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
A6 F1 I0 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 minE 1,933,684 C→T 35.1% E253E (GAG→GAA)  lysS ← lysine tRNA synthetase, constitutive

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,933,6840CT35.1% 135.4 / 116.9 131E253E (GAG→GAA) lysSlysine tRNA synthetase, constitutive
Reads supporting (aligned to +/- strand):  ref base C (43/42);  new base T (30/16);  total (73/58)
Fisher's exact test for biased strand distribution p-value = 1.41e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.62e-01

Only 100 of 136 total aligned reads displayed.

GTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCA  >  minE/1933616‑1933754
                                                                    |                                                                      
gTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCt                                                                       <  1:3970881/70‑1 (MQ=255)
gTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCt                                                                       <  1:675221/70‑1 (MQ=255)
 tGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCg                                                                     <  1:1146341/71‑1 (MQ=255)
 tGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTca                                                                     <  1:554714/71‑2 (MQ=255)
  gAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCg                                                                     >  1:4582207/1‑70 (MQ=255)
   aaCTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGaa                                                                   <  1:430150/71‑1 (MQ=255)
   aaCTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGaa                                                                   <  1:4527674/71‑1 (MQ=255)
   aaCTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGaa                                                                   <  1:4827354/71‑1 (MQ=255)
   aaCTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTcaa                                                                    <  1:2987779/70‑3 (MQ=255)
     ctctGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGc                                                                 <  1:2892083/71‑1 (MQ=255)
     ctctGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGc                                                                 <  1:4084731/71‑1 (MQ=255)
     ctctGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGc                                                                 <  1:5195268/71‑1 (MQ=255)
        tGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGa                                                                    <  1:4519719/65‑1 (MQ=255)
        tGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGa                                                                    <  1:4923416/65‑1 (MQ=255)
        tGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGccac                                                              >  1:1408252/1‑71 (MQ=255)
        tGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGccac                                                              >  1:4228905/1‑71 (MQ=255)
        tGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGccac                                                              >  1:2777119/1‑71 (MQ=255)
        tGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGc                                                                 <  1:1602887/68‑1 (MQ=255)
        tGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTAAGGTTGATTTCGAATACACGCTCGAAGccac                                                              >  1:2157608/1‑71 (MQ=255)
         gggTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTACGAATACACGCTCGAAGccac                                                              >  1:2774212/1‑70 (MQ=255)
          ggTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAg                                                                  >  1:2616005/1‑65 (MQ=255)
          ggTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGccacc                                                             <  1:4870123/70‑1 (MQ=255)
            ttATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAAccgccta                                                           >  1:4819371/1‑68 (MQ=255)
            ttATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCgcctac                                                          <  1:3838952/71‑1 (MQ=255)
              aTGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCaaaa                                                                  >  1:277397/1‑60 (MQ=255)
              aTGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCgcctacaa                                                        >  1:748797/1‑69 (MQ=255)
              aTGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCgcctaca                                                         <  1:1084518/70‑2 (MQ=255)
               tGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGcca                                                               >  1:5042931/1‑63 (MQ=255)
                 aCGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAaccac                                                       >  1:1326860/1‑69 (MQ=255)
                 aCGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAAccacca                                                     <  1:2818589/71‑1 (MQ=255)
                  cGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAg                                                    <  1:1516433/71‑1 (MQ=255)
                     aCGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACg                                                 >  1:1033978/1‑71 (MQ=255)
                      cGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGaa                                                                   <  1:4410153/52‑1 (MQ=255)
                        gAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGgcacc                                                             >  1:421049/1‑56 (MQ=255)
                        gAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCtt                                              >  1:2675331/1‑71 (MQ=255)
                        gAAATACCTTCATTACGGAAGTTATGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGttt                                              >  1:3821128/1‑71 (MQ=255)
                         aaaTACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCg                                                                     <  1:3268977/47‑1 (MQ=255)
                         aaaTACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGcca                                                               >  1:376949/1‑53 (MQ=255)
                         aaaTACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGcca                                                               >  1:1239092/1‑53 (MQ=255)
                         aaaTACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTg                                             <  1:4666974/71‑1 (MQ=255)
                           aTACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGttt                                              >  1:5186520/1‑68 (MQ=255)
                              ccTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCgcctacaa                                                        >  1:3994674/1‑53 (MQ=255)
                              ccTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTacaac                                                       >  1:1873826/1‑56 (MQ=255)
                              ccTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATa                                        <  1:4856855/71‑1 (MQ=255)
                               cTTCGTTACGGAAGTTTCGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTAc                                       <  1:3647018/71‑1 (MQ=255)
                               cTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTAc                                       <  1:187276/71‑1 (MQ=255)
                                ttCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGccacca                                                            <  1:3893942/49‑1 (MQ=255)
                                ttCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGccacca                                                            <  1:5360544/49‑1 (MQ=255)
