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
A108 F1 I1 R1 80 195.1 12639756 93.3% 11792892 75.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA REL606 4,164,802 A→G E1316G (GAG→GGG)  rpoB → DNA‑directed RNA polymerase subunit beta

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*REL6064,164,8020AG99.1% 880.7 / ‑2.4 215E1316G (GAG→GGG) rpoBDNA‑directed RNA polymerase subunit beta
Reads supporting (aligned to +/- strand):  ref base A (2/0);  new base G (106/106);  total (108/107)
Fisher's exact test for biased strand distribution p-value = 4.98e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.66e-01

Only 100 of 219 total aligned reads displayed.

CCGTTAAGTCTGATGACGTGAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGA  >  REL606/4164730‑4164874
                                                                        |                                                                        
ccGTTAAGTCTGATGACGTGAACGGTCTTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGcc                                                                       >  1:1394155/1‑76 (MQ=255)
 cGTTAAGTCTGATGACGTGAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCg                                                                      >  1:5464149/1‑76 (MQ=255)
 cGTTAAGTCTGATGACGTGAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCg                                                                      >  1:5290524/1‑76 (MQ=255)
  gTTAAGTCTGATGACGTGAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCgg                                                                     >  2:1041503/1‑76 (MQ=255)
  gTTAAGTCTGATGACGTAAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCgg                                                                     <  1:4891549/76‑1 (MQ=255)
   ttAAGTCTGATGACGTGAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCggg                                                                    <  1:3369042/76‑1 (MQ=255)
   ttAAGTCTGATGACGTGAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCggg                                                                    >  2:5232875/1‑76 (MQ=255)
    tAAGTCTGATGACGTGAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGc                                                                   >  1:5809470/1‑76 (MQ=255)
    tAAGTCTGATGACGTGAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGc                                                                   >  1:2203333/1‑76 (MQ=255)
     aaGTCTGATGACGTGAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCa                                                                  >  2:4060931/1‑76 (MQ=255)
      aGTCTGATGACGTGAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCAt                                                                 <  1:4939847/76‑1 (MQ=255)
       gTCTGATGACGCGAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATg                                                                <  1:4820904/76‑1 (MQ=255)
        tCTGATGACGTGAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGc                                                               >  1:313855/1‑76 (MQ=255)
         cTGATGACGTGAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGcc                                                              >  2:1379770/1‑76 (MQ=255)
         cTGATGACGTGAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGcc                                                              <  1:1599927/76‑1 (MQ=255)
          tgatgaGGTGAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGTGCCGGGCATGCCa                                                             <  2:1759205/76‑1 (MQ=255)
          tgatgaCGTGAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCa                                                             <  1:660699/76‑1 (MQ=255)
           gatgaCGTGAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAg                                                            <  2:4683717/76‑1 (MQ=255)
           gatgaCGTGAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAg                                                            <  2:4787374/76‑1 (MQ=255)
            atgaCGTGAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGa                                                           >  2:5544898/1‑76 (MQ=255)
            atgaCGTGAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGa                                                           <  1:5687155/76‑1 (MQ=255)
                    taCGGTCGTACCAAGATGTATAAAAACATCGTGGAGGGCAACCATCAGATGGGGCCGGGCATGCCTGTATCCTTCa                                                   >  2:3138649/2‑76 (MQ=255)
                    aaCGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCa                                                   >  1:964968/1‑76 (MQ=255)
                    aaCGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCa                                                   <  1:3670061/76‑1 (MQ=255)
                    aaCGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCa                                                   >  2:2107426/1‑76 (MQ=255)
                    aaCGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCa                                                   >  2:877078/1‑76 (MQ=255)
                     aCGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCaa                                                  <  1:3926097/76‑1 (MQ=255)
                     aCGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCaa                                                  <  2:1289792/76‑1 (MQ=255)
                      cGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAAc                                                 <  2:6047014/76‑1 (MQ=255)
                      cGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAAc                                                 <  2:362679/76‑1 (MQ=255)
                          cGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTAt                                             >  1:4216628/1‑76 (MQ=255)
                          cGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTAt                                             >  1:4187003/1‑76 (MQ=255)
                          cGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTAt                                             >  2:4369057/1‑76 (MQ=255)
                          cGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTAt                                             >  1:106791/1‑76 (MQ=255)
                           gTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTAtt                                            <  1:3249/76‑1 (MQ=255)
                           gTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTAtt                                            >  1:5444057/1‑76 (MQ=255)
                            tACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTAttg                                           >  2:2488500/1‑76 (MQ=255)
                            tACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTAttg                                           >  1:5429321/1‑76 (MQ=255)
                            tACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTAttg                                           >  1:3090986/1‑76 (MQ=255)
                            tACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTAttg                                           <  2:1086845/76‑1 (MQ=255)
                             aCCAAGATGTATAAAAACATCGTGGACGGCAAGCGTCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTAttgt                                          <  1:2395519/76‑1 (MQ=255)
                             aCCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTAttgt                                          >  2:5119435/1‑76 (MQ=255)
                              ccAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTAttgtt                                         <  2:4246680/76‑1 (MQ=255)
                              ccAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGAATGCCAGAATCCTTCAACGTAttgtt                                         <  1:2587925/76‑1 (MQ=255)
                               cAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTAttgttg                                        >  1:84097/1‑76 (MQ=255)
                               cAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTAttgttg                                        <  1:2838992/76‑1 (MQ=255)
                                aaGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGa                                       <  1:5755749/76‑1 (MQ=255)
                                 aGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGaa                                      <  1:2084162/76‑1 (MQ=255)
