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 F21 I0 R2 370 72.1 3738297 91.5% 3420541 62.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,933,109 G→T 5.6% A445D (GCC→GAC) ‡ lysS ← lysine tRNA synthetase, constitutive

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,933,1090GT 5.6% 307.1 / 2.4 88A445D (GCC→GAC) ‡lysSlysine tRNA synthetase, constitutive
Reads supporting (aligned to +/- strand):  ref base G (37/46);  new base T (2/3);  total (39/49)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.35e-01

CATGTTCCAGTGCGGTGACGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTT  >  minE/1933041‑1933178
                                                                    |                                                                     
cATGTTCCAGTGCGGTGACGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGc                                                                      >  1:2928523/1‑70 (MQ=255)
cATGTTCCAGTGCGGTGACGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGc                                                                      >  1:1051824/1‑70 (MQ=255)
cATGTTCCAGTGCGGTGACGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCa                                                                     <  1:3094420/71‑1 (MQ=255)
  tGTTCCAGTGCGGTGACGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCaa                                                                    >  1:1490286/1‑70 (MQ=255)
  tGTTCCAGTGCGGTGACGTAATCTTCATCGTAGAACATCGCTTCGTCATCACCTGCGTCTTTCGCGGCAAc                                                                   >  1:18462/1‑71 (MQ=255)
    ttCCAGTGCGGTGACGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCt                                                                 <  1:759415/71‑1 (MQ=255)
       cAGTGCGGTGACGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGa                                                               <  1:3269500/70‑1 (MQ=255)
        aGTGCGGTGACGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATc                                                             <  1:2998201/71‑1 (MQ=255)
        aGTGCGGTGACGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATc                                                             >  1:1103143/1‑71 (MQ=255)
         gTGCGGTGACGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATcc                                                            <  1:3042917/71‑1 (MQ=255)
         gTGCGGTGACGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATcc                                                            <  1:1522501/71‑1 (MQ=255)
          tGCGGTGACGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATc                                                             >  1:428054/1‑69 (MQ=255)
          tGCGGTGACGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCa                                                           <  1:1812253/71‑1 (MQ=255)
            cGGTGACGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATc                                                             >  1:1443407/1‑67 (MQ=255)
            cGGTGACGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAg                                                          >  1:1657954/1‑70 (MQ=255)
             ggTGACGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGa                                                        <  1:63412/71‑1 (MQ=255)
             ggTGACGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGa                                                        <  1:3274528/71‑1 (MQ=255)
             ggTGACGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGa                                                        <  1:329462/71‑1 (MQ=255)
               tGACGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCgg                                                                       <  1:2850521/54‑1 (MQ=255)
               tGACGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATc                                                             <  1:2559082/64‑1 (MQ=255)
               tGACGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATc                                                             <  1:3302034/64‑1 (MQ=255)
                 aCGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGc                                                     <  1:3302403/70‑1 (MQ=255)
                 aCGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGc                                                     <  1:3032348/70‑1 (MQ=255)
                 aCGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCg                                                    >  1:2173432/1‑71 (MQ=255)
                  cGTAATCTTCGTCATAGAACATGGCTTCGTCGTCACCTGCAGCTTTAGCATTAACCTGTTCCTGGAAACGt                                                   >  1:1458125/1‑71 (MQ=255)
                  cGTAATCTTCGTCATAGAACATGGCTTCGTCGTCACCTGCAGCTTTAGCATTAACCTGTTCCTGGAAACGt                                                   >  1:362217/1‑71 (MQ=255)
                  cGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGt                                                   <  1:145945/71‑1 (MQ=255)
                  cGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGt                                                   <  1:32075/71‑1 (MQ=255)
                    tAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTg                                                 >  1:1401504/1‑71 (MQ=255)
                    tAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTg                                                 <  1:203329/71‑1 (MQ=255)
                     aaTCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAg                                                          >  1:3703943/1‑61 (MQ=255)
                     aaTCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAg                                                          >  1:1231354/1‑61 (MQ=255)
                     aaTCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTgc                                                >  1:533772/1‑71 (MQ=255)
                     aaTCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTgc                                                >  1:3236910/1‑71 (MQ=255)
                      aTCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTgcg                                               >  1:3440040/1‑71 (MQ=255)
                         ttCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGa                                                               >  1:3635250/1‑52 (MQ=255)
                         ttCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGa                                                               >  1:1545752/1‑52 (MQ=255)
                          tCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCt                                            >  1:3617230/1‑70 (MQ=255)
                           cATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCaa                                                                    >  1:951007/1‑45 (MQ=255)
                           cATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTgcgc                                              >  1:1914762/1‑67 (MQ=255)
                           cATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTgcgc                                              <  1:583430/67‑1 (MQ=255)
                           cATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTgcgc                                              >  1:579646/1‑67 (MQ=255)
                           cATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGcc                                             <  1:2997881/68‑1 (MQ=255)
                           cATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCt                                            <  1:2874433/69‑1 (MQ=255)
                           cATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCt                                            <  1:1402321/69‑1 (MQ=255)
                            aTCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTg                                           <  1:1111011/69‑1 (MQ=255)
