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 F1 I0 R2 532 47.8 3863072 94.9% 3666055 61.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 236,107 A→C 92.7% 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.gb236,1070AC92.7% 3581.8 / 116.7 1106E14A (GAA→GCA) dnaQDNA polymerase III epsilon subunit
Reads supporting (aligned to +/- strand):  ref base A (36/46);  new base C (547/477);  total (583/523)
Fisher's exact test for biased strand distribution p-value = 1.08e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.42e-01

Only 100 of 1144 total aligned reads displayed.

AAACGACAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCGTT  >  W3110S.gb/236038‑236174
                                                                     |                                                                   
aaaCGACAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGa                                                                     >  1:550842/1‑70 (MQ=255)
 caactCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGcaa                                                                   >  1:1567319‑M2/6‑71 (MQ=255)
 caactCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGcaa                                                                   >  1:3520078‑M2/6‑71 (MQ=255)
 caactCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGcaa                                                                   >  1:859275‑M2/6‑71 (MQ=255)
 caactCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGcaa                                                                   >  1:3102999‑M2/6‑71 (MQ=255)
  aactCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAac                                                                  >  1:1848928‑M2/5‑71 (MQ=255)
   cGACAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAac                                                                  >  1:938943/1‑70 (MQ=255)
      cAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAaccacc                                                              >  1:2895960/1‑71 (MQ=255)
      cAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAaccac                                                               <  1:707892/70‑1 (MQ=255)
       aaGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCg                                                             >  1:1215911/1‑71 (MQ=255)
       aaGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCg                                                             >  1:1252945/1‑71 (MQ=255)
       aaGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCg                                                             >  1:538775/1‑71 (MQ=255)
           cTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTAt                                                         >  1:2858691/1‑71 (MQ=255)
              aCATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATg                                                        <  1:3132648/69‑1 (MQ=255)
              aCATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGaa                                                      >  1:81827/1‑71 (MQ=255)
              aCATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGa                                                       <  1:2565971/70‑1 (MQ=255)
              aCATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGaa                                                      >  1:2165297/1‑71 (MQ=255)
               cATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                     >  1:3307806/1‑71 (MQ=255)
                aTAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAcc                                                    <  1:1434167/71‑1 (MQ=255)
                aTAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                     >  1:1490487/1‑70 (MQ=255)
                aTAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                     >  1:734324/1‑70 (MQ=255)
                   aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAac                                                                  >  1:1074229/1‑54 (MQ=255)
                   aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                     >  1:582002/1‑67 (MQ=255)
                   aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                   <  1:663680/69‑1 (MQ=255)
                     tGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAtt                                               <  1:105243/71‑1 (MQ=255)
                     tGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAtt                                               <  1:2556930/71‑1 (MQ=255)
                      gACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                   >  1:1795859/1‑66 (MQ=255)
                       aCCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGaa                                                      <  1:2977738/62‑1 (MQ=255)
                       aCCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTg                                              <  1:3732190/70‑1 (MQ=255)
                       aCCGCTATGAGCACTGCAATTACACGCCAGATCGTTATCGCTACCGCAac                                                                  >  1:3393880/1‑50 (MQ=255)
                           cTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTgcg                                         <  1:2762871/71‑1 (MQ=255)
                             aTGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAac                                                                  <  1:1393023/44‑1 (MQ=255)
                             aTGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCa                                       >  1:633261/1‑71 (MQ=255)
                              tgtgCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGATGCGCAc                                      <  1:3834281/68‑1 (MQ=255)
                                aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCg                                                             >  1:1909382/1‑46 (MQ=255)
                                aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGaa                                                      >  1:502339/1‑53 (MQ=255)
                                aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGa                                                 >  1:2189924/1‑58 (MQ=255)
                                 gCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAtt                                               <  1:2290693/59‑1 (MQ=255)
                                  cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAaccac                                                               >  1:1470006/1‑42 (MQ=255)
                                  cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAt                                                >  1:3636367/1‑57 (MQ=255)
                                  cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                  <  1:391024/71‑1 (MQ=255)
                                  cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                  <  1:3544504/71‑1 (MQ=255)
                                   aCTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                  <  1:1760328/70‑1 (MQ=255)
                                    cTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCa                                       <  1:2221323/64‑1 (MQ=255)
                                    cTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                  >  1:3268345/1‑69 (MQ=255)
                                    cTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                  <  1:3239007/69‑1 (MQ=255)
                                      gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGa                                                 >  1:2111151/1‑52 (MQ=255)
                                      gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCa                                       >  1:1187018/1‑62 (MQ=255)
