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 1,211,301 A→G 32.8% F17F (TTT→TTC)  cspC ← stress protein, member of the CspA‑family

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,211,3010AG32.8% 186.9 / 113.3 134F17F (TTT→TTC) cspCstress protein, member of the CspA‑family
Reads supporting (aligned to +/- strand):  ref base A (44/46);  new base G (23/21);  total (67/67)
Fisher's exact test for biased strand distribution p-value = 8.54e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.27e-01

Only 100 of 143 total aligned reads displayed.

CCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTG  >  minE/1211233‑1211371
                                                                    |                                                                      
 cATTGCTCTGGATGGCGGTGAAATGGACGAAAACGTCTTTGCTGCCATCATCAGGAGTGATAAAGCCaaa                                                                      <  1:951577/70‑1 (MQ=9)
 cATTGCTCTGGATGGCGGTGAAATGGACGAAAACGTCTTTGCTGCCATCATCAGGAGTGATAAAGCCaaa                                                                      <  1:5092732/70‑1 (MQ=9)
  aTTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAAc                                                                    >  1:3805245/1‑71 (MQ=255)
  aTTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAAc                                                                    >  1:597120/1‑71 (MQ=255)
   ttACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCaa                                                                       <  1:3383326/67‑1 (MQ=255)
      gtcTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCtt                                                                 <  1:1279319/68‑1 (MQ=12)
      gtcTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCtt                                                                 <  1:4722556/68‑1 (MQ=12)
      ctcTGGATGGCGGTGAAATGGACGAAAACGTCTTTGCTGCCATCATCAGGAGTGATAAAGCCAAAACCttt                                                                <  1:2084618/69‑1 (MQ=9)
      cccTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCtt                                                                 <  1:3886370/70‑1 (MQ=255)
      cccTGGATAGCGGAGAAGTGTACGAACACATCTTTGATGCCATCAGCCGGAGTAATGAAGCCAAAACCtt                                                                 >  1:4280542/1‑70 (MQ=255)
      cccTGGATAGCGGAGAAGTGTAAGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCtt                                                                 <  1:4050024/70‑1 (MQ=255)
        cTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAg                                                              <  1:3836516/71‑1 (MQ=255)
         tGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGa                                                             >  1:290164/1‑71 (MQ=255)
           gATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGa                                                             >  1:4172713/1‑69 (MQ=255)
           gATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACt                                                           >  1:2843540/1‑71 (MQ=255)
           gATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACt                                                           <  1:523556/71‑1 (MQ=12)
               gCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGtt                                                       <  1:153090/71‑1 (MQ=255)
                cagagaAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCAtta                                                      <  1:1167976/69‑2 (MQ=255)
                cagagaAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCAtt                                                       <  1:3159219/68‑1 (MQ=12)
                cGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTa                                                               <  1:5060615/62‑1 (MQ=255)
                 ggAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGa                                                     <  1:5539536/71‑1 (MQ=255)
                 ggAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGa                                                     <  1:303111/71‑1 (MQ=255)
                 ggAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGa                                                     <  1:1613290/71‑1 (MQ=255)
                  gagaAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGAc                                                            >  1:3861295/1‑63 (MQ=12)
                  gagaAGTGTACGAACACGTCTTTGCTGCCGTCTTCAGGAGTAATGAAACCGAATCCtttg                                                               <  1:1869002/60‑2 (MQ=12)
                      aGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCAc                                                <  1:4487975/71‑1 (MQ=255)
                          tACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTaa                                            >  1:702603/1‑71 (MQ=255)
                          tACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTaa                                            >  1:2964801/1‑71 (MQ=255)
                          tACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTa                                             <  1:2181620/70‑1 (MQ=255)
                          tACGAACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCAtttta                                            >  1:4551257/1‑69 (MQ=255)
                          gaCGAAAACGTCTTTGCTGCCATCATCAGGAGTGATAAAGCCAAAAc                                                                    >  1:893405/2‑47 (MQ=12)
                           aCGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAAc                                                                    >  1:3856104/1‑46 (MQ=255)
                           aCGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAAc                                                                    >  1:2164978/1‑46 (MQ=255)
                            cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTaaa                                                    >  1:3629146/1‑61 (MQ=9)
                            cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAAc                                                   >  1:2622983/1‑62 (MQ=9)
                            cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAAc                                                   >  1:2731558/1‑62 (MQ=9)
                            cGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAAcc                                          <  1:4801092/71‑1 (MQ=255)
                              aaCACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAAcgtt                                        <  1:4154567/71‑4 (MQ=12)
                               acacATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGa                                       <  1:3971008/71‑1 (MQ=255)
                               acacATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGa                                       >  1:2078914/1‑71 (MQ=255)
                                cacaTCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCAc                                                <  1:3855277/61‑1 (MQ=255)
                                  cgtCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCt                                    >  1:3944241/3‑71 (MQ=12)
                                  caTCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCt                                    <  1:4781149/71‑1 (MQ=255)
                                  caTCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCt                                    <  1:1152790/71‑1 (MQ=255)
                                   aTCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCtt                                   <  1:4970200/71‑1 (MQ=255)
