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 1,211,298 G→A 31.2% G18G (GGC→GGT)  cspC ← stress protein, member of the CspA‑family

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,211,2980GA31.2% 216.0 / 109.5 144G18G (GGC→GGT) cspCstress protein, member of the CspA‑family
Reads supporting (aligned to +/- strand):  ref base G (49/50);  new base A (22/23);  total (71/73)
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 146 total aligned reads displayed.

TGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCT  >  minE/1211228‑1211364
                                                                      |                                                                  
tGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAg                                                                    >  1:1975074/1‑71 (MQ=255)
  aaaccATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAAcc                                                                  <  1:663283/68‑1 (MQ=12)
   aGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGcc                                                                  >  1:431655/1‑70 (MQ=255)
     ccATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCaaa                                                               <  1:2245700/71‑1 (MQ=255)
     ccATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCaaa                                                               <  1:2066571/71‑1 (MQ=255)
      cATTGCTCTGGATGGCGGTGAAATGGACGAAAACGTCTTTGCTGCCATCATCAGGAGTGATAAAGCCaaa                                                               <  1:951577/70‑1 (MQ=9)
           gtcTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCtt                                                          <  1:1279319/68‑1 (MQ=12)
           gtcTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCtt                                                          <  1:4722556/68‑1 (MQ=12)
           cccTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCtt                                                          <  1:3886370/70‑1 (MQ=255)
           cccTGGATAGCGGAGAAGTGTAAGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCtt                                                          <  1:4050024/70‑1 (MQ=255)
            tcTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATcc                                                            <  1:35234/66‑1 (MQ=12)
             cTGGATAGCGGAGAAGTGTACGAACACATCTTTTCTGCCATCAGCCGGAGTAATGAAGCCAAAACCtt                                                          >  1:2917133/1‑68 (MQ=255)
             cTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAg                                                       <  1:3836516/71‑1 (MQ=255)
              tGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCtt                                                          >  1:4297971/1‑67 (MQ=12)
              tGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGa                                                      >  1:290164/1‑71 (MQ=255)
               ggATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGAc                                                     >  1:1426323/1‑71 (MQ=255)
                gATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACt                                                    <  1:523556/71‑1 (MQ=12)
                    gCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGc                                                                   >  1:3857525/1‑52 (MQ=255)
                    gCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTa                                                        <  1:3655965/63‑1 (MQ=255)
                     cagagaAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCAtta                                               <  1:1167976/69‑2 (MQ=255)
                     cagagaAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCAtt                                                <  1:3159219/68‑1 (MQ=12)
                     cagagaAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCAtt                                                >  1:4202839/3‑70 (MQ=12)
                     cGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTa                                                        <  1:5060615/62‑1 (MQ=255)
                      ggAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGa                                              <  1:1613290/71‑1 (MQ=255)
                      ggAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGa                                              <  1:303111/71‑1 (MQ=255)
                       gagaAGTGTACGAACACGTCTTTGCTGCCGTCTTCAGGAGTAATGAAACCGAATCCtttg                                                        <  1:1869002/60‑2 (MQ=12)
                         gaAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAAc                                            >  1:5097356/1‑70 (MQ=255)
                           aGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCAc                                         <  1:4487975/71‑1 (MQ=255)
                             tgtAAGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAAccg                                                                 <  1:1828006/45‑2 (MQ=2)
                             tgtAAGAACACGTCATTGCTGCCGTCTTCCGGAGTAATGATACCGAATCCtt                                                          <  1:3246410/52‑1 (MQ=255)
                               tACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTaa                                     >  1:702603/1‑71 (MQ=255)
                               tACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTaa                                     >  1:2964801/1‑71 (MQ=255)
                               tACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTa                                                        >  1:3796598/1‑52 (MQ=255)
                               tACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGt                                                 >  1:2812273/1‑59 (MQ=255)
                               tACGAACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCAtttta                                     >  1:4551257/1‑69 (MQ=255)
                               gaCGAAAACGTCTTTGCTGCCATCATCAGGAGTGATAAAGCCAAAAc                                                             >  1:893405/2‑47 (MQ=12)
                                aCGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAAc                                                             >  1:2164978/1‑46 (MQ=255)
                                aCGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAAc                                                             >  1:3856104/1‑46 (MQ=255)
                                 cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTaaa                                             >  1:3629146/1‑61 (MQ=9)
                                 cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAAc                                            >  1:2731558/1‑62 (MQ=9)
                                 cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAAc                                            >  1:2622983/1‑62 (MQ=9)
                                 cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAAcg                                   >  1:4127071/1‑70 (MQ=12)
                                 cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAAcg                                   >  1:192844/1‑70 (MQ=12)
                                 cGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAAcc                                   <  1:4801092/71‑1 (MQ=255)
                                   aaCACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAAcgtt                                 <  1:4154567/71‑4 (MQ=12)
                                   aaCACATCTTTACTACCATCAACAGGAGAAATAAAGccga                                                                >  1:1592686/1‑38 (MQ=9)
                                   aaCACATCTTTACTACCATCAACAGGAGAAATAAAGccga                                                                >  1:1525315/1‑38 (MQ=9)
                                   aaCACATCTTTACTACCATCAACAGGAGAAATAAAGccga                                                                >  1:5206818/1‑38 (MQ=9)
                                    acacATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGa                                <  1:3624785/71‑1 (MQ=255)
