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 1,211,268 A→G 38.8% D28D (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
*minE1,211,2680AG38.8% 156.2 / 145.0 139D28D (GAT→GAC) cspCstress protein, member of the CspA‑family
Reads supporting (aligned to +/- strand):  ref base A (43/42);  new base G (28/26);  total (71/68)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01

Only 100 of 144 total aligned reads displayed.

AACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTT  >  minE/1211202‑1211338
                                                                  |                                                                      
  cGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTtg                                                                  <  1:1692410/71‑1 (MQ=255)
    cgcTGACCTTCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTtgc                                                                 <  1:5022279/68‑1 (MQ=255)
     tCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTtgctg                                                               >  1:4519688/1‑71 (MQ=255)
       tGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTtgctgc                                                              >  1:468109/1‑70 (MQ=255)
        gACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCa                                                            >  1:5551196/1‑71 (MQ=255)
             tCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGc                                                       >  1:3933927/1‑71 (MQ=255)
             tCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCtt                                                                    <  1:3821948/58‑1 (MQ=255)
             tCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCtt                                                                    <  1:1788695/58‑1 (MQ=255)
             tCAGCAAGAGTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCtt                                                                    <  1:5328213/58‑1 (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)
                  cAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCt                                                                     >  1:5316754/1‑52 (MQ=255)
                  aagagTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAg                                                  >  1:2641007/2‑71 (MQ=255)
                     agTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTaa                                               <  1:4061192/71‑1 (MQ=16)
                      gTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAAt                                              <  1:5394219/71‑1 (MQ=255)
                      gTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAAt                                              >  1:2661813/1‑71 (MQ=255)
                      gTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAAt                                              <  1:2078635/71‑1 (MQ=255)
                      gTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAAt                                              >  1:2186337/1‑71 (MQ=255)
                      gTTTTAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAAt                                              <  1:1547175/71‑1 (MQ=16)
                        tttAAAACCATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGccg                                                            <  1:5545042/55‑2 (MQ=16)
                         ttGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGa                                            <  1:1533115/70‑1 (MQ=255)
                         ttGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGa                                            <  1:2205268/70‑1 (MQ=255)
                           gAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATc                                                                      >  1:661413/1‑42 (MQ=255)
                            aaaccATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAAcc                                        <  1:663283/68‑1 (MQ=12)
                             aGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGcc                                        >  1:431655/1‑70 (MQ=255)
                               ccATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCttt                                                                   >  1:1058512/1‑41 (MQ=19)
                               ccATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCaaa                                     <  1:2245700/71‑1 (MQ=255)
                               ccATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCaaa                                     <  1:2066571/71‑1 (MQ=255)
                                cATTGCTCTGGATGGCGGTGAAATGGACGAAAACGTCTTTGCTGCCATCATCAGGa                                                   >  1:3652710/1‑56 (MQ=2)
                                cATTGCTCTGGATGGCGGTGAAATGGACGAAAACGTCTTTGCTGCCATCATCAGGAGTGATAAAGCCaaa                                     <  1:5092732/70‑1 (MQ=9)
                                cATTGCTCTGGATGGCGGTGAAATGGACGAAAACGTCTTTGCTGCCATCATCAGGAGTGATAAAGCCaaa                                     <  1:951577/70‑1 (MQ=9)
                                cATTAGTCTGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGa                                                   >  1:2581149/1‑56 (MQ=12)
                                 aTTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAAc                                   >  1:597120/1‑71 (MQ=255)
                                 aTTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAAc                                   >  1:3805245/1‑71 (MQ=255)
                                  ttACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCaa                                      <  1:3383326/67‑1 (MQ=255)
                                    aCCCTGGATAGCGGAGAAGTGTACGAACACATCtt                                                                    <  1:2290882/35‑1 (MQ=255)
                                    aCCCTGGATAGCGGAGAAGTGTACGAACACATCtt                                                                    <  1:1814370/35‑1 (MQ=255)
                                    aCCCTGGATAGCGGAGAAGTGTACGAACACATCtt                                                                    <  1:2382160/35‑1 (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)
                                     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)
                                        tGGATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCtt                                >  1:4297971/1‑67 (MQ=12)
                                         ggATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGAc                           >  1:1426323/1‑71 (MQ=255)
                                          gATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGa                            >  1:4172713/1‑69 (MQ=255)
                                          gATTGCAGAGAAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACt                          <  1:523556/71‑1 (MQ=12)
                                           aTAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCgg                                                    >  1:5179639/1‑44 (MQ=255)
                                              gCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGc                                         >  1:3857525/1‑52 (MQ=255)
                                               cagagaAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCAtt                      <  1:3159219/68‑1 (MQ=12)
