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 F3 I0 R1 560 56.4 4650532 94.9% 4413354 59.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 236,107 A→C 93.7% 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.gb236,1070AC93.7% 3382.0 / 88.2 1014E14A (GAA→GCA) dnaQDNA polymerase III epsilon subunit
Reads supporting (aligned to +/- strand):  ref base A (37/28);  new base C (498/449);  total (536/478)
Fisher's exact test for biased strand distribution p-value = 5.23e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

Only 100 of 1053 total aligned reads displayed.

AAACGACAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCGTTGA  >  W3110S.gb/236038‑236176
                                                                     |                                                                     
 caactCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGcaa                                                                     >  1:1268980‑M2/6‑71 (MQ=255)
  aactCAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGcaa                                                                     >  1:4544318‑M2/5‑70 (MQ=255)
      cAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAaccacc                                                                >  1:4037774/1‑71 (MQ=255)
       aaGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCg                                                               >  1:2833008/1‑71 (MQ=255)
        aGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGTTCGTTCTCGCTACCGCAACCACCgg                                                              <  1:1443504/71‑1 (MQ=255)
        aGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCgg                                                              <  1:2095509/71‑1 (MQ=255)
         gTCTGACATAAATGACCGCTATGAGCACTGCAATTACACTCCAGATCGTTCTCGCTACCGCAACCACCGGt                                                             <  1:595023/71‑1 (MQ=255)
            tGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTa                                                            <  1:3242567/69‑1 (MQ=255)
              aCATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTAt                                                           <  1:1136327/68‑1 (MQ=255)
              aCATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGa                                                         <  1:4441181/70‑1 (MQ=255)
                 tAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATg                                                          <  1:4287636/66‑1 (MQ=255)
                 tAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                       <  1:3353914/69‑1 (MQ=255)
                   aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGcaa                                                                     >  1:2061660/1‑53 (MQ=255)
                   aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAGCCACCGGTATGAAc                                                       >  1:1360507/1‑67 (MQ=255)
                   aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                       >  1:1005307/1‑67 (MQ=255)
                   aaTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                       >  1:1787222/1‑67 (MQ=255)
                    aTGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAg                                                    <  1:3742230/69‑1 (MQ=255)
                       aCCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGcaa                                                                     >  1:3438436/1‑49 (MQ=255)
                       aCCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTgg                                               >  1:2810203/1‑71 (MQ=255)
                       aCCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTg                                                <  1:4314327/70‑1 (MQ=255)
                         cGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTg                                             >  1:183207/1‑71 (MQ=255)
                           cTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTgcg                                           <  1:1964541/71‑1 (MQ=255)
                           cTATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTg                                             >  1:2529818/1‑69 (MQ=255)
                            tATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGcaa                                                                     >  1:1921956/1‑44 (MQ=255)
                            tATGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTgcg                                           >  1:3125392/1‑70 (MQ=255)
                              tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTAt                                                           <  1:709084/52‑1 (MQ=255)
                              tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCa                                         <  1:2640156/70‑1 (MQ=255)
                                 gCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTgg                                               >  1:1871565/1‑61 (MQ=255)
                                 gCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTAt                                     <  1:4152399/71‑1 (MQ=255)
                                  cACTGCAATTACACGCCAGATCGTTCTCTCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                    <  1:928857/71‑1 (MQ=255)
                                  cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCTCCGGTATGAACCAGATTGGTGCGCACTATg                                    <  1:1101144/71‑1 (MQ=255)
                                  cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                    <  1:807489/71‑1 (MQ=255)
                                  cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                    <  1:1688375/71‑1 (MQ=255)
                                    cTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGaa                                  <  1:2253981/71‑1 (MQ=255)
                                     tGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                     <  1:2315647/51‑1 (MQ=255)
                                     tGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCAc                                        <  1:3794221/64‑1 (MQ=255)
                                      gCAATTACACGCCAGATCGTTCTCGCTACCGCAac                                                                    >  1:4120904/1‑35 (MQ=38)
                                      gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGaa                                                        >  1:2919383/1‑47 (MQ=39)
                                      gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCa                                         >  1:276069/1‑62 (MQ=255)
                                       cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGc                               >  1:4179747/1‑71 (MQ=255)
                                       cAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGc                               >  1:3066727/1‑71 (MQ=255)
                                        aaTTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAg                                                    >  1:2386623/1‑49 (MQ=39)
                                        aaTTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGcc                              <  1:1190325/71‑1 (MQ=255)
                                         aTTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCca                             >  1:3405778/1‑71 (MQ=255)
                                         aTTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCca                             <  1:1720205/71‑1 (MQ=255)
                                          ttACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                                    <  1:2703753/63‑1 (MQ=255)
                                          ttACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                            <  1:2211291/71‑1 (MQ=255)
                                           tACACGCCAGATCGTTCTCGCTACCGCAACCACCGTTATg                                                          >  1:347734/1‑40 (MQ=255)
