Predicted mutation
evidence seq id position mutation freq annotation gene description
RA AP009048 71,109 T→C 25.5% T241T (ACT→ACC araC → DNA‑binding transcriptional dual regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AP00904871,1090TC25.5% 172.3 / 64.2 97T241T (ACT→ACCaraCDNA‑binding transcriptional dual regulator
Reads supporting (aligned to +/- strand):  ref base T (30/42);  new base C (7/17);  total (38/59)
Fisher's exact test for biased strand distribution p-value = 3.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 103 total aligned reads displayed.

TTAGGGATTAGCGTCTTAAGCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATCAACTCTATTTCTCGCGAGTA  >  AP009048/71041‑71178
                                                                    |                                                                     
ttAGGGATTAGCGTCTTAAGCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTa                                                                      >  1:113923/1‑70 (MQ=255)
  aGGGATTAGCGTCTTAAGCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTAccc                                                                   >  1:1381761/1‑71 (MQ=255)
  aGGGATTAGCGTCTTAAGCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTAcc                                                                    <  1:2506671/70‑1 (MQ=255)
   gggATTAGCGTCTTAAGCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCg                                                                  <  1:3038304/71‑1 (MQ=255)
    ggATTAGCGTCTTAAGCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCg                                                                  >  1:2664018/1‑70 (MQ=255)
     gATTAGCGTCTTAAGCTGGCGCGAGGACCAACGTATCAGCCAGGCGAAGCTGCTTTTGAGCACCACCCg                                                                  <  1:1210610/69‑1 (MQ=255)
     gATTAGCGTCTTAAGCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGa                                                                <  1:3793083/71‑1 (MQ=255)
      aTTAGCGTCTTAAGCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGa                                                                >  1:1072028/1‑70 (MQ=255)
          gCGTCTTAAGCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGcc                                                            >  1:3442576/1‑70 (MQ=255)
          gCGTCTTAAGCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGcc                                                            <  1:2832758/70‑1 (MQ=255)
          gCGTCTTAAGCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGcc                                                            >  1:2640585/1‑70 (MQ=255)
           cGTCTTAAGCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTa                                                          <  1:5009363/71‑1 (MQ=255)
           cGTCTTAAGCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTa                                                          >  1:4340919/1‑71 (MQ=255)
           cGTCTTAAGCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTa                                                          <  1:3555347/71‑1 (MQ=255)
           cGTCTTAAGCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTa                                                          <  1:4349324/71‑1 (MQ=255)
             tCTTAAGCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCg                                                                  <  1:1642497/61‑1 (MQ=255)
             tCTTAAGCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATc                                                        >  1:1959777/1‑71 (MQ=255)
             tCTTAAGCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATc                                                        <  1:4126133/71‑1 (MQ=255)
              cTTAAGCTGGCGCGAGGACCAACGTATCAGCCAGGCGAAGCTGCTTTTGAGCACCACCCGGATGCCTATCg                                                       >  1:2156700/1‑71 (MQ=255)
                 aaGCTGGCGCGAGGACCAACGTATCAGCCAGGCGAAGCTGCTTTTGAGCACCACCCGGATGCCTATCGc                                                      <  1:4682167/69‑1 (MQ=255)
                 aaGCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGc                                                             >  1:2334096/1‑62 (MQ=255)
                  aGCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCa                                                    <  1:1990277/70‑1 (MQ=255)
                   gCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCAcc                                                  <  1:2468171/71‑1 (MQ=255)
                    cTGGCGCGAGGACCAACGTATCAGCCAGGCGAAGCTGCTTTTGAGCACCACGCGGATGCCTAt                                                         <  1:2616167/63‑1 (MQ=255)
                    cTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCg                                                 <  1:4979896/71‑1 (MQ=255)
                     tGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCg                                                                  <  1:1684754/53‑1 (MQ=255)
                        cgcgAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCgtcgg                                             >  1:2820478/1‑71 (MQ=255)
                         gcgAGGACCAACGTATCAGCCAGGCGAAGCTGCTTTTGAGCACCACCCGGATGCCTATCGCCACCgtcggt                                            <  1:3497401/71‑1 (MQ=255)
                         gcgAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGa                                                                >  1:653168/1‑51 (MQ=255)
                             ggACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGc                                         >  1:1560542/1‑70 (MQ=255)
                             ggACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCa                                        <  1:1725680/71‑1 (MQ=255)