                                               cGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTa                                                <  1:1732270/44‑1 (MQ=255)
                                               cGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTa                              <  1:5060615/62‑1 (MQ=255)
                                                ggAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGa                    <  1:5539536/71‑1 (MQ=255)
                                                ggAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGa                    <  1:303111/71‑1 (MQ=255)
                                                 gagaAGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGAc                           >  1:2598203/1‑63 (MQ=12)
                                                 gagaAGTGTACGAACACGTCTTTGCTGCCGTCTTCAGGAGTAATGAAACCGAATCCtttg                              <  1:1869002/60‑2 (MQ=12)
                                                 gagaAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAAt                                              >  1:3001490/1‑44 (MQ=255)
                                                 gagaAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAAt                                              >  1:120909/1‑44 (MQ=255)
                                                   gaAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAAc                  >  1:5097356/1‑70 (MQ=255)
                                                    aaGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCtt                                <  1:3736081/55‑1 (MQ=255)
                                                     aGTGTACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCAc               <  1:4487975/71‑1 (MQ=255)
                                                       tgtACGAACACATCTTTGCTGCCATCAGCCGGAGTa                                                <  1:5235387/36‑1 (MQ=255)
                                                        gtACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATg                                             >  1:1348652/1‑38 (MQ=18)
                                                        gtACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATg                                             >  1:3088576/1‑38 (MQ=18)
                                                        gtACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATg                                             >  1:1775226/1‑38 (MQ=18)
                                                        gtACGAACACATCTTTGCTGCCATCAGCCGGAGTAATg                                             <  1:1027758/38‑1 (MQ=255)
                                                         tACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGaa                                           <  1:5693580/39‑1 (MQ=17)
                                                         tACGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTaa           >  1:2964801/1‑71 (MQ=255)
                                                         tACGAACACATCTTTGCTGCCATCAGCCGGAGTAAt                                              >  1:4421765/1‑36 (MQ=255)
                                                         tACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTa                              >  1:4843779/1‑52 (MQ=255)
                                                         tACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTa                              >  1:3796598/1‑52 (MQ=255)
                                                         tACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGt                       >  1:2812273/1‑59 (MQ=255)
                                                         gaCGAAAACGTCTTTGCTGCCATCATCAGGAGTGATAAAGCCAAAAc                                   >  1:893405/2‑47 (MQ=12)
                                                          aCGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAAc                                   >  1:1208086/1‑46 (MQ=255)
                                                          aCGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAAc                                   >  1:3856104/1‑46 (MQ=255)
                                                          aCGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAAc                                   >  1:2164978/1‑46 (MQ=255)
                                                           cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATg                                             >  1:4512650/1‑35 (MQ=12)
                                                           cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGa                                            >  1:2873384/1‑36 (MQ=12)
                                                           cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGa                                            >  1:2849694/1‑36 (MQ=12)
                                                           cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGa                                            >  1:2823655/1‑36 (MQ=12)
                                                           cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTaaa                   >  1:3629146/1‑61 (MQ=9)
                                                           cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAAc                  >  1:2731558/1‑62 (MQ=9)
                                                           cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAAc                  >  1:2622983/1‑62 (MQ=9)
                                                           cGAACACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAAcg         >  1:192844/1‑70 (MQ=12)
                                                           cGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAAcc         <  1:4801092/71‑1 (MQ=255)
                                                            gAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCt        >  1:3011678/1‑71 (MQ=255)
                                                            gAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCt        >  1:4944556/1‑71 (MQ=255)
                                                             aaCACGTCTTTGCTGCCGTCTTCCGGAGTAATGAAACCGAATCCTTTGGACTCATTAAACCACTTAAcgtt       <  1:4154567/71‑4 (MQ=12)
                                                             aaCACATCTTTACTACCATCAACAGGAGAAATAAAGccga                                      >  1:1525315/1‑38 (MQ=9)
                                                             aaCACATCTTTACTACCATCAACAGGAGAAATAAAGccga                                      >  1:1592686/1‑38 (MQ=9)
                                                              acacATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGa      <  1:3624785/71‑1 (MQ=255)
                                                               cacaTCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCAc               <  1:476376/61‑1 (MQ=255)
                                                               cacaTCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCAc               <  1:3855277/61‑1 (MQ=255)
                                                                 caTCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCt   <  1:4781149/71‑1 (MQ=255)
                                                                 caTCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCt   <  1:1152790/71‑1 (MQ=255)
                                                                  |                                                                      
AACGTTCTGACCTTCAGCCAGAGTTTTGAAGCCATTACCCTGGATAGCGGAGAAGTGTACGAACACATCTTTGCTGCCATCAGCCGGAGTAATGAAGCCAAAACCTTTAGACTCGTTGAACCACTTAACCTGACCTT  >  minE/1211202‑1211338

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