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 R2 52 68.8 5189613 98.4% 5106579 62.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,809,581 G→A 29.6% 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.gb2,809,5810GA29.6% 152.2 / 80.1 98G52G (GGG→GGA) mprADNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (33/36);  new base A (17/12);  total (50/48)
Fisher's exact test for biased strand distribution p-value = 3.80e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.33e-01

Only 100 of 101 total aligned reads displayed.

GACTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTT  >  W3110S.gb/2809512‑2809648
                                                                     |                                                                   
gACTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGa                                                                    >  1:1751632/1‑71 (MQ=255)
 aCTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAt                                                                   >  1:4953942/1‑71 (MQ=255)
   tCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                  >  1:2571982/1‑70 (MQ=255)
     gTCTTTGCATGCACATGCAAAGCAAGATGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                               >  1:4238993/1‑71 (MQ=255)
        tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTTAc                                                               >  1:3024737/1‑68 (MQ=255)
        tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                               >  1:501883/1‑68 (MQ=255)
         ttGCATGCACATGCAAAGCAAGCTGCTGGACAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACgaga                                                           >  1:3476539/1‑71 (MQ=255)
          tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                             <  1:3111265/68‑1 (MQ=255)
           gcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGAc                                                          <  1:1163288/70‑1 (MQ=255)
            catgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACg                                                         <  1:4953775/70‑1 (MQ=255)
             atgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgtt                                                       >  1:2973774/1‑71 (MQ=255)
              tgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttg                                                      >  1:3272409/1‑71 (MQ=255)
               gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgt                                                     >  1:5100386/1‑71 (MQ=255)
                  catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGa                                                                    >  1:5073051/1‑53 (MQ=255)
                    tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                 <  1:109520/70‑1 (MQ=255)
                     gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATg                                                >  1:1731198/1‑70 (MQ=255)
                      caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAt                                                                   >  1:1664935/1‑50 (MQ=255)
                      caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                              >  1:1943461/1‑71 (MQ=255)
                      caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                              <  1:4617411/71‑1 (MQ=255)
                       aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGc                                              >  1:4295992/1‑70 (MQ=255)
                       aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCg                                             >  1:3046028/1‑71 (MQ=255)
                       aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCg                                             <  1:1479374/71‑1 (MQ=255)
                       aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGAc                                                          >  1:3164835/1‑58 (MQ=255)
                       aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                    >  1:1135085/1‑64 (MQ=255)
                       aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCg                                             >  1:2093240/1‑71 (MQ=255)
                       aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCg                                             <  1:4177920/71‑1 (MQ=255)
                          gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGc                                              <  1:760473/67‑1 (MQ=255)
                           caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTg                                          <  1:29662/70‑1 (MQ=255)
                           caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                         <  1:3906102/71‑1 (MQ=255)
                           caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                         >  1:1991128/1‑71 (MQ=255)
                            aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTg                                          <  1:4306342/69‑1 (MQ=255)
                             agcTTCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                        <  1:1637719/70‑1 (MQ=255)
                             agcTGCTGGAGAACCGCAATAAAATTCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAtt                                       <  1:2069616/71‑1 (MQ=255)
                              gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                      <  1:4855931/71‑1 (MQ=255)
                               ctgctgGAGAAACGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTAc                                     >  1:603797/1‑71 (MQ=255)
                                tgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                    <  1:4587310/55‑1 (MQ=255)
                                 gctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                 <  1:4141581/57‑1 (MQ=255)
                                  ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACg                                    <  1:4594267/69‑1 (MQ=255)
                                  ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGc                                   <  1:4361612/70‑1 (MQ=255)
                                     gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTgg                                <  1:803570/70‑1 (MQ=255)
                                      agaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTgg                                <  1:3742792/69‑1 (MQ=255)
                                      agaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAg                              >  1:3352083/1‑71 (MQ=255)
                                        aaCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGCCGTTGATTACGCTGGAGtc                            >  1:2904310/1‑71 (MQ=255)
                                         aCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                        >  1:2693819/1‑58 (MQ=255)
                                          ccGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGttt                                                   <  1:48012/46‑1 (MQ=255)
                                          ccGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtctc                          <  1:1150365/71‑1 (MQ=255)
                                            gCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAAGGCGTTGATTACGCTGGAGTCTCAg                        >  1:2553834/1‑71 (MQ=255)
                                            gCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTg                                          >  1:1815411/1‑53 (MQ=255)
                                             cAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAgg                       <  1:3208795/71‑1 (MQ=255)
                                              aaTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                           <  1:3817868/50‑1 (MQ=255)
                                              aaTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAgg                       >  1:1399496/1‑70 (MQ=255)
                                              aaTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGa                      <  1:1455087/71‑1 (MQ=255)
                                              aaTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAgg                       >  1:3475731/1‑70 (MQ=255)
                                               ataataTGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                    <  1:2782842/40‑1 (MQ=255)
                                               aTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                     <  1:1860097/71‑1 (MQ=255)
                                               aTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                     <  1:2033450/71‑1 (MQ=255)
                                               aTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                     <  1:706783/71‑1 (MQ=255)
                                               aTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                     <  1:2565829/71‑1 (MQ=255)
                                               aTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGa                      >  1:3369567/1‑70 (MQ=255)
                                               aTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGa                      >  1:2176928/1‑70 (MQ=255)
                                               aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                     <  1:4427921/71‑1 (MQ=255)
                                                tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGttt                                                   <  1:2925307/40‑1 (MQ=255)
                                                tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                         >  1:2292125/1‑50 (MQ=255)
                                                tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                     >  1:3025498/1‑70 (MQ=255)
                                                 aaaaTGCTTAAGGCTCAGGGGATTAACGAGACGTTGTTTa                                                  >  1:1162142/1‑40 (MQ=255)
                                                 aaaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTgg                                >  1:4499816/1‑58 (MQ=255)
                                                 aaaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                   >  1:2211909/1‑71 (MQ=255)
                                                  aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGt                             >  1:3201182/1‑60 (MQ=255)
                                                   aaTGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                    <  1:3506744/36‑1 (MQ=255)
                                                   aaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTg                                          <  1:4378490/46‑1 (MQ=255)
                                                   aaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCt                                  >  1:4342091/1‑54 (MQ=255)
                                                   aaTGCTGAAGGCTCAGGGGATTAACGAGACGGTGTTTATGGCGTTg                                          <  1:3431773/46‑1 (MQ=255)
                                                   aaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc                  <  1:4413242/70‑1 (MQ=255)
                                                    aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                <  1:3992828/71‑1 (MQ=255)
                                                     tGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                >  1:2038628/1‑70 (MQ=255)
                                                       cTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                     >  1:58590/1‑63 (MQ=255)
                                                       cTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg             >  1:2665520/1‑71 (MQ=255)
                                                       cTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg             <  1:1844290/71‑1 (MQ=255)
                                                       cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcaca              <  1:4273889/70‑1 (MQ=255)
                                                       cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg             <  1:3327820/71‑1 (MQ=255)
                                                         gAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg             <  1:4673392/69‑1 (MQ=255)
                                                          aaGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa           <  1:2745488/70‑1 (MQ=255)
                                                          aaGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt          >  1:2847497/1‑71 (MQ=255)
                                                          aaGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt          <  1:4140492/71‑1 (MQ=255)
                                                          aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt          >  1:2228509/1‑71 (MQ=255)
                                                           aGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaa                    >  1:5078279/1‑60 (MQ=255)
                                                           aGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaa                    >  1:180791/1‑60 (MQ=255)
                                                           aGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc                  >  1:3558982/1‑62 (MQ=255)
                                                           aGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt         <  1:3042778/71‑1 (MQ=255)
                                                           aGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt         <  1:2713122/71‑1 (MQ=255)
                                                           aGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt         <  1:1980487/71‑1 (MQ=255)
                                                           aGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                               >  1:2755066/1‑49 (MQ=255)
                                                            ggCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAtt         >  1:4556135/1‑70 (MQ=255)
                                                              cTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                <  1:684175/61‑1 (MQ=255)
                                                               tCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAg      >  1:1168785/1‑70 (MQ=255)
                                                                cAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTa                                      >  1:122094/1‑37 (MQ=255)
                                                                 aGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCt   >  1:1544418/1‑71 (MQ=255)
                                                                  ggggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCtt  <  1:2428726/71‑1 (MQ=255)
                                                                  ggggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCtt  <  1:75944/71‑1 (MQ=255)
                                                                   gggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcaca              >  1:1751570/1‑58 (MQ=255)
                                                                     |                                                                   
GACTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTT  >  W3110S.gb/2809512‑2809648

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