                                    tCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTg                                                      <  1:5642545/51‑1 (MQ=255)
                                    tCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTa                                             <  1:4881688/60‑1 (MQ=255)
                                    tCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTa                                             <  1:5158342/60‑1 (MQ=255)
                                     cTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAAc                                                                    >  1:4205672/1‑36 (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                                 <  1:3678572/68‑1 (MQ=255)
                                         gctgcCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCt                             >  1:3595011/1‑71 (MQ=255)
                                         gctgcCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCt                             >  1:5137044/1‑71 (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)
                                               aTCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCa                       <  1:5384946/71‑1 (MQ=255)
                                                tCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCt                             <  1:2535722/64‑1 (MQ=255)
                                                tCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCt                             <  1:3575/64‑1 (MQ=255)
                                                tCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCAt                      <  1:1346808/71‑1 (MQ=255)
                                                tCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCAt                      >  1:5457350/1‑71 (MQ=255)
                                                  aGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCttt                           >  1:4610099/1‑64 (MQ=255)
                                                  aGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCAtt                     >  1:3981886/1‑70 (MQ=255)
                                                    ccGTAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAAc                                           >  1:3683862/1‑46 (MQ=12)
                                                    ccGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTa                                             <  1:3480573/44‑1 (MQ=255)
                                                    ccGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAAc                                           >  1:2053871/1‑46 (MQ=16)
                                                    ccGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCTTTAATCTTAGACAtcaa                   <  1:3496766/70‑4 (MQ=255)
                                                    ccGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCTTTAATCTTAGACAtcaa                   <  1:4366361/70‑4 (MQ=255)
                                                    ccGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCTTTAATCTTAGACAtcaa                   <  1:3476175/70‑4 (MQ=255)
                                                    ccGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCTTTAATCTTAGACAtca                    <  1:3627065/69‑3 (MQ=255)
                                                    ccGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCTTTAATCTTAGACAtca                    <  1:3136418/69‑3 (MQ=255)
                                                      ggAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCa                       <  1:2943115/64‑1 (MQ=255)
                                                      ggAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGaaa                <  1:3067404/71‑1 (MQ=255)
                                                      ggAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGaaa                <  1:3113148/71‑1 (MQ=255)
                                                        aGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCAtt                     >  1:3768443/1‑64 (MQ=255)
                                                          tAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCtt                                   <  1:4339395/48‑1 (MQ=255)
                                                          tAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCtt                                   <  1:1822953/48‑1 (MQ=255)
                                                          tAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGaaa                <  1:4087591/67‑1 (MQ=255)
                                                           aaTGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCttt                                  <  1:3264398/48‑1 (MQ=255)
                                                            aTGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTaa                                >  1:172183/1‑49 (MQ=255)
                                                            aTGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTaa                                >  1:4980506/1‑49 (MQ=255)
                                                            aTGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTcc          <  1:2504374/71‑1 (MQ=255)
                                                            aTGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTcc          >  1:3092134/1‑71 (MQ=255)
                                                            aTGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTcc          <  1:3240707/71‑1 (MQ=255)
                                                             tGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCAt                      <  1:4771719/58‑1 (MQ=255)
                                                             tGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCAt                      <  1:5568382/58‑1 (MQ=255)
                                                               aaGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGaaaaa              >  1:1909686/1‑64 (MQ=255)
                                                               aaGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGaaaaa              >  1:2473115/1‑64 (MQ=255)
                                                               aaGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGaaaaa              >  1:4413746/1‑64 (MQ=255)
                                                                 gCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCt         >  1:2943908/1‑67 (MQ=255)
                                                                  ccAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTTcc                        <  1:2447139/51‑1 (MQ=255)
                                                                   cAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGAt    >  1:2456088/1‑70 (MQ=255)
                                                                    aaaaCCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATc                              <  1:2119062/43‑1 (MQ=255)
                                                                    aaaaCCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGcc                        <  1:3424188/49‑1 (MQ=255)
                                                                    aaaaCCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCAt                      >  1:2056603/1‑51 (MQ=255)
                                                                    aaaaCCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTg  <  1:3300760/71‑1 (MQ=255)
                                                                    |                                                                      
CCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTG  >  minE/1211233‑1211371

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