                            aTCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTg                                           <  1:555642/69‑1 (MQ=255)
                             tCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAAcc                                                                  >  1:2607090/1‑45 (MQ=255)
                             tCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAAcc                                                                  >  1:3648783/1‑45 (MQ=255)
                             tCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAAcc                                                                  >  1:2213243/1‑45 (MQ=255)
                               gTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCgg                                                                       >  1:773258/1‑38 (MQ=255)
                               gTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCgg                                                                       >  1:2483467/1‑38 (MQ=255)
                                tAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCa                                                                     <  1:1275139/39‑1 (MQ=255)
                                tAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCa                                                                     <  1:337496/39‑1 (MQ=255)
                                tAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCa                                                                     <  1:1207189/39‑1 (MQ=255)
                                tAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCa                                                                     <  1:2501002/39‑1 (MQ=255)
                                tAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTg                                           <  1:1001371/65‑1 (MQ=255)
                                tAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTc                                     >  1:1351967/1‑71 (MQ=255)
                                  gAACATGGCTTCGTCGTCACCTGCAGCTTTAGCATTAACCTGTTCCTGGAAACGTTCAGCCTGATCTTct                                    <  1:3668796/70‑2 (MQ=255)
                                  gAACATGGCTTCGTCGTCACCTGCAGCTTTAGCATTAACCTGTTCCTGGAAACGTTCAGCCTGATCTTct                                    <  1:1929007/70‑2 (MQ=255)
                                  gAACATGGCTTCGTCGTCACCTGCAGCTTTAGCATTAACCTGTTCCTGGAAACGTTCAGCCTGATCTTct                                    <  1:620064/70‑2 (MQ=255)
                                  gAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCcg                                   <  1:2842864/71‑1 (MQ=255)
                                  gAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCcg                                   >  1:132471/1‑71 (MQ=255)
                                     cATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAg                                                      >  1:459341/1‑49 (MQ=255)
                                       tCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCa                              <  1:1515315/71‑1 (MQ=255)
                                         gCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCAtt                            <  1:3721822/71‑1 (MQ=255)
                                          cTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCAtt                            <  1:3697729/70‑1 (MQ=255)
                                          cTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCAtt                            <  1:1217093/70‑1 (MQ=255)
                                            tcgtcgTCACTTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAg                         >  1:697240/1‑71 (MQ=255)
                                            tcgtcgTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAg                         >  1:1412372/1‑71 (MQ=255)
                                             cgtcgtCACCTGCGTCTTTCGCGGCAACCTGATCCa                                                           <  1:1345239/36‑1 (MQ=255)
                                             cgtcgtCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCa                          <  1:1258963/69‑1 (MQ=255)
                                              gtcgtcACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGc                        <  1:3613428/70‑1 (MQ=255)
                                              gtcgtcACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGc                        <  1:2839302/70‑1 (MQ=255)
                                              gtcgtcACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGc                        <  1:3617753/70‑1 (MQ=255)
                                              gtcgtcACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGc                        <  1:2069330/70‑1 (MQ=255)
                                                 gtcACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGc                    <  1:1010574/71‑1 (MQ=255)
                                                 gtcACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGc                    >  1:1750396/1‑71 (MQ=255)
                                                 gtcACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGc                    <  1:1563464/71‑1 (MQ=255)
                                                  tcACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGt                                                   <  1:802717/39‑1 (MQ=255)
                                                  tcACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGc                    >  1:3115832/1‑70 (MQ=255)
                                                   cACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTg                                           <  1:2378735/46‑1 (MQ=255)
                                                      cTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAg               <  1:2981397/71‑1 (MQ=255)
                                                      cTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAg               >  1:754459/1‑71 (MQ=255)
                                                      cTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAg               >  1:3469767/1‑71 (MQ=255)
                                                      cTGCGTCTTTCGAGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAg               >  1:1614046/1‑71 (MQ=255)
                                                       tGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTc                                     <  1:3439401/48‑1 (MQ=255)
                                                        gCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGcc             >  1:636305/1‑71 (MQ=255)
                                                          gTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGt           >  1:2522874/1‑71 (MQ=255)
                                                          gTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGt           >  1:1159005/1‑71 (MQ=255)
                                                                 gcgGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGAt    <  1:2583566/71‑1 (MQ=255)
                                                                   ggCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGAttt  <  1:2997836/71‑1 (MQ=255)
                                                                   ggCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGAttt  >  1:297682/1‑71 (MQ=255)
                                                                    gCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGAttt  >  1:1889561/1‑70 (MQ=255)
                                                                    |                                                                     
CATGTTCCAGTGCGGTGACGTAATCTTCATCGTAGAACATCGCTTCGTCGTCACCTGCGTCTTTCGCGGCAACCTGATCCAGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTT  >  minE/1933041‑1933178

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