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
A122 F1 I1 R1 27 151.2 10056804 92.4% 9292486 76.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA REL606 3,464,820 C→T R150H (CGC→CAC)  ompR ← osmolarity response regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*REL6063,464,8200CT98.8% 343.7 / ‑3.4 84R150H (CGC→CAC) ompRosmolarity response regulator
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (16/67);  total (16/68)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.31e-01

GACCAGTGCCTTCAGTACCGCAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGCGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCTGTGACGGTGTGCCTGGCAGTT  >  REL606/3464750‑3464892
                                                                       |                                                                         
gcccAGTGCCTTCAGTACCGCAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑a                                                                     <  1:1331738/74‑1 (MQ=255)
gACCAGTGCCTTCAGTACCGCAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑a                                                                     <  1:4216740/76‑1 (MQ=255)
gACCAGTGCCTTCAGTACCGCAAACTCACCGCTGGTGAGCGGCATCGGCTCCCCCTCCC‑GGAACACTTCTTGCGtc                                                                      >  2:1786309/1‑75 (MQ=255)
   cAGTGCCTTCAGTCCCGCAAACTCACCGCTGGTGTGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCg                                                                  <  1:1791464/76‑1 (MQ=255)
   cAGTGCCTTCAGTACCGCAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCg                                                                  <  2:2162085/76‑1 (MQ=255)
       gCCTTCAGTACCGCAACCTCACCGCTGGGGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGt                                                              <  1:4759291/76‑1 (MQ=255)
        ctttCAGTACCGCAACCTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGtt                                                             <  1:69944/74‑1 (MQ=255)
        ccTTCAGTCCCGCAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGtt                                                             <  1:144374/76‑1 (MQ=255)
        ccTTCAGTACCGCAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGtt                                                             <  1:4712362/76‑1 (MQ=255)
        ccTTCAGTACCGCAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGtt                                                             <  1:4972788/76‑1 (MQ=255)
        ccTTCAGTACCGCAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGtt                                                             <  1:2344899/76‑1 (MQ=255)
         cTTCAGTACCGCAACCTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTa                                                            <  1:3972086/76‑1 (MQ=255)
         cTTCAGTACCGCAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTa                                                            <  1:4792287/76‑1 (MQ=255)
         cTTCAGTACCGCAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTa                                                            <  2:101164/76‑1 (MQ=255)
          ttCAGTACCGCAAACTCCCCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTaa                                                           <  2:4106327/76‑1 (MQ=255)
          ttCAGTACCGCAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTaa                                                           <  1:4577935/76‑1 (MQ=255)
          ttCAGTACCGCAAACTCACCGCTGGGGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTaa                                                           <  2:2452739/76‑1 (MQ=255)
           tCAGTACCGCAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAg                                                          <  2:4833895/76‑1 (MQ=255)
            cAGTACCGCAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGt                                                         <  1:4849902/76‑1 (MQ=255)
            cAGTACCGCAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGt                                                         <  2:1112702/76‑1 (MQ=255)
            cAGTACCGCAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGt                                                         <  2:3166136/76‑1 (MQ=255)
             aGTACCGCAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGtt                                                        <  1:93145/76‑1 (MQ=255)
             aGTACCGCAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGCGCGT‑ACCGAGGTTAAGtt                                                        <  2:1029725/76‑1 (MQ=255)
              gtcccGCAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGttt                                                       <  2:2218881/73‑1 (MQ=255)
              gTACCGCAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGttt                                                       <  1:4839860/76‑1 (MQ=255)
              gTACCGCAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGttt                                                       <  2:4533535/76‑1 (MQ=255)
                  cGCAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAAc                                                   <  1:1503702/76‑1 (MQ=255)
                    cAAAGTCCCCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACtt                                                 <  1:1071954/76‑1 (MQ=255)
                    cAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACtt                                                 <  1:3115468/76‑1 (MQ=255)
                    cAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACtt                                                 <  2:3384700/76‑1 (MQ=255)
                     aaaCTCACCGCTGGTTGGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTa                                                <  1:3638977/76‑1 (MQ=255)
                     aaaCTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTa                                                <  2:1210783/76‑1 (MQ=255)
                     aaaCTCACCGCTGGTGAGCGGCATCGGCTCCCCTTCCC‑CGGACAATTCTTGCGTGCCCCGGGTTAAGTTTTAAttt                                                 >  2:4106687/1‑76 (MQ=255)
                     aaaCTCACCGCTGGTGAGCGGCATCGGCTCCCCCTCGC‑CGGATATTTCCTGCGT‑GCCCGGGGTAAACTTGAAAttt                                                >  2:3574776/1‑75 (MQ=255)
                     aaaCTCACCGCTGGTGAGCGGCATCGGCTCCCCCTCCC‑GGGGCACTTTTTGGGT‑ACCGAGGGTAAGTTTGTACttt                                                >  2:635384/1‑75 (MQ=255)
                     aaaCTCACCGCTGGTGAGCGGCATCGGCTCCCCCTCCC‑CGGGCGCTTCGCGAGT‑ACCGAGGTTAAAGTTGAAAttt                                                >  2:3411229/1‑75 (MQ=255)
                     aaaCTCACCGCTGGTGAGCGGCATCGGCTCCCCCTCCC‑CGGACACTTCTTGCGG‑ACCGAGGGTGAGTTTTTACttt                                                >  2:4475671/1‑75 (MQ=255)
                      aaCTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTAc                                               <  1:4505067/76‑1 (MQ=255)
                        cTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCg                                             <  1:4584308/76‑1 (MQ=255)
                        cTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCg                                             <  1:1234395/76‑1 (MQ=255)
                        cTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCg                                             <  2:3153567/76‑1 (MQ=255)
                         tCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGa                                            <  2:2612747/76‑1 (MQ=255)
                         tCACCGCTGGTGAGCGGCATCGGCTCCCCCTCGCGGGAACTTTTTTTGCG‑‑ACCGAGGGTAAGGTTTGACTTAcagc                                            >  2:1959381/1‑73 (MQ=255)