                                       cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTAt                                   >  1:3162675/1‑65 (MQ=255)
                                       cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGaa                                >  1:3038715/1‑68 (MQ=255)
                                       cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGc                             >  1:3583182/1‑71 (MQ=255)
                                       cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGc                             >  1:1370375/1‑71 (MQ=255)
                                       cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGc                             >  1:2943610/1‑71 (MQ=255)
                                       cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGc                             >  1:892993/1‑71 (MQ=255)
                                       cAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAg                               <  1:3767302/69‑1 (MQ=255)
                                        aaTTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGcc                            <  1:2829203/71‑1 (MQ=255)
                                          ttACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                     <  1:921867/44‑1 (MQ=38)
                                           tACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                          >  1:1871236/1‑70 (MQ=255)
                                           tACACGCCAGATAGTTCTCGCTACCGCAACCACCGGTATGaa                                                      >  1:1120311/1‑42 (MQ=37)
                                            acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                   >  1:3606820/1‑44 (MQ=38)
                                            acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                          >  1:3426774/1‑69 (MQ=255)
                                             cacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAg                       <  1:2597537/71‑1 (MQ=255)
                                             cacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAg                       <  1:2041869/71‑1 (MQ=255)
                                               cGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGACACAAGAt                     <  1:1340557/71‑1 (MQ=255)
                                                 ccAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATc                    <  1:1295234/70‑1 (MQ=255)
                                                 ccAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCa                   <  1:1699856/71‑1 (MQ=255)
                                                 ccAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCa                   <  1:2264776/71‑1 (MQ=255)
                                                   aGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACaa                        >  1:2395749/1‑64 (MQ=255)
                                                   aGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                 >  1:270701/1‑71 (MQ=255)
                                                   aGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAAGCCACAAGATCAtt                 <  1:1592597/71‑1 (MQ=255)
                                                    gATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAtt                                               <  1:471494/40‑1 (MQ=38)
                                                    gATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGa                                 <  1:2082645/54‑1 (MQ=255)
                                                     aTCGTTCTCGGTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAt                  >  1:3664908/1‑68 (MQ=255)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAtt                                               <  1:424375/39‑1 (MQ=37)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                 >  1:3348133/1‑69 (MQ=255)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTga               <  1:2059956/71‑1 (MQ=255)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTga               <  1:2526065/71‑1 (MQ=255)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTga               <  1:3710846/71‑1 (MQ=255)
                                                     aTCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCCCACTATGa                                 <  1:1007940/53‑1 (MQ=255)
                                                      tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                 >  1:1962465/1‑68 (MQ=255)
                                                      tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                 >  1:1514733/1‑68 (MQ=255)
                                                      tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                 >  1:2684345/1‑68 (MQ=255)
                                                      tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCCCACTATGAAGGCCACAAGATCAtt                 >  1:1641851/1‑68 (MQ=255)
                                                       cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTg                                              >  1:3191080/1‑38 (MQ=37)
                                                       cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                  >  1:306977/1‑50 (MQ=255)
                                                       cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                 >  1:2332788/1‑67 (MQ=255)
                                                       cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                 >  1:773780/1‑67 (MQ=255)
                                                        gTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGAt            <  1:201083/71‑1 (MQ=255)
                                                         ttCTCGCTACCGCAACCACCGGTATGAACCAGAtt                                               <  1:2624540/35‑1 (MQ=37)
                                                         ttCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTgcgc                                        <  1:1030880/42‑1 (MQ=38)
                                                         ttCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGa                                 <  1:2433570/49‑1 (MQ=39)
                                                           ctcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTg          <  1:1166460/70‑1 (MQ=255)
                                                           ctcGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGa                      >  1:2371150/1‑58 (MQ=255)
                                                            tcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCa                   >  1:3787196/1‑60 (MQ=255)
                                                              gctACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACaa                        >  1:3457784/3‑53 (MQ=255)
                                                              gctACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGAt                     >  1:2133434/3‑56 (MQ=255)
                                                              gctACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTgaga             >  1:3486830/3‑64 (MQ=255)
                                                              gctACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTgaga             >  1:3013691/3‑64 (MQ=255)
                                                                tACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCg    >  1:278608/1‑71 (MQ=255)
                                                                  ccGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCg    <  1:2486802/69‑1 (MQ=255)
                                                                     |                                                                   
AAACGACAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCGTT  >  W3110S.gb/236038‑236174

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