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 1,211,280 A→G 32.0% D24D (GAT→GAC)  cspC ← stress protein, member of the CspA‑family

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,211,2800AG32.0% 209.4 / 119.6 147D24D (GAT→GAC) cspCstress protein, member of the CspA‑family
Reads supporting (aligned to +/- strand):  ref base A (47/53);  new base G (25/22);  total (72/75)
Fisher's exact test for biased strand distribution p-value = 5.96e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 149 total aligned reads displayed.

GACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCA  >  minE/1211210‑1211350
                                                                      |                                                                      
gACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCa                                                                        >  1:5551196/1‑71 (MQ=255)
     tCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGc                                                                   >  1:2276753/1‑71 (MQ=255)
      cAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAg                                                                    <  1:3489174/69‑1 (MQ=255)
      cAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAg                                                                    <  1:1528557/69‑1 (MQ=255)
      cAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGc                                                                   <  1:1600824/70‑1 (MQ=255)
       aGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCg                                                                 <  1:2632015/71‑1 (MQ=255)
           agagTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGact                                                             <  1:2794389/71‑3 (MQ=255)
           agagTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAg                                                              >  1:5312850/1‑70 (MQ=255)
           agagTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGt                                                             <  1:1759384/71‑1 (MQ=255)
             agTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTaa                                                           <  1:5371059/71‑1 (MQ=255)
             agTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTaa                                                           <  1:4061192/71‑1 (MQ=16)
              gTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAAt                                                          <  1:2078635/71‑1 (MQ=255)
              gTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAAt                                                          >  1:2661813/1‑71 (MQ=255)
              gTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAAt                                                          >  1:2186337/1‑71 (MQ=255)
              gTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAAt                                                          <  1:5075619/71‑1 (MQ=255)
              gTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAAt                                                          <  1:5394219/71‑1 (MQ=255)
              gTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAAt                                                          <  1:1547175/71‑1 (MQ=16)
               ttttGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATg                                                         <  1:4816761/71‑1 (MQ=255)
                 ttGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGa                                                        <  1:2655222/70‑1 (MQ=255)
                 ttGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGa                                                        <  1:1533115/70‑1 (MQ=255)
                    aaaccATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAAcc                                                    <  1:663283/68‑1 (MQ=12)
                     aGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGcc                                                    >  1:431655/1‑70 (MQ=255)
                       ccATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCaaa                                                 <  1:2066571/71‑1 (MQ=255)
                       ccATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCaaa                                                 <  1:2245700/71‑1 (MQ=255)
                        cATTGCTCTGGATGGCGGTGAAATGGACGAAAACGTCTTTGCTGCCATCATCAGGa                                                               >  1:3652710/1‑56 (MQ=2)
                        cATTGCTCTGGATGGCGGTGAAATGGACGAAAACGTCTTTGCTGCCATCATCAGGAGTGATAAAGCCaaa                                                 <  1:951577/70‑1 (MQ=9)
                        cATTGCTCTGGATGGCGGTGAAATGGACGAAAACGTCTTTGCTGCCATCATCAGGAGTGATAAAGCCaaa                                                 <  1:5092732/70‑1 (MQ=9)
                        cATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGa                                                               >  1:2581149/1‑56 (MQ=12)
                         aTTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAAc                                               >  1:597120/1‑71 (MQ=255)
                         aTTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAAc                                               >  1:3805245/1‑71 (MQ=255)
                             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)
                               cTGGATAGCGGAGAAGTGTACGAACACATCTTTTCTGCCATCAGCCGGAGTAATGAAGCCAAAACCtt                                            >  1:2917133/1‑68 (MQ=255)
                                tGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGaaac                                                     >  1:5419329/1‑56 (MQ=18)
                                tGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGa                                        >  1:290164/1‑71 (MQ=255)
                                  gATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGa                                        >  1:4172713/1‑69 (MQ=255)
                                  gATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACt                                      >  1:2843540/1‑71 (MQ=255)
                                      gCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTa                                          <  1:3655965/63‑1 (MQ=255)
                                       cagagaAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCAtt                                  <  1:3159219/68‑1 (MQ=12)
                                       cGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTa                                                            <  1:1732270/44‑1 (MQ=255)
                                        ggAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGa                                <  1:303111/71‑1 (MQ=255)
                                        ggAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGa                                <  1:5539536/71‑1 (MQ=255)
                                        ggAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGa                                <  1:1613290/71‑1 (MQ=255)
                                         gagaAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGAc                                       >  1:2598203/1‑63 (MQ=12)
                                         gagaAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGAc                                       >  1:3861295/1‑63 (MQ=12)
                                         gagaAGTGTACGAACACGTCTTTGCTGCCGTCTTCAGGAGTAATGAAACCGAATCCtttg                                          <  1:1869002/60‑2 (MQ=12)