                            ccGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAg                                         <  2:2599683/76‑1 (MQ=255)
                            ccGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAg                                         <  2:3710667/76‑1 (MQ=255)
                              gCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCa                                       <  2:4212001/76‑1 (MQ=255)
                               cTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCaa                                      <  1:4477041/76‑1 (MQ=255)
                                tGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAAt                                     <  2:2910582/76‑1 (MQ=255)
                                 ggTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAAtt                                    <  1:3893280/76‑1 (MQ=255)
                                 ggTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAAtt                                    <  1:1111913/76‑1 (MQ=255)
                                 ggTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAAtt                                    <  1:3350844/76‑1 (MQ=255)
                                 ggTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGCTTGAACTTACCGAAAGCAAtt                                    <  2:1423490/76‑1 (MQ=255)
                                  gtgtGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTa                                   <  1:813274/76‑1 (MQ=255)
                                  gTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTa                                   <  1:2711555/76‑1 (MQ=255)
                                  gTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTa                                   <  2:4551747/76‑1 (MQ=255)
                                  gTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTa                                   <  1:2343964/76‑1 (MQ=255)
                                   tGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTAc                                  <  1:4330395/76‑1 (MQ=255)
                                   tGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTAc                                  <  1:3547165/76‑1 (MQ=255)
                                   tGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTAc                                  <  1:37041/76‑1 (MQ=255)
                                     aGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCg                                <  1:660168/76‑1 (MQ=255)
                                      gCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGc                               <  2:3907579/76‑1 (MQ=255)
                                      gCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGc                               <  1:2645637/76‑1 (MQ=255)
                                        ggCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCct                             <  1:1211482/76‑1 (MQ=255)
                                         gCATCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCctc                            <  2:3935559/76‑1 (MQ=255)
                                           aTCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCtt                          <  1:3952405/76‑1 (MQ=255)
                                            tCGGCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTc                         <  1:1012720/76‑1 (MQ=255)
                                              ggCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCt                       <  1:1395052/76‑1 (MQ=255)
                                               gCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCtg                      <  1:550727/76‑1 (MQ=255)
                                               gCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCtg                      <  2:2744076/76‑1 (MQ=255)
                                               gCTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCtg                      <  1:4701973/76‑1 (MQ=255)
                                                cTCGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCtgt                     <  1:4543986/76‑1 (MQ=255)
                                                  cGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCTGTGa                   <  2:701833/76‑1 (MQ=255)
                                                  cGTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCTGTGa                   <  1:4322709/76‑1 (MQ=255)
                                                   gTCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCTGTGAc                  >  1:3477390/1‑76 (MQ=255)
                                                    tCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCTGTGACg                 >  2:148954/1‑76 (MQ=255)
                                                    tCTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCTGTGACg                 >  2:847764/1‑76 (MQ=255)
                                                     cTTCGC‑GGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCTGTGACgg                >  1:4290246/1‑76 (MQ=255)
                                                        cgc‑gGAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCTGTGACGgtgt             <  2:1199376/76‑1 (MQ=255)
                                                            ggAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCTGTGACGGTGTGcc          >  2:48779/1‑76 (MQ=255)
                                                             gAACATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCTGTGACGGTGTGCCt         >  1:1537642/1‑76 (MQ=255)
                                                              aaCATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCTGTGACGGTGTGCCTg        >  2:273067/1‑76 (MQ=255)
                                                                cATTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCTGTGACGGTGTGCCTGGc      >  1:690727/1‑76 (MQ=255)
                                                                 aTTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCTGTGACGGTGTGCCTGGCa     >  2:2774449/1‑76 (MQ=255)
                                                                 aTTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCTGTGACGGTGTGCCTGGCa     >  2:4002646/1‑76 (MQ=255)
                                                                 aTTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCTGTGACGGTGTGCCTGGCa     <  1:1922276/76‑1 (MQ=255)
                                                                 aTTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCTGTGACGGTGTGCCTGGCa     >  1:4991435/1‑76 (MQ=255)
                                                                 aTTTCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCTGTGACGGTGTGCCTGGCa     >  1:4758355/1‑76 (MQ=255)
                                                                  tttCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCTGTGACGGTGTGCCTGGCAg    >  1:2090163/1‑76 (MQ=255)
                                                                  tttCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCTGTGACGGTGTGCCTGGCAg    >  1:486193/1‑76 (MQ=255)
                                                                   ttCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCTGTGACGGTGTGCCTGGCAgt   >  1:1500212/1‑76 (MQ=255)
                                                                    tCGTGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCTGTGACGGTGTGCCTGGCAgtt  >  1:2209953/1‑76 (MQ=255)
                                                                       |                                                                         
GACCAGTGCCTTCAGTACCGCAAACTCACCGCTGGTGAGCGGCATCGGCTCGTCTTCGC‑GGAACATTTCGCGCGT‑ACCGAGGTTAAGTTTGAACTTACCGAAAGCAATTACCGCCTCTTCCTGTGACGGTGTGCCTGGCAGTT  >  REL606/3464750‑3464892

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A