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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,771,324 C→G 33.6% T298T (ACC→ACG)  pheA → fused chorismate mutase P and prephenate dehydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,771,3240CG33.6% 106.3 / 79.6 104T298T (ACC→ACG) pheAfused chorismate mutase P and prephenate dehydratase
Reads supporting (aligned to +/- strand):  ref base C (31/38);  new base G (16/19);  total (47/57)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 104 total aligned reads displayed.

CCGATTTGTGGTGTTGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGCAACAAGCCGGTGCGCTGGTTGAAGCGTTGCTGGTACTGCGCAAC  >  minE/1771264‑1771390
                                                            |                                                                  
ccGATTTGTGGTGTTTGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            <  1:2754477/69‑1 (MQ=255)
ccGATTTGTGGTGTTGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            <  1:1785911/69‑1 (MQ=255)
ccGATTTGTGGTGTTGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            <  1:1998288/69‑1 (MQ=255)
ccGATTTGTGGTGTTGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            <  1:2002308/69‑1 (MQ=255)
ccGATTTGTGGTGTTGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            <  1:2096426/69‑1 (MQ=255)
ccGATTTGTGGTGTTGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            <  1:211654/69‑1 (MQ=255)
ccGATTTGTGGTGTTGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            <  1:212174/69‑1 (MQ=255)
ccGATTTGTGGTGTTGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            <  1:2733098/69‑1 (MQ=255)
ccGATTTGTGGTGTTGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            <  1:3229258/69‑1 (MQ=255)
ccGATTTGTGGTGTTGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            <  1:1206101/69‑1 (MQ=255)
ccGATTTGTGGTGTTGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            <  1:490337/69‑1 (MQ=255)
ccGATTTGTGGTGTTGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            <  1:495910/69‑1 (MQ=255)
ccGATTTGTGGTGTTGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            <  1:1064857/69‑1 (MQ=255)
             ttGGCTCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            >  1:735223/1‑56 (MQ=255)
             ttGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            <  1:3367483/56‑1 (MQ=255)
             ttGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            <  1:2807901/56‑1 (MQ=255)
             ttGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            <  1:3410133/56‑1 (MQ=255)
             ttGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            <  1:273342/56‑1 (MQ=255)
             ttGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            >  1:44943/1‑56 (MQ=255)
             ttGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            <  1:2396195/56‑1 (MQ=255)
             ttGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            <  1:2285115/56‑1 (MQ=255)
             ttGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            >  1:2220504/1‑56 (MQ=255)
             ttGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            <  1:2014123/56‑1 (MQ=255)
             ttGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            <  1:504917/56‑1 (MQ=255)
             ttGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            <  1:1023897/56‑1 (MQ=255)
             ttGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACgttgtt                                                            >  1:1394478/1‑56 (MQ=255)
               ggCGCGTAAAGCCATTAACGTGTCTTATCAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGc                                              >  1:1938850/1‑68 (MQ=255)
               ggCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGc                                              >  1:1531858/1‑68 (MQ=255)
               ggCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGc                                              >  1:590305/1‑68 (MQ=255)
               ggCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGc                                              >  1:551968/1‑68 (MQ=255)
               ggCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGc                                              >  1:1217758/1‑68 (MQ=255)
               ggCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGc                                              >  1:2643978/1‑68 (MQ=255)
               ggCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGc                                              >  1:2599677/1‑68 (MQ=255)
               ggCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGc                                              >  1:2575015/1‑68 (MQ=255)
               ggCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGc                                              >  1:2528540/1‑68 (MQ=255)
               ggCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGc                                              >  1:2440122/1‑68 (MQ=255)
               ggCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGc                                              >  1:2159373/1‑68 (MQ=255)
               ggCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGc                                              >  1:1460677/1‑68 (MQ=255)
               ggCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGc                                              >  1:1987940/1‑68 (MQ=255)
                       aaGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGCAACAAGCCg                                     >  1:1117048/1‑69 (MQ=255)
                       aaGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGCAACAAGCCg                                     >  1:3372630/1‑69 (MQ=255)
                       aaGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGCAACAAGCCg                                     >  1:1188807/1‑69 (MQ=255)
                       aaGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGCAACAAGCCg                                     >  1:2224302/1‑69 (MQ=255)
                               aaCGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAAt                                                         <  1:3340823/41‑1 (MQ=255)
                               aaCGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAAt                                                         <  1:2462141/41‑1 (MQ=255)
                               aaCGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAAt                                                         <  1:3080837/41‑1 (MQ=255)
                               aaCGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAAt                                                         <  1:1340186/41‑1 (MQ=255)
                               aaCGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAAt                                                         <  1:231440/41‑1 (MQ=255)
                               aaCGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAAt                                                         <  1:1240266/41‑1 (MQ=255)
                               aaCGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAAt                                                         <  1:1391569/41‑1 (MQ=255)
                               aaCGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGCAACAAGCCGGTGCGCTg                             >  1:1095703/1‑69 (MQ=255)
                               aaCGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGCAACAAGCCGGTGCGCTg                             >  1:734919/1‑69 (MQ=255)
                               aaCGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGCAACAAGCCGGTGCGCTg                             >  1:1968513/1‑69 (MQ=255)
                                aCGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAAt                                                         <  1:1832470/40‑1 (MQ=255)
                                      cTGACCAGGTTCCGGCGAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTgcac                               <  1:1328209/60‑3 (MQ=255)
                                      cTGACCAGGTTCCGGCGAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTgcac                               <  1:277542/60‑3 (MQ=255)
                                      cTGACCAGGTTCCGGCGAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTgcac                               <  1:1967681/60‑3 (MQ=255)
                                      cTGACCAGGTTCCGGCGAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTgcac                               <  1:1313670/60‑3 (MQ=255)
                                      cTGACCAGGTTCCGGCGAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTgcac                               <  1:1251039/60‑3 (MQ=255)
                                      cTGACCAGGTTCCGGCGAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTgcac                               <  1:2900506/60‑3 (MQ=255)
                                      cTGACCAGGTTCCGGCGAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTgcac                               <  1:3178099/60‑3 (MQ=255)
                                      cTGACCAGGTTCCGGCGAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTgcac                               <  1:1668904/60‑3 (MQ=255)
                                      cTGACCAGGTTCCGGCGAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTgcac                               <  1:10778/60‑3 (MQ=255)
                                      cTGACCAGGTTCCGGCGAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTgcac                               <  1:747767/60‑3 (MQ=255)
                                      cTGACCAGGTTCCGGCGAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTgcac                               <  1:836072/60‑3 (MQ=255)
                                      cTGACCAGGTTCCGGCGAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTgcac                               <  1:269201/60‑3 (MQ=255)
                                      cTGACCAGGTTCCGGCGAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTgcac                               <  1:1741580/60‑3 (MQ=255)
                                      cTGACCAGGTTCCGGCGAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTgcac                               <  1:1828267/60‑3 (MQ=255)
                                       tGACCAGGTTCCGGCTAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTgcac                               <  1:1517943/59‑3 (MQ=255)
                                       tGACCAGGTTCCGGCGAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTgcac                               <  1:113709/59‑3 (MQ=255)
                                           cAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGCAACAAGCCGGTGCGCTGGTTGAAGCGTTg                 >  1:2727331/1‑69 (MQ=255)
                                           cAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGCAACAAGCCGGTGCGCTGGTTGAAGCGTTg                 >  1:883445/1‑69 (MQ=255)
                                           cAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGCAACAAGCCGGTGCGCTGGTTGAAGCGTTg                 >  1:1001385/1‑69 (MQ=255)
                                           cAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGCAACAAGCCGGTGCGCTGGTTGAAGCGTTg                 >  1:1457783/1‑69 (MQ=255)
                                           cAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGCAACAAGCCGGTGCGCTGGTTGAAGCGTTg                 >  1:14571/1‑69 (MQ=255)
                                           cAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGCAACAAGCCGGTGCGCTGGTTGAAGCGTTg                 >  1:432234/1‑69 (MQ=255)
                                           cAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGCAACAAGCCGGTGCGCTGGTTGAAGCGTTg                 >  1:1787649/1‑69 (MQ=255)
                                               ttCCGGCGAAAACCACGTTGTTAATGGCGACCGGGCAACAAGCCGGTGCGCTGGTTGAAGCGTTGCTgg             <  1:1576004/69‑1 (MQ=255)
                                               ttCCGGAGAAAACCACGTTGTTAATGGCGACCGGGCAACAAGCCGGTGCGCTGGTTGAAGCGTTGCTgg             <  1:1025498/69‑1 (MQ=255)
                                                 ccGGCGAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTgcac                               <  1:3250107/49‑3 (MQ=255)
                                                   ggCGAAAACCACGTTGTTAATGGCGACCGGGCAACAAGCCGGTGCGCTGGTTGAAGCGTTGCTGGTAc          <  1:2690177/68‑1 (MQ=255)
                                                      gAAACCGACGTTGTTAATGGCGACCGGACAACAAGCTGGTGCACTGGTTGAAGCGTTGCTGGTACTgc       >  1:852876/1‑68 (MQ=255)
                                                      gAAAACGCCGTTGTTAATGGCGACCGGACAACAAGCTGGTGCACTGGTTGAAGCGTTGCTGGTACTgc       >  1:2597290/1‑68 (MQ=255)
                                                      gAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTGCACTGGTTGAGGCGTTGCTGGTACTgc       >  1:2978361/1‑68 (MQ=255)
                                                      gAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTGCACTGGTTGAAGCGTTGCTGGTACTgc       >  1:2040256/1‑68 (MQ=255)
                                                      gAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTGCACTGGTTGAAGCGTTGCTGGTACTgc       >  1:1924985/1‑68 (MQ=255)
                                                      gAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTGCACTGGTTGAAGCGTTGCTGGTACTgc       >  1:1478192/1‑68 (MQ=255)
                                                      gAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTGCACTGGTTGAAGCGTTGCTGGTACTgc       >  1:1497305/1‑68 (MQ=255)
                                                      gAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTGCACTGGTTGAAGCGTTGCTGGTACTgc       >  1:2868517/1‑68 (MQ=255)
                                                      gAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTGCACTGGTTGAAGCGTTGCTGGTACTgc       >  1:374823/1‑68 (MQ=255)
                                                      gAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTGCACTGGTTGAAGCGTTGCTGGTACTgc       >  1:1850802/1‑68 (MQ=255)
                                                      gAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTGCACTGGTTGAAGCGTTGCTGGTACTgc       >  1:3318248/1‑68 (MQ=255)
                                                      gAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTGCACTGGTTGAAGCGTTGCTGGTACTgc       >  1:2255611/1‑68 (MQ=255)
                                                      gAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTGCACTGGTTGAAGCGTTGCTGGTACTgc       >  1:3187071/1‑68 (MQ=255)
                                                      gAAAACGACGTTGTTAATGGCGACCGGACAACAAGCTGGTGCACTGGTTGAAGCGTTGCTGGTACTg        >  1:1920307/1‑67 (MQ=255)
                                                          aCCACGTTGTTAATGGCGACCGGGCAACAAGCCGGTGCGCTGGTTGAAGCGTTGCTGGTACTGCGCAAc  <  1:2307794/69‑1 (MQ=255)
                                                          aCCACGTTGTTAATGGCGACCGGGCAACAAGCCGGTGCGCTGGTTGAAGCGTTGCTGGTACTGCGCAAc  <  1:1413439/69‑1 (MQ=255)
                                                          aCCACGTTGTTAATGGCGACCGGGCAACAAGCCGGTGCGCTGGTTGAAGCGTTGCTGGTACTGCGCAAc  <  1:1409380/69‑1 (MQ=255)
                                                          aCCACGTTGTTAATGGCGACCGGGCAACAAGCCGGTGCGCTGGTTGAAGCGTTGCTGGTACTGCGCAAc  <  1:1681917/69‑1 (MQ=255)
                                                          aCCACGTTGTTAATGGCGACCGGGCAACAAGCCGGTGCGCTGGTTGAAGCGTTGCTGGTACTGCGCAAc  <  1:756077/69‑1 (MQ=255)
                                                            |                                                                  
CCGATTTGTGGTGTTGGCGCGTAAAGCCATTAACGTGTCTGATCAGGTTCCGGCGAAAACCACGTTGTTAATGGCGACCGGGCAACAAGCCGGTGCGCTGGTTGAAGCGTTGCTGGTACTGCGCAAC  >  minE/1771264‑1771390

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