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
A1 F8 I0 R1 311 50.1 4085234 95.9% 3917739 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 236,107 A→C 88.4% 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
*W3110S.gb236,1070AC88.4% 1818.0 / 111.7 572E14A (GAA→GCA) dnaQDNA polymerase III epsilon subunit
Reads supporting (aligned to +/- strand):  ref base A (34/33);  new base C (280/225);  total (314/258)
Fisher's exact test for biased strand distribution p-value = 5.14e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.86e-01

Only 100 of 596 total aligned reads displayed.

AAACGACAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCGTT  >  W3110S.gb/236038‑236174
                                                                     |                                                                   
 caactCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGcaa                                                                   >  1:1022094‑M2/6‑71 (MQ=255)
 caactCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGcaa                                                                   >  1:3606880‑M2/6‑71 (MQ=255)
 caactCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGcaa                                                                   >  1:3777601‑M2/6‑71 (MQ=255)
 caactCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGcaa                                                                   >  1:568087‑M2/6‑71 (MQ=255)
 caactCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTAACGcaa                                                                   >  1:3650829‑M2/6‑71 (MQ=255)
 caactCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTACTCGCTACCGcaa                                                                   >  1:1006154‑M2/6‑71 (MQ=255)
   actCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAac                                                                  >  1:2032748‑M2/4‑70 (MQ=255)
    ctCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAacca                                                                >  1:2440776‑M2/3‑71 (MQ=255)
    ctCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAac                                                                  >  1:3226639‑M2/3‑69 (MQ=255)
      cAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAacc                                                                 >  1:1506670/1‑68 (MQ=255)
       aaGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCg                                                             >  1:1767881/1‑71 (MQ=255)
           cTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAac                                                                  >  1:1199979/1‑62 (MQ=255)
            tGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTAt                                                         >  1:889027/1‑70 (MQ=255)
              aCATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATg                                                        <  1:301152/69‑1 (MQ=255)
              aCATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATg                                                        <  1:1858113/69‑1 (MQ=255)
              aCATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGaa                                                      >  1:4035271/1‑71 (MQ=255)
              aCATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGaa                                                      >  1:125752/1‑71 (MQ=255)
                 tAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                   <  1:2764144/71‑1 (MQ=255)
                 tAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                   <  1:3250115/71‑1 (MQ=255)
                  aaaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                     >  1:1294613/1‑68 (MQ=255)
                   aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGt                                                           >  1:682343/1‑61 (MQ=255)
                   aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                     >  1:3342117/1‑67 (MQ=255)
                     tGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAtt                                               <  1:3920359/71‑1 (MQ=255)
                         cGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTGCCGCAACCACCGGTATGAACCAGATTGGTg                                           >  1:446402/1‑71 (MQ=255)
                           cTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTgcg                                         <  1:3476331/71‑1 (MQ=255)
                           cTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTgcg                                         <  1:859202/71‑1 (MQ=255)
                             aTGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCa                                       >  1:1436978/1‑71 (MQ=255)
                              tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGt                                                           <  1:2665495/50‑1 (MQ=255)
                              tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                   <  1:2909253/58‑1 (MQ=255)
                              tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                   <  1:3287080/58‑1 (MQ=255)
                              tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCa                                       >  1:2470122/1‑70 (MQ=255)
                              tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCAc                                      >  1:497165/1‑71 (MQ=255)
                              tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCAc                                      <  1:3729591/71‑1 (MQ=255)
                              tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCAc                                      <  1:802422/71‑1 (MQ=255)
                              tGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCAc                                      <  1:195763/71‑1 (MQ=255)
                                aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACt                                     <  1:3703785/70‑1 (MQ=255)
                                aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTa                                    >  1:2505958/1‑71 (MQ=255)
                                aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTa                                    >  1:4080507/1‑71 (MQ=255)
                                aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTa                                    >  1:660282/1‑71 (MQ=255)
                                aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTa                                    >  1:3200530/1‑71 (MQ=255)
                                  cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                  <  1:2876429/71‑1 (MQ=255)
                                  cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                  <  1:2123273/71‑1 (MQ=255)
                                  cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                  <  1:543844/71‑1 (MQ=255)
                                  cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                  <  1:1738640/71‑1 (MQ=255)
                                  cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGATATGAACCAGATTGGTGCGCACTATg                                  <  1:2960348/71‑1 (MQ=255)
                                   aCTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                  <  1:2721329/70‑1 (MQ=255)
                                    cTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATg                                                        <  1:3540138/47‑1 (MQ=39)
                                    cTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                  >  1:179626/1‑69 (MQ=255)
                                    cTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                  >  1:3435846/1‑69 (MQ=255)
                                     tGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCgg                                                            <  1:1349679/42‑1 (MQ=255)
                                     tGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATg                                                        <  1:1980032/46‑1 (MQ=39)
                                     tGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                   <  1:2677089/51‑1 (MQ=255)
                                      gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                              >  1:3169424/1‑71 (MQ=255)
                                      gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                              >  1:471618/1‑71 (MQ=255)
                                      gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                              >  1:1930927/1‑71 (MQ=255)
                                      gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                              >  1:2374772/1‑71 (MQ=255)
                                      gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAg                               >  1:1702514/1‑70 (MQ=255)
                                       cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATg                                                        >  1:3035869/1‑44 (MQ=38)
                                       cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGa                                                 >  1:2243210/1‑51 (MQ=255)
                                       cAAATACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGc                             >  1:331845/1‑71 (MQ=255)
                                          ttACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                  <  1:2556656/63‑1 (MQ=255)
                                            acacGCCAGATCGTTCTCGCTACCGCAACCACCgg                                                            <  1:2840276/35‑1 (MQ=38)
                                            acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                          >  1:1585215/1‑69 (MQ=255)
                                            acacGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTa                                    >  1:2190151/1‑59 (MQ=255)
                                             cacGCCAGATCGTTCTCGCTACCGCAACCACCTGTATGAACCAGATTGGTGCGCACTATGAAGGCCACaa                        <  1:1319653/70‑1 (MQ=255)
                                             cacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACaa                        <  1:1057781/70‑1 (MQ=255)
                                             cacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAg                       <  1:715444/71‑1 (MQ=255)
                                               cGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGa                      >  1:1886847/1‑70 (MQ=255)
                                               cGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTACGAAGGCcac                          >  1:1825425/1‑66 (MQ=255)
                                                gCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGAt                     <  1:3122919/70‑1 (MQ=255)
                                                gCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATc                    <  1:1103667/71‑1 (MQ=255)
                                                   aGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGa                                                 >  1:1627909/1‑39 (MQ=37)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                   <  1:1613673/35‑1 (MQ=37)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTg                                              <  1:762095/40‑1 (MQ=38)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACaa                        <  1:154240/62‑1 (MQ=255)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCa                   <  1:3977410/67‑1 (MQ=255)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTga               <  1:1224569/71‑1 (MQ=255)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTga               <  1:3503811/71‑1 (MQ=255)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTga               <  1:2072509/71‑1 (MQ=255)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTga               <  1:3939764/71‑1 (MQ=255)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTga               <  1:1492336/71‑1 (MQ=255)
                                                     aTCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                 >  1:3819390/1‑69 (MQ=255)
                                                      tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                 >  1:2591890/1‑68 (MQ=255)
                                                      tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTgag              <  1:2349559/71‑1 (MQ=255)
                                                       cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                 >  1:2811411/1‑67 (MQ=255)
                                                       cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                 >  1:3082781/1‑67 (MQ=255)
                                                       cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTg                                              >  1:600271/1‑38 (MQ=255)
                                                         ttCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGAtt           <  1:1663651/71‑1 (MQ=255)
                                                         ttCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGAtt           <  1:2173566/71‑1 (MQ=255)
                                                           ctcGCTACCGCAACCACCGGTATGAACCAGATTgg                                             >  1:385024/1‑35 (MQ=37)
                                                           ctcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGAtt           <  1:3884650/69‑1 (MQ=255)
                                                           ctcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTgg         >  1:3358147/1‑71 (MQ=255)
                                                           ctcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTgg         >  1:229094/1‑71 (MQ=255)
                                                            tcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTga               <  1:3413179/64‑1 (MQ=255)
                                                              gctACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTgg         <  1:952022/66‑1 (MQ=255)
                                                              gctACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGt        <  1:1153720/67‑1 (MQ=255)
                                                              gctACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGt        <  1:139796/67‑1 (MQ=255)
                                                                 aCCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCa                   <  1:2647240/55‑1 (MQ=255)
                                                                 aCCGAAACCACCGGTATGAACCTGATTGGTGCGCACTATg                                  <  1:1125082/40‑1 (MQ=255)
                                                                  ccGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCGtt  >  1:2020265/1‑71 (MQ=255)
                                                                     |                                                                   
AAACGACAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCGTT  >  W3110S.gb/236038‑236174

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A