                                           tACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                                >  1:1408693/1‑66 (MQ=255)
                                           tACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCcac                            <  1:903696/70‑1 (MQ=255)
                                            acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTa                                                            >  1:3286589/1‑37 (MQ=37)
                                            acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATg                                                          >  1:3849893/1‑39 (MQ=37)
                                            acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTgcg                                           >  1:498440/1‑54 (MQ=255)
                                            acacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCca                             >  1:249969/1‑68 (MQ=255)
                                             cacGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAg                         <  1:66576/71‑1 (MQ=255)
                                               cGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGa                                                         <  1:215393/37‑1 (MQ=37)
                                               cGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGAt                       <  1:1058842/71‑1 (MQ=255)
                                                gCCAGATCGTTCTCGCTACCGCAACCACCTGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATc                      <  1:956708/71‑1 (MQ=255)
                                                gCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGaa                                  >  1:3918483/1‑59 (MQ=255)
                                                gCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGAt                       >  1:4255857/1‑70 (MQ=255)
                                                gCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAACAt                       >  1:4592920/1‑70 (MQ=255)
                                                 ccAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCa                     <  1:2676913/71‑1 (MQ=255)
                                                  cAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAt                    <  1:464752/71‑1 (MQ=255)
                                                   aGATCGTTCTCGCTACCGCAACCACCGGTATGAAc                                                       <  1:847111/35‑1 (MQ=37)
                                                    gATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTgg                                               >  1:4499241/1‑42 (MQ=38)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCa                                                     <  1:407695/35‑1 (MQ=37)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGAt                                                  <  1:3614522/38‑1 (MQ=37)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCCCAAGATCATTga                 <  1:1757247/71‑1 (MQ=255)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTga                 <  1:3012303/71‑1 (MQ=255)
                                                     aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTga                 <  1:2019460/71‑1 (MQ=255)
                                                     aTCGTCCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATc                      <  1:4357746/66‑1 (MQ=255)
                                                      tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                   >  1:244874/1‑68 (MQ=255)
                                                      tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                   >  1:3517581/1‑68 (MQ=255)
                                                      tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                   >  1:2953816/1‑68 (MQ=255)
                                                      tCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTga                 <  1:398280/70‑1 (MQ=255)
                                                      tCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTga                 <  1:3315616/70‑1 (MQ=255)
                                                      tCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTga                 <  1:1235211/70‑1 (MQ=255)
                                                       cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACaa                          >  1:3707967/1‑60 (MQ=255)
                                                       cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt                   >  1:619324/1‑67 (MQ=255)
                                                        gTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTa                                      <  1:1655360/47‑1 (MQ=39)
                                                        gTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTgaga               <  1:1312964/70‑1 (MQ=255)
                                                        gTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGAt              <  1:1549877/71‑1 (MQ=255)
                                                        gTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGAt              <  1:4379027/71‑1 (MQ=255)
                                                        gTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGAt              <  1:753954/71‑1 (MQ=255)
                                                         ttCTCGCTACCGCAACCACCGGTATGAACCAGATTgg                                               >  1:3565869/1‑37 (MQ=37)
                                                         ttCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACaa                          <  1:3893819/58‑1 (MQ=255)
                                                         ttCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATc                      <  1:1489431/62‑1 (MQ=255)
                                                         ttCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGAtt             <  1:2612267/71‑1 (MQ=255)
                                                         ttCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGAtt             >  1:534185/1‑71 (MQ=255)
                                                         ttCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGAt              <  1:2571706/70‑1 (MQ=255)
                                                         ttCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGAt              <  1:3175074/70‑1 (MQ=255)
                                                          tctcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCa                     >  1:4224066/1‑62 (MQ=255)
                                                           ctcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTgaga               >  1:569753/1‑67 (MQ=255)
                                                           ctcGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTgg           >  1:3677061/1‑71 (MQ=255)
                                                             cgctACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGAGCATTGAGATTg            <  1:2341404/65‑1 (MQ=255)
                                                              gctACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGt          <  1:3639860/67‑1 (MQ=255)
                                                              gctACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGc        >  1:2869382/3‑71 (MQ=255)
                                                                  ccGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCGACAAGATCATTgaga               >  1:2743622/1‑60 (MQ=255)
                                                                  ccGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCGtt    >  1:2901970/1‑71 (MQ=255)
                                                                    gAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCGTTGa  <  1:1600673/71‑1 (MQ=255)
                                                                     |                                                                     
AAACGACAAGTCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAGATTGGTGCCGTTGA  >  W3110S.gb/236038‑236176

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A