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 F2 I1 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA Exported 214,931 A→C 69.6% E14A (GAA→GCA)  dnaQ → DNA polymerase III epsilon subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported214,9310AC69.6% 499.8 / 188.0 282E14A (GAA→GCA) dnaQDNA polymerase III epsilon subunit
Reads supporting (aligned to +/- strand):  ref base A (57/29);  new base C (89/107);  total (146/136)
Fisher's exact test for biased strand distribution p-value = 1.81e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.79e-01

Only 100 of 291 total aligned reads displayed.

AAACGACAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCGTTG  >  Exported/214862‑214999
                                                                     |                                                                    
     aCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAaccac                                                                >  1:2762524/1‑71 (MQ=255)
       aaGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCg                                                              >  1:2895135/1‑71 (MQ=255)
        aGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCgg                                                             <  1:4200709/71‑1 (MQ=255)
         gTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGt                                                            <  1:722835/71‑1 (MQ=255)
         gTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCgg                                                             >  1:1561748/1‑70 (MQ=255)
           cTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGaaa                                                                    >  1:347227/1‑61 (MQ=255)
              aCATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGt                                                            >  1:3118508/1‑66 (MQ=255)
              aCATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATg                                                         <  1:2161693/69‑1 (MQ=255)
              aCATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATg                                                         <  1:3069095/69‑1 (MQ=255)
               cATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                      <  1:1058026/71‑1 (MQ=255)
                aTAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAAc                                                      >  1:1584096/1‑70 (MQ=255)
                 tAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCgg                                                             <  1:1453806/62‑1 (MQ=255)
                 tAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATg                                                         <  1:1701821/66‑1 (MQ=255)
                 tAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                    <  1:3985398/71‑1 (MQ=255)
                 tAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                    <  1:2533216/71‑1 (MQ=255)
                 tAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                    <  1:2223219/71‑1 (MQ=255)
                 tAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAAc                                                      >  1:4872087/1‑69 (MQ=255)
                 tAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAAc                                                      >  1:769434/1‑69 (MQ=255)
                   aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAAc                                                      >  1:5332594/1‑67 (MQ=255)
                     tGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGAtt                                                <  1:5252121/71‑1 (MQ=255)
                       aCCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTg                                               <  1:4337078/70‑1 (MQ=255)
                       aCCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTg                                               <  1:3443424/70‑1 (MQ=255)
                       aCCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTg                                               <  1:661856/70‑1 (MQ=255)
                       aCCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTg                                               <  1:2616441/70‑1 (MQ=255)
                       aCCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTg                                               <  1:1046752/70‑1 (MQ=255)
                         cGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTg                                            >  1:3537097/1‑71 (MQ=255)
                             aTGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAaccac                                                                >  1:5367890/1‑47 (MQ=255)
                             aTGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAaccac                                                                >  1:428507/1‑47 (MQ=255)
                              tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAg                                                   <  1:1617940/59‑1 (MQ=255)
                              tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAg                                                   <  1:5265950/59‑1 (MQ=255)
                              tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAtt                                                <  1:3829310/62‑1 (MQ=255)
                              tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCAc                                       <  1:968480/71‑1 (MQ=255)
                              tGAGCACTGCAATTACACGCCAGATCGTTCCCGCTACCGCAACCACCGGTATGAACCAGAtt                                                <  1:2793237/62‑1 (MQ=255)
                               gAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGa                                                  >  1:2124255/1‑59 (MQ=255)
                               gAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCAc                                       >  1:4682582/1‑70 (MQ=255)
                                aGCACTTCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCa                                        >  1:3908/1‑68 (MQ=255)
                                aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTa                                     >  1:2058186/1‑71 (MQ=255)
                                aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTa                                     >  1:892572/1‑71 (MQ=255)
                                 gCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAt                                                 <  1:1344784/58‑1 (MQ=255)
                                  cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   <  1:2712182/71‑1 (MQ=255)
                                  cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   <  1:5182075/71‑1 (MQ=255)
                                     tGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGa                                                        <  1:1721683/47‑1 (MQ=255)
                                      gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                               >  1:3641491/1‑71 (MQ=255)
                                      gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                               >  1:573601/1‑71 (MQ=255)
                                      gCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTAt                                                          >  1:2186730/1‑44 (MQ=255)
                                       cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTa                                     >  1:2348307/1‑64 (MQ=255)
                                       cAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGAACTATGAAGGc                              >  1:3488354/1‑71 (MQ=255)
                                         aTTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                      <  1:2448811/45‑1 (MQ=38)
                                          ttACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   <  1:5153662/63‑1 (MQ=255)