                                         gagaAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAAt                                                          >  1:120909/1‑44 (MQ=255)
                                         gagaAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAAt                                                          >  1:3001490/1‑44 (MQ=255)
                                            aaGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCtt                                            <  1:3736081/55‑1 (MQ=255)
                                             aGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCAc                           <  1:4487975/71‑1 (MQ=255)
                                               tgtACGAACACATCTTTGCTGCCATCAGCCGGAGTa                                                            <  1:5235387/36‑1 (MQ=255)
                                               tgtAAGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAAccg                                                   <  1:1828006/45‑2 (MQ=2)
                                               tgtAAGAACACGTCATTGCTGCCGTCTTCCGGAGTAATGATACCGAATCCtt                                            <  1:3246410/52‑1 (MQ=255)
                                                gtACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATg                                                         >  1:1348652/1‑38 (MQ=18)
                                                gtACGAACACATCTTTGCTGCCATCAGCCGGAGTAATg                                                         <  1:1027758/38‑1 (MQ=255)
                                                 tACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGaaa                                                      <  1:4490316/40‑2 (MQ=17)
                                                 tACGAACACATCTTTGCTGCCATCAGCCGGAGTAAt                                                          >  1:4421765/1‑36 (MQ=255)
                                                 tACGAACACATCTTTGCTGCCATCAGCCGGAGTAAt                                                          >  1:3011408/1‑36 (MQ=255)
                                                 tACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTa                                          >  1:4843779/1‑52 (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                                               >  1:3856104/1‑46 (MQ=255)
                                                  aCGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAAc                                               >  1:1208086/1‑46 (MQ=255)
                                                   cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGa                                                        >  1:2849694/1‑36 (MQ=12)
                                                   cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGa                                                        >  1:3804661/1‑36 (MQ=12)
                                                   cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAAc                              >  1:2622983/1‑62 (MQ=9)
                                                   cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAAcg                     >  1:192844/1‑70 (MQ=12)
                                                   cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAAc                      <  1:3081630/70‑1 (MQ=12)
                                                    gAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCt                    >  1:4944556/1‑71 (MQ=255)
                                                     aaCACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAAcgtt                   <  1:4154567/71‑4 (MQ=12)
                                                     aaCACATCTTTACTACCATCAACAGGAGAAATAAAGccga                                                  >  1:1397473/1‑38 (MQ=9)
                                                     aaCACATCTTTACTACCATCAACAGGAGAAATAAAGccga                                                  >  1:5206818/1‑38 (MQ=9)
                                                     aaCACATCTTTACTACCATCAACAGGAGAAATAAAGccga                                                  >  1:1525315/1‑38 (MQ=9)
                                                      acacATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGa                  <  1:3624785/71‑1 (MQ=255)
                                                      acacATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGa                  <  1:3971008/71‑1 (MQ=255)
                                                       cacaTCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCAc                           <  1:476376/61‑1 (MQ=255)
                                                       cacaTCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCAc                           <  1:3855277/61‑1 (MQ=255)
                                                         cgtCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAACGTTACCt               >  1:3944241/3‑71 (MQ=12)
                                                         caTCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCt               <  1:1152790/71‑1 (MQ=255)
                                                         caTCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCt               <  1:4781149/71‑1 (MQ=255)
                                                           tCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAg                                         >  1:4588488/1‑43 (MQ=255)
                                                           tCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTa                        <  1:5158342/60‑1 (MQ=255)
                                                            cTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAAc                                               >  1:4205672/1‑36 (MQ=255)
                                                            cTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTaa                       >  1:5689306/1‑60 (MQ=255)
                                                             tttGGTGCCATCAGCCGGAGTAATGAAGCCAAAACCt                                             >  1:5021466/1‑37 (MQ=255)
                                                             tttGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCtttgg                                         <  1:1025835/41‑3 (MQ=12)
                                                             tttGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCtttg                                          <  1:4885998/40‑2 (MQ=12)
                                                             tttGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTg                   >  1:5654221/1‑63 (MQ=255)
                                                               tgctgcCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTa            <  1:3454643/68‑1 (MQ=255)
                                                               tgctgcCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTa            <  1:2164328/68‑1 (MQ=255)
                                                               tgctgcCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTa            <  1:3678572/68‑1 (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)
                                                                    ccATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGc    >  1:1797797/1‑71 (MQ=255)
                                                                      |                                                                      
GACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTTTAATCTTTGCCA  >  minE/1211210‑1211350

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