                             ggACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCa                                        <  1:772709/71‑1 (MQ=255)
                                ccAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATg                                     <  1:4473757/71‑1 (MQ=255)
                                ccAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATg                                     <  1:1645925/71‑1 (MQ=255)
                                 cAACGTATCAGCCAGGCGAAGCTGCTTTTGAGCACCACCCGGATGCCTATCGCCACCGTCGGTCGCAATGt                                    <  1:1881769/71‑1 (MQ=255)
                                 cAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCAc                                                   <  1:2502989/56‑1 (MQ=255)
                                 cAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGt                                    <  1:4416068/71‑1 (MQ=255)
                                 cAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGt                                    <  1:4686538/71‑1 (MQ=255)
                                 cAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGt                                    >  1:1820761/1‑71 (MQ=255)
                                  aaCGTATCAGCCAGGCGAAGCTGCTTTTGAGCACCACCCGGATGCCTATCGCCACCgtcg                                              >  1:172232/1‑60 (MQ=255)
                                  aaCGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGtt                                   >  1:3452967/1‑71 (MQ=255)
                                   aCGTATCAGCCAGGCGAAGCTGCTTTTGAGCACCACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTg                                  >  1:4957236/1‑71 (MQ=255)
                                   aCGTATCAGCCAGGCGAAGCTGCTTTTGAGCACCACACGGATGCCTATCGCCACAgtcgg                                             >  1:4346418/1‑60 (MQ=255)
                                   aCGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTg                                  >  1:1555022/1‑71 (MQ=255)
                                     gCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTg                                  >  1:4780198/1‑69 (MQ=255)
                                      cATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGtt                               >  1:2679282/1‑71 (MQ=255)
                                        ttAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGTtttt                             <  1:713509/71‑1 (MQ=255)
                                        ttAGTCAGGCGAAGCTGCTTTTAAGCACTACCCGGATGCCTATCGCCACCgt                                                <  1:1607947/52‑1 (MQ=255)
                                         tAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTAt                                                         >  1:1791790/1‑42 (MQ=255)
                                         tAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGcc                                                     >  1:3217216/1‑46 (MQ=255)
                                         tAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCgtcggt                                            >  1:3536565/1‑55 (MQ=255)
                                          agccAGGCGAAGCTGCTTTTGAGCACCACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGa                           >  1:798275/4‑71 (MQ=255)
                                          agccAGGCGAAGCTGCTTTTGAGCACCACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGa                           >  1:4758692/4‑71 (MQ=255)
                                           gTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGtttt                             <  1:4425096/68‑1 (MQ=255)
                                           gTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGAc                          <  1:887605/71‑1 (MQ=255)
                                            tCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCg                                                       >  1:69150/1‑41 (MQ=255)
                                            tCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCg                                                       >  1:4626014/1‑41 (MQ=255)
                                            tCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACg                         <  1:832790/71‑1 (MQ=255)
                                            ccAGGCGAAGCTGCTTTTGAGCACCACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACg                         <  1:2714598/70‑1 (MQ=255)
                                             cAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGtt                                   <  1:544581/60‑1 (MQ=255)
                                             cAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGttt                              >  1:3004405/1‑65 (MQ=255)
                                             cAGGCGAAGCTGCTTTTGAGCACAACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTgg                                 >  1:122391/1‑62 (MQ=255)
                                              aGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCgtcgg                                             <  1:836815/49‑1 (MQ=255)
                                              aGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGttt                              >  1:863081/1‑64 (MQ=255)
                                              aGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGtt                               >  1:1698685/1‑63 (MQ=255)
                                              aGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGa                        <  1:3361751/70‑1 (MQ=255)
                                              aGGCGAAGCTGCTTTTGAGCACCACCCGGATGCCTATCGCCACCGTCGGTCGCaa                                       <  1:1320761/55‑1 (MQ=255)
