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 1,211,304 A→T 32.2% G16G (GGT→GGA)  cspC ← stress protein, member of the CspA‑family

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,211,3040AT32.2% 201.1 / 122.7 134G16G (GGT→GGA) cspCstress protein, member of the CspA‑family
Reads supporting (aligned to +/- strand):  ref base A (44/46);  new base T (22/21);  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 = 1.62e-01

Only 100 of 144 total aligned reads displayed.

ATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTGTT  >  minE/1211235‑1211373
                                                                     |                                                                     
aTTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAAc                                                                      >  1:597120/1‑71 (MQ=255)
aTTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAAc                                                                      >  1:3805245/1‑71 (MQ=255)
    gtcTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCtt                                                                   <  1:4722556/68‑1 (MQ=12)
    gtcTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCtt                                                                   <  1:1279319/68‑1 (MQ=12)
    ctcTGGATGGCGGTGAAATGGACGAAAACGTCTTTGCTGCCATCATCAGGAGTGATAAAGCCAAAACCttt                                                                  <  1:2084618/69‑1 (MQ=9)
    cccTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCtt                                                                   <  1:3886370/70‑1 (MQ=255)
     tcTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATcc                                                                     <  1:35234/66‑1 (MQ=12)
      cTGGATAGCGGAGAAGTGTACGAACACATCTTTTCTGCCATCAGCCGGAGTAATGAAGCCAAAACCtt                                                                   >  1:2917133/1‑68 (MQ=255)
       tGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCtt                                                                   >  1:4297971/1‑67 (MQ=12)
       tGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGa                                                               >  1:290164/1‑71 (MQ=255)
         gATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGa                                                               >  1:4172713/1‑69 (MQ=255)
         gATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACt                                                             <  1:523556/71‑1 (MQ=12)
             gCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTa                                                                 <  1:3655965/63‑1 (MQ=255)
             gCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGtt                                                         <  1:153090/71‑1 (MQ=255)
              cagagaAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCAtta                                                        <  1:1167976/69‑2 (MQ=255)
              cagagaAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCAtt                                                         >  1:4202839/3‑70 (MQ=12)
              cGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTa                                                                 <  1:5060615/62‑1 (MQ=255)
               ggAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGa                                                       <  1:5539536/71‑1 (MQ=255)
               ggAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGa                                                       <  1:1613290/71‑1 (MQ=255)
               ggAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGa                                                       <  1:303111/71‑1 (MQ=255)
                gagaAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGAc                                                              >  1:3861295/1‑63 (MQ=12)
                gagaAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGAc                                                              >  1:2598203/1‑63 (MQ=12)
                gagaAGTGTACGAACACGTCTTTGCTGCCGTCTTCAGGAGTAATGAAACCGAATCCtttg                                                                 <  1:1869002/60‑2 (MQ=12)
                   aaGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCtt                                                                   <  1:3736081/55‑1 (MQ=255)
                      tgtAAGAACACGTCATTGCTGCCGTCTTCCGGAGTAATGATACCGAATCCtt                                                                   <  1:3246410/52‑1 (MQ=255)
                        tACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTaa                                              >  1:2964801/1‑71 (MQ=255)
                        tACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTa                                                                 >  1:3796598/1‑52 (MQ=255)
                        tACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGt                                                          >  1:2812273/1‑59 (MQ=255)
                        tACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTa                                               <  1:2181620/70‑1 (MQ=255)
                        tACGAACACATCTTTAGAGCCATCGTCAGGAGTGATGAAGCCGAAGCCTTTGTCAGCGTTGAACCAtttta                                              >  1:4551257/1‑69 (MQ=255)
                        gaCGAAAACGTCTTTGCTGCCATCATCAGGAGTGATAAAGCCAAAAc                                                                      >  1:893405/2‑47 (MQ=12)
                         aCGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAAc                                                                      >  1:2164978/1‑46 (MQ=255)
                          cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAAc                                                     >  1:2731558/1‑62 (MQ=9)
                          cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAAcg                                            >  1:4127071/1‑70 (MQ=12)
                          cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAAc                                             <  1:3081630/70‑1 (MQ=12)
                          cGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAAcc                                            <  1:4801092/71‑1 (MQ=255)
                           gAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCt                                           >  1:4944556/1‑71 (MQ=255)
                           gAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCt                                           >  1:3011678/1‑71 (MQ=255)
                             acacATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGa                                         <  1:3971008/71‑1 (MQ=255)
                             acacATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGa                                         <  1:3624785/71‑1 (MQ=255)
                              cacaTCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCAc                                                  <  1:3855277/61‑1 (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                                                                >  1:4588488/1‑43 (MQ=255)
                                  tCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTg                                                        <  1:5642545/51‑1 (MQ=255)
                                  tCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTa                                               <  1:5158342/60‑1 (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)
                                    tttGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTaa                                  >  1:4453267/1‑71 (MQ=255)
                                      tgctgcCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCTTTaa                                  <  1:3695205/69‑1 (MQ=255)
                                      tgctgcCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTa                                   <  1:3454643/68‑1 (MQ=255)
                                      tgctgcCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTa                                   <  1:3678572/68‑1 (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                               <  1:3575/64‑1 (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)
                                                  ccGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTa                                               <  1:3480573/44‑1 (MQ=255)
                                                  ccGGAGTAATGAAACCGAATCCTTTGGACTCATTaaa                                                      >  1:3854253/1‑37 (MQ=12)
                                                  ccGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAAc                                             >  1:2053871/1‑46 (MQ=16)
                                                  ccGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCTTTAATCTTAGACAtcaa                     <  1:3476175/70‑4 (MQ=255)
                                                  ccGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCTTTAATCTTAGACAtca                      <  1:3136418/69‑3 (MQ=255)
                                                  ccGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCTTTAATCTTAGACAtca                      <  1:3627065/69‑3 (MQ=255)
                                                    ggAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGaaa                  <  1:3067404/71‑1 (MQ=255)
                                                      aGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCTTTAATCtta                             >  1:810974/1‑57 (MQ=16)
                                                       gTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTAcc                                       >  1:3366984/1‑47 (MQ=9)
                                                        tAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCtt                                     <  1:4339395/48‑1 (MQ=255)
                                                        tAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCtt                                     <  1:1822953/48‑1 (MQ=255)
                                                        tAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGaaa                  <  1:4087591/67‑1 (MQ=255)
                                                          aTGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTaa                                  >  1:172183/1‑49 (MQ=255)
                                                          aTGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTaa                                  >  1:4980506/1‑49 (MQ=255)
                                                          aTGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTcc            <  1:3240707/71‑1 (MQ=255)
                                                          aTGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTcc            >  1:3116939/1‑71 (MQ=255)
                                                          aTGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTcc            >  1:3877377/1‑71 (MQ=255)
                                                          aTGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTcc            >  1:3092134/1‑71 (MQ=255)
                                                           tGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCAt                        <  1:5568382/58‑1 (MQ=255)
                                                             aaGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGaaaaa                >  1:1909686/1‑64 (MQ=255)
                                                             aaGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGaaaaa                >  1:2473115/1‑64 (MQ=255)
                                                             aaGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGaaaaa                >  1:2466670/1‑64 (MQ=255)
                                                             aaGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGaaaaa                >  1:4413746/1‑64 (MQ=255)
                                                               gCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCt           >  1:2943908/1‑67 (MQ=255)
                                                                ccAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTTcc                          <  1:2447139/51‑1 (MQ=255)
                                                                  aaaaCCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATc                                <  1:2119062/43‑1 (MQ=255)
                                                                  aaaaCCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCAt                        >  1:2056603/1‑51 (MQ=255)
                                                                  aaaaCCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTg    <  1:3300760/71‑1 (MQ=255)
                                                                   aaaCCTTTAGACTCGTTGAACCACTTAACCTGACCTTTa                                   <  1:56089/39‑1 (MQ=255)
                                                                   aaaCCTTTAGACTCGTTGAACCACTTAACCTGACCTTTa                                   <  1:4757809/39‑1 (MQ=255)
                                                                    aaCCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTGtt  >  1:292420/1‑71 (MQ=255)
                                                                     |                                                                     
ATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCATTTGAAAAATTCCTTAGATTGTT  >  minE/1211235‑1211373

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