                                   aTGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAag                                    <  1:1836754/76‑1 (MQ=255)
                                    tGTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAaga                                   <  2:2113864/76‑1 (MQ=255)
                                     gTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAagag                                  <  2:1506341/76‑1 (MQ=255)
                                     gTATAAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAagag                                  >  2:2559739/1‑76 (MQ=255)
                                      tataAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAgaga                                 <  1:3794158/76‑1 (MQ=255)
                                      tataAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAgaga                                 >  1:2168891/1‑76 (MQ=255)
                                        taAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGAtt                               <  1:3820398/76‑1 (MQ=255)
                                        taAAAACATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGAtt                               >  2:2036937/1‑76 (MQ=255)
                                           aaaCATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGAttcgt                            >  2:4553256/1‑76 (MQ=255)
                                           aaaCATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGAttcgt                            <  1:6214822/76‑1 (MQ=255)
                                             aCATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGAttcgttc                          <  2:4514499/76‑1 (MQ=255)
                                             aCATCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGAttcgttc                          <  1:5959361/76‑1 (MQ=255)
                                               aTCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGTGATTCGTTCGc                        >  1:2003136/1‑76 (MQ=255)
                                               aTCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGc                        >  2:5558768/1‑76 (MQ=255)
                                               aTCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGc                        <  1:4494928/76‑1 (MQ=255)
                                                tCGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCt                       <  2:5403705/76‑1 (MQ=255)
                                                 cGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTg                      <  2:4937126/76‑1 (MQ=255)
                                                 cGTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTg                      >  2:4608188/1‑76 (MQ=255)
                                                  gTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTgg                     >  2:4488084/1‑76 (MQ=255)
                                                  gTGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTgg                     <  1:3526749/76‑1 (MQ=255)
                                                   tGGACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTggg                    >  1:4631620/1‑76 (MQ=255)
                                                    ggACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGt                   <  1:466587/76‑1 (MQ=255)
                                                    ggACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGt                   >  1:872326/1‑76 (MQ=255)
                                                     gACGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTa                  >  2:483437/1‑76 (MQ=255)
                                                      aCGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTAt                 <  2:3209561/76‑1 (MQ=255)
                                                      aCGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTAt                 >  2:3827455/1‑76 (MQ=255)
                                                      aCGGCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTAt                 >  2:5840326/1‑76 (MQ=255)
                                                       cGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATc                >  2:2773146/1‑76 (MQ=255)
                                                        ggCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCa               >  1:1183402/1‑76 (MQ=255)
                                                        ggCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCa               <  2:3984797/76‑1 (MQ=255)
                                                        ggCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCa               <  2:5464149/76‑1 (MQ=255)
                                                        ggCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCa               >  2:2671483/1‑76 (MQ=255)
                                                         gCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCaa              >  1:3337103/1‑76 (MQ=255)
                                                         gCAACCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCaa              <  1:4146582/76‑1 (MQ=255)
                                                           aaCCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACa            <  1:1878091/76‑1 (MQ=255)
                                                           aaCCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACa            <  2:3236178/76‑1 (MQ=255)
                                                           aaCCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACa            <  2:536839/76‑1 (MQ=255)
                                                            aCCATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACAt           >  1:165689/1‑76 (MQ=255)
                                                              cATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCg         <  1:4588217/76‑1 (MQ=255)
                                                              cATCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCg         <  1:1481790/76‑1 (MQ=255)
                                                               aTCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGa        >  1:2384811/1‑76 (MQ=255)
                                                               aTCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGa        >  1:5227675/1‑76 (MQ=255)
                                                               aTCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGa        >  2:774026/1‑76 (MQ=255)
                                                                tCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGaa       >  1:5670912/1‑76 (MQ=255)
                                                                tCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGaa       <  2:2279107/76‑1 (MQ=255)
                                                                tCAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGaa       >  1:5370861/1‑76 (MQ=255)
                                                                 cAGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAAc      >  1:3979592/1‑76 (MQ=255)
                                                                  aGATGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACt     >  2:2887235/1‑76 (MQ=255)
                                                                  aGATGGGGACGGGCATGCCACCATACTTCAACGTATTGTAGACAGACATTCGTTCGCTGGGTATCAACATCGAACt     <  2:348324/76‑1 (MQ=255)
                                                                    aTGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTgg   >  2:4035774/1‑76 (MQ=255)
                                                                    aTGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTgg   >  2:6224313/1‑76 (MQ=255)
                                                                     tGGGGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAATATATTCGTTCGCTGGGTATCAACATCGAACTGGa  <  2:1312937/76‑1 (MQ=255)
                                                                        |                                                                        
CCGTTAAGTCTGATGACGTGAACGGTCGTACCAAGATGTATAAAAACATCGTGGACGGCAACCATCAGATGGAGCCGGGCATGCCAGAATCCTTCAACGTATTGTTGAAAGAGATTCGTTCGCTGGGTATCAACATCGAACTGGA  >  REL606/4164730‑4164874

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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