                                          ttACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   <  1:4833620/63‑1 (MQ=255)
                                          ttACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                   <  1:2677149/63‑1 (MQ=255)
                                          ttACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGa                                  <  1:3465458/64‑1 (MQ=255)
                                          ttACACGCCAGATCGTTCTCGATACCGAAACCACCgg                                                             <  1:1532122/37‑1 (MQ=255)
                                           tACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGa                                  >  1:4364473/1‑63 (MQ=255)
                                           tACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                           >  1:3384746/1‑70 (MQ=255)
                                           tACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                           >  1:2005258/1‑70 (MQ=255)
                                            acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGaaac                                                     >  1:5050722/1‑41 (MQ=37)
                                            acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGa                                                  >  1:812832/1‑46 (MQ=39)
                                            acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGa                                                  >  1:4737579/1‑46 (MQ=39)
                                            acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCa                                        >  1:789121/1‑56 (MQ=255)
                                            acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGaa                                 >  1:2206126/1‑63 (MQ=255)
                                            acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAg                                >  1:4802311/1‑64 (MQ=255)
                                             cacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAg                        <  1:4036351/71‑1 (MQ=255)
                                               cGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                           >  1:4628701/1‑66 (MQ=255)
                                               cGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGAt                      <  1:1781687/71‑1 (MQ=255)
                                               cGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGAt                      <  1:1379114/71‑1 (MQ=255)
                                                  cAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAt                   <  1:1033091/71‑1 (MQ=255)
                                                  cAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAt                   >  1:1834579/1‑71 (MQ=255)
                                                  cAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAt                   >  1:2953/1‑71 (MQ=255)
                                                   aGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTAt                                    <  1:1102196/53‑1 (MQ=255)
                                                   aGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTAt                                    <  1:113424/53‑1 (MQ=255)
                                                   aGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTAt                                    <  1:3702314/53‑1 (MQ=255)
                                                   aGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                  <  1:5519357/71‑1 (MQ=255)
                                                    gATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTgcg                                          <  1:4480789/46‑1 (MQ=39)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTga                <  1:4264386/71‑1 (MQ=255)
                                                     aTCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCa                    <  1:3879901/67‑1 (MQ=255)
                                                      tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                  >  1:4110164/1‑68 (MQ=255)
                                                      tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                  >  1:414121/1‑68 (MQ=255)
                                                      tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTgag               <  1:4215524/71‑1 (MQ=255)
                                                       cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGaa                                 >  1:588952/1‑52 (MQ=255)
                                                         ttCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGAtt            <  1:2294966/71‑1 (MQ=255)
                                                         ttCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGAtt            >  1:4858960/1‑71 (MQ=255)
                                                         ttCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGAtt            >  1:5544988/1‑71 (MQ=255)
                                                          tctcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACaa                         >  1:2079529/1‑57 (MQ=255)
                                                          tctcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCa                    <  1:3199217/62‑1 (MQ=255)
                                                           ctcGCTACCGCAACCACCGGTATGAACCAGATTgg                                              >  1:4951174/1‑35 (MQ=37)
                                                           ctcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTgg          >  1:3154679/1‑71 (MQ=255)
                                                           ctcGCTACAGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGaa                                 >  1:2580880/1‑48 (MQ=255)
                                                           ctcGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGAt             <  1:1471673/68‑1 (MQ=255)
                                                            tcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGc                              <  1:3022627/50‑1 (MQ=255)
                                                            tcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCca                            <  1:4913546/52‑1 (MQ=255)
                                                            tcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCca                            <  1:1227792/52‑1 (MQ=255)
                                                            tcGATACCGAAACCACCGGTATGAACCAGATTGGTgcg                                          >  1:3580809/1‑38 (MQ=255)
                                                            tcGATACCGAAACCACCGGTATGAACCAGATTGGTgcg                                          >  1:3713011/1‑38 (MQ=255)
                                                               ctACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGcc      <  1:28618/70‑1 (MQ=255)
                                                               aTACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGcc      <  1:562589/71‑1 (MQ=255)
                                                                 aCCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTg        >  1:1897845/1‑67 (MQ=255)
                                                                  ccGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                           <  1:1967610/47‑1 (MQ=255)
                                                                  ccGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCGtt   >  1:544660/1‑71 (MQ=255)
                                                                   cGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCGTTg  <  1:1318611/71‑1 (MQ=255)
                                                                     |                                                                    
AAACGACAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCGTTG  >  Exported/214862‑214999

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