                                    acacATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGa                                <  1:3971008/71‑1 (MQ=255)
                                    acacATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGa                                >  1:2078914/1‑71 (MQ=255)
                                     cacaTCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCAc                                         <  1:476376/61‑1 (MQ=255)
                                       caTCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCt                             <  1:4781149/71‑1 (MQ=255)
                                       caTCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCt                             <  1:1152790/71‑1 (MQ=255)
                                        aTCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCtt                            <  1:4970200/71‑1 (MQ=255)
                                         tCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAg                                                       >  1:1835602/1‑43 (MQ=255)
                                         tCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTa                                      <  1:4881688/60‑1 (MQ=255)
                                          cTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAAc                                                             >  1:4205672/1‑36 (MQ=255)
                                          cTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTaa                                     >  1:5689306/1‑60 (MQ=255)
                                           tttGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCtttgg                                                       <  1:1025835/41‑3 (MQ=12)
                                           tttGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCtttg                                                        <  1:4885998/40‑2 (MQ=12)
                                           tttGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTg                                 >  1:5654221/1‑63 (MQ=255)
                                             tgctgcCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCTTTaa                         <  1:3695205/69‑1 (MQ=255)
                                             tgctgcCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTa                          <  1:2164328/68‑1 (MQ=255)
                                             tgctgcCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTa                          <  1:3454643/68‑1 (MQ=255)
                                              gctgcCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCt                      >  1:5137044/1‑71 (MQ=255)
                                              gctgcCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCt                      >  1:3595011/1‑71 (MQ=255)
                                               ctgcCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCTTTAATCtt                     <  1:5041135/71‑1 (MQ=255)
                                               ctgcCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCTTTAATCt                      <  1:3743808/70‑1 (MQ=255)
                                                tgcCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTa                          <  1:402581/65‑1 (MQ=255)
                                                  ccATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGc                  >  1:1797797/1‑71 (MQ=255)
                                                     tCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCt                      <  1:2535722/64‑1 (MQ=255)
                                                     tCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCAt               <  1:1346808/71‑1 (MQ=255)
                                                     tCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCAt               >  1:5457350/1‑71 (MQ=255)
                                                       ttccGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCa                                          >  1:4018360/3‑42 (MQ=255)
                                                       ttccGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCa                                          >  1:3968665/3‑42 (MQ=255)
                                                       aGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTaa                                     >  1:5227390/1‑47 (MQ=255)
                                                       aGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCttt                    >  1:4610099/1‑64 (MQ=255)
                                                         ccGTAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAAc                                    >  1:3683862/1‑46 (MQ=12)
                                                         ccGGAGTAATGAAACCGAATCCTTTGGACTCATTaaa                                             >  1:3854253/1‑37 (MQ=12)
                                                         ccGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCTTTAATCTTAGACAtcaa            <  1:4366361/70‑4 (MQ=255)
                                                         ccGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCTTTAATCTTAGACAtcaa            <  1:3476175/70‑4 (MQ=255)
                                                         ccGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCTTTAATCTTAGACAtcaa            <  1:3496766/70‑4 (MQ=255)
                                                         ccGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCTTTAATCTTAGACAtca             <  1:3136418/69‑3 (MQ=255)
                                                           ggAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGaaa         <  1:3067404/71‑1 (MQ=255)
                                                           ggAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGaaa         <  1:3113148/71‑1 (MQ=255)
                                                             aGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCAtt              >  1:3768443/1‑64 (MQ=255)
                                                              gTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTAcc                              >  1:3366984/1‑47 (MQ=9)
                                                                aaTGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCttt                           <  1:3264398/48‑1 (MQ=255)
                                                                 aTGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTaa                         >  1:4980506/1‑49 (MQ=255)
                                                                 aTGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTaa                         >  1:172183/1‑49 (MQ=255)
                                                                 aTGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTcc   <  1:2504374/71‑1 (MQ=255)
                                                                 aTGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTcc   >  1:3092134/1‑71 (MQ=255)
                                                                 aTGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTcc   >  1:3877377/1‑71 (MQ=255)
                                                                  tGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCAt               <  1:5568382/58‑1 (MQ=255)
                                                                  tGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCt  <  1:541882/71‑1 (MQ=255)
                                                                    aaGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGaaaaa       >  1:2466670/1‑64 (MQ=255)
                                                                    aaGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGaaaaa       >  1:560782/1‑64 (MQ=255)
                                                                    aaGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGaaaaa       >  1:4413746/1‑64 (MQ=255)
                                                                      gCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCt  >  1:2943908/1‑67 (MQ=255)
                                                                      |                                                                  
TGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCT  >  minE/1211228‑1211364

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