                                ttCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTa                                        >  1:604968/1‑69 (MQ=255)
                                ttCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAAcc                                                                <  1:1435071/45‑1 (MQ=25)
                                  cattACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAgc                                    >  1:4430100/3‑70 (MQ=255)
                                  cGTTACGGAAGTTACGGTTGATTTCGAATACACGCTc                                                                      >  1:5012709/1‑37 (MQ=255)
                                  cGTTACGGAAGTTACGGTTGATTTCGAATACACGCTc                                                                      >  1:2656446/1‑37 (MQ=255)
                                  cGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGcc                                                                >  1:2008424/1‑43 (MQ=255)
                                  cGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAgg                                          >  1:1963701/1‑65 (MQ=255)
                                   attACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAgc                                    <  1:1080444/69‑2 (MQ=255)
                                   attACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAgc                                    <  1:2252117/69‑2 (MQ=255)
                                   attACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTA‑AACCAGACGTTTCAGATACAGCTc                                  >  1:2459265/2‑71 (MQ=255)
                                      aCGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAAccgcc                                                             >  1:282983/1‑42 (MQ=19)
                                      aCGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTcc                                 >  1:5351536/1‑70 (MQ=255)
                                      aCGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCg                                >  1:5008196/1‑71 (MQ=255)
                                      aCGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTcc                                 <  1:2260078/70‑1 (MQ=255)
                                      aCGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCg                                >  1:3371058/1‑71 (MQ=255)
                                          aaGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATa                                        >  1:5596705/1‑59 (MQ=255)
                                          aaGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATa                                        >  1:5252360/1‑59 (MQ=255)
                                          aaGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATa                                        >  1:4202604/1‑59 (MQ=255)
                                          aaGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATa                                        >  1:917003/1‑59 (MQ=255)
                                          aaGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAg                                     >  1:1566166/1‑62 (MQ=255)
                                          aaGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGgcgc                            <  1:2875600/71‑1 (MQ=255)
                                          aaGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGgcgc                            <  1:288199/71‑1 (MQ=255)
                                            gTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGa                          <  1:4795269/71‑1 (MQ=255)
                                            gTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCtt                                              <  1:515468/51‑1 (MQ=255)
                                            gTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCtt                                              <  1:3097117/51‑1 (MQ=255)
                                              tACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATa                        >  1:2469760/1‑71 (MQ=255)
                                               aCGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACgt                                                >  1:2275108/1‑45 (MQ=12)
                                               aCGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATa                        >  1:4185953/1‑70 (MQ=255)
                                               aCGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGgcgc                            >  1:5387034/1‑66 (MQ=255)
                                                cGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATACg                      >  1:4656395/1‑71 (MQ=255)
                                                 ggTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACG‑TTCAGATACAGCTCCGGCGCGATACGCa                    <  1:201603/71‑1 (MQ=255)
                                                 ggTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGc                     <  1:3248809/71‑1 (MQ=255)
                                                 ggTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGc                     <  1:5289292/71‑1 (MQ=255)
                                                   ttGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATACGCa                    <  1:665385/70‑1 (MQ=255)
                                                   ttGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAg                   >  1:3631369/1‑71 (MQ=255)
                                                      aTTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATa                <  1:4404712/71‑1 (MQ=255)
                                                        ttCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACa              >  1:2757169/1‑71 (MQ=255)
                                                         tCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACa              >  1:490592/1‑70 (MQ=255)
                                                         tCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACa              >  1:3019741/1‑70 (MQ=255)
                                                         tCGAATACACGCTCGAAGCCACCAACCACCAGACGCt                                               >  1:4662182/1‑37 (MQ=255)
                                                         tCGAATACACGCTCGAAGCCACCAACCACCAGACGCt                                               >  1:2582511/1‑37 (MQ=255)
                                                              tACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTc          >  1:4741747/1‑69 (MQ=255)
                                                                 acGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGAt     <  1:2723919/71‑1 (MQ=255)
                                                                  cGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTAc               >  1:2664894/1‑60 (MQ=255)
                                                                  cGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTAc               >  1:1303601/1‑60 (MQ=255)
                                                                  cGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTAc               >  1:1057842/1‑60 (MQ=255)
                                                                  cGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCgaga      <  1:3263218/69‑1 (MQ=255)
                                                                  cGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATc    <  1:5599401/71‑1 (MQ=255)
                                                                  cGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATc    <  1:2306737/71‑1 (MQ=255)
                                                                   gCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATcc   <  1:3558803/71‑1 (MQ=255)
                                                                    cTCGAAGCCACCAACCACCTGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCa  <  1:2373747/71‑1 (MQ=255)
                                                                    cTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGc                     >  1:1373156/1‑52 (MQ=255)
                                                                    |                                                                      
GTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCA  >  minE/1933616‑1933754

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