                                               ggCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGtttt                             <  1:2641050/64‑1 (MQ=255)
                                               ggCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATc                      <  1:3877917/71‑1 (MQ=255)
                                               ggCGAAGCTGCTTTTGAGCACCACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATc                      <  1:2943791/71‑1 (MQ=255)
                                                gCGAAGCTGTTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATCa                     <  1:818701/71‑1 (MQ=255)
                                                gCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATCa                     <  1:614153/71‑1 (MQ=255)
                                                gCGAAGCTGCTTTTGAGCACCACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATc                      <  1:1068693/70‑1 (MQ=255)
                                                  gAAGCTGCTTTTGAGCACTACCAGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATCAAc                   <  1:2253437/71‑1 (MQ=255)
                                                    aGCTGCTTTTGAGCACCACCCGGATTCCTATCGCCACCGTCGGTCGCAATGTTGGtttt                             <  1:4030416/59‑1 (MQ=255)
                                                     gctgctTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATCAActc                 >  1:2092522/1‑70 (MQ=255)
                                                      ctgctTTTGAGCACCACCCGGATGCCTATCGCCACCGTCGGTCGCAATg                                     <  1:3769388/49‑1 (MQ=255)
                                                        gctTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTg                            <  1:1916165/56‑1 (MQ=255)
                                                         ctTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATCAACTCTAttt            <  1:3561080/71‑1 (MQ=255)
                                                         ctTTTGAGCACCACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATCAACTCTAt              <  1:3491189/69‑1 (MQ=255)
                                                          ttttGAGCACTACCCGGATGCCTATCGCCACCgtcggt                                            <  1:4512676/38‑1 (MQ=255)
                                                          ttttGAGCACTACCCGGATGCCTATCGCCACCGTCTGTCGCAATGTTGGTTTTGa                           <  1:3216711/55‑1 (MQ=255)
                                                          ttttGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGa                           <  1:2452169/55‑1 (MQ=255)
                                                          ttttGAGCACCACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGtttt                             <  1:1217900/53‑1 (MQ=255)
                                                          ttttGAGCACCACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATCAActct                <  1:5001334/66‑1 (MQ=255)
                                                           tttGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGa                           <  1:3433345/54‑1 (MQ=255)
                                                           tttGAGCACCACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATc                      <  1:2188632/59‑1 (MQ=255)
                                                            ttGAGCACCACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATCaa                    >  1:4457699/1‑60 (MQ=255)
                                                            ttGAGCACCACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATCAACTCTATTtc           <  1:3916328/69‑1 (MQ=255)
                                                             tGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTg                            <  1:172887/51‑1 (MQ=255)
                                                             tGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATCAACTCTATTTCTcg        >  1:4950473/1‑71 (MQ=255)
                                                                 cACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATCAACTCTATTTCTcg        >  1:4854600/1‑67 (MQ=255)
                                                                   cTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGAc                          >  1:4726753/1‑47 (MQ=255)
                                                                   cTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATCAACTCTATTTCTCGCGAGTa  >  1:3169570/1‑71 (MQ=255)
                                                                    tACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGtt                               >  1:1172072/1‑41 (MQ=255)
                                                                    tACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGAc                          <  1:5050550/46‑1 (MQ=255)
                                                                    tACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGAc                          <  1:1607723/46‑1 (MQ=255)
                                                                    tACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACg                         <  1:2443458/47‑1 (MQ=255)
                                                                    tACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATc                      <  1:1970935/50‑1 (MQ=255)
                                                                    tACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTACGATc                      <  1:1272615/49‑1 (MQ=39)
                                                                    |                                                                     
TTAGGGATTAGCGTCTTAAGCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATCAACTCTATTTCTCGCGAGTA  >  AP009048/71041‑71178

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: