:2370267/1‑70 (MQ=255)
                                                     gCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAgg                          >  1:875543/1‑62 (MQ=255)
                                                      cTGAAGGCTCATGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcaca                 >  1:1531452/1‑70 (MQ=255)
                                                      cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg                <  1:4264789/71‑1 (MQ=255)
                                                      cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg                <  1:2488318/71‑1 (MQ=255)
                                                       tGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                              <  1:1230954/40‑1 (MQ=255)
                                                       tGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    <  1:369827/50‑1 (MQ=255)
                                                        gAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGt               >  1:3073366/1‑70 (MQ=255)
                                                         aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                            >  1:4485310/1‑40 (MQ=255)
                                                         aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                  >  1:2442672/1‑50 (MQ=255)
                                                         aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa              <  1:3965147/70‑1 (MQ=255)
                                                          aGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt            >  1:1894320/1‑71 (MQ=255)
                                                            gCTCATGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                   <  1:1251687/62‑1 (MQ=255)
                                                             cTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                      >  1:3876315/1‑58 (MQ=255)
                                                             cTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAg         >  1:2188135/1‑71 (MQ=255)
                                                              tCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:2227103/36‑1 (MQ=255)
                                                              tCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:2927432/36‑1 (MQ=255)
                                                              tCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                   >  1:4130174/1‑60 (MQ=255)
                                                              tCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGc        >  1:3741216/1‑71 (MQ=255)
                                                                aGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                         >  1:1845603/1‑36 (MQ=255)
                                                                    |                                                                      
ACTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCTG  >  W3110S.gb/2809513‑2809651

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