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 2,572,707 T→C 37.9% intergenic (+1475/‑304) yibH → / → ysaB hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,572,7070TC37.9% 129.0 / 168.2 167intergenic (+1475/‑304)yibH/ysaBhypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (58/45);  new base C (39/24);  total (98/69)
Fisher's exact test for biased strand distribution p-value = 5.19e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

Only 100 of 183 total aligned reads displayed.

AACAGGTGGCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTA  >  minE/2572637‑2572777
                                                                      |                                                                      
aaCAGGTGGCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCacct                                                                        <  1:3974861/71‑1 (MQ=255)
aaCAGGTGGCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCacct                                                                        <  1:3079356/71‑1 (MQ=255)
    ggTGGCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCacctacct                                                                    >  1:3298856/1‑71 (MQ=255)
     gTGGCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCtt                                                                   >  1:2416482/1‑71 (MQ=255)
      tGGCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTc                                                                  <  1:1357980/71‑1 (MQ=255)
        gCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTc                                                                  >  1:4964614/1‑69 (MQ=255)
        gCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTc                                                                  >  1:1142815/1‑69 (MQ=255)
        gCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCa                                                                <  1:1422235/71‑1 (MQ=255)
            aTCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGcc                                                             <  1:3723592/70‑1 (MQ=255)
             tCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCa                                                           <  1:2969901/71‑1 (MQ=255)
                cAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTc                                                                  <  1:2106058/61‑1 (MQ=255)
                cAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTc                                                                  <  1:1032664/61‑1 (MQ=255)
                cAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATc                                                        >  1:73009/1‑71 (MQ=255)
                cAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATc                                                        >  1:5319246/1‑71 (MQ=255)
                cAAGGGGATCGATTCCAGAAATAGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAAt                                                         >  1:55964/1‑70 (MQ=255)
                 aaGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTc                                                                  <  1:917203/60‑1 (MQ=255)
                 aaGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCg                                                       >  1:1465919/1‑71 (MQ=255)
                 aaGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCg                                                       >  1:4834487/1‑71 (MQ=255)
                   ggggATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCg                                                       >  1:2091529/1‑69 (MQ=255)
                      gATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGcc                                                  >  1:1086747/1‑71 (MQ=255)
                       aTCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCt                                                 <  1:423499/71‑1 (MQ=255)
                           aTTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCaccta                                                                       <  1:3775956/45‑1 (MQ=255)
                              ccAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCa                                                                >  1:5590047/1‑49 (MQ=255)
                              ccAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgtgt                                           <  1:1882051/70‑1 (MQ=255)
                               cAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTta                                         <  1:2017498/71‑1 (MQ=255)
                                 gagaTCGGATTCAACGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGatat                                        <  1:1170903/67‑1 (MQ=255)
                                 gAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgtg                                            <  1:3999812/66‑1 (MQ=255)
                                  aaaTCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTg                                                >  1:2153154/1‑61 (MQ=255)
                                    aTCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgt                                             <  1:4897259/62‑1 (MQ=255)
                                    aTCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCg                                    <  1:1734648/71‑1 (MQ=255)
                                     tCGGATTCAACGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAATCGGatc                                                   <  1:2424029/55‑3 (MQ=255)
                                     ccGGATTCAACGGATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGc                                   >  1:1660448/2‑71 (MQ=255)
                                     ccGGATTCAACGGATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGc                                   >  1:1231848/2‑71 (MQ=255)
                                      cGGATTCAACGGATACTGATAAAAATTCCATCCCCCTTTCAg                                                               <  1:171590/42‑1 (MQ=255)
                                        ggTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGcccc                                <  1:2673676/71‑1 (MQ=255)
                                         attCAGCGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCgg                                                      <  1:5664344/47‑1 (MQ=255)
                                         attCAGCGGATACGCATACAGACTCCATCCCCCCTCCAGCCCTATCGGGTCCTGAGTGATATACCGCCCct                               <  1:2205840/70‑1 (MQ=255)
                                         attCAACGGATACTGATACATATTCCATCCACCTCTCAACCCAATCGGGTCCGGGGTGATATACCGccc                                 >  1:3231085/2‑69 (MQ=255)
                                          ttCAGCGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCTCCCctg                              >  1:4336450/1‑71 (MQ=255)
                                          ttCAACGTATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTta                                         >  1:2577749/1‑60 (MQ=255)
                                          ttCAACGGATACTGATACATATTCCATCCACCTCTCAACCCAATCGGGTCCGGGGTGATATAcc                                     >  1:1843433/1‑64 (MQ=255)
                                          ttCAACGGATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAgt                                             <  1:5182467/56‑1 (MQ=255)
                                          ttCAACGGATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGccccag                              >  1:1136220/1‑69 (MQ=255)
                                          ttCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCaa                                                          <  1:2808058/43‑1 (MQ=255)
                                          ttCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCaa                                                          <  1:1049083/43‑1 (MQ=255)
                                           tCAACGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCGCCCctg                              >  1:27694/1‑70 (MQ=255)
                                           tCAACGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCGCCCct                               >  1:4019555/1‑69 (MQ=255)
                                            cAACGGATACTGATACATATTCCATCCACCTCTCAACCCAATCGGGTCCGGGGTGATATACCGCCCctgc                             <  1:5249456/70‑1 (MQ=255)
                                            cAACGGATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGatc                                                   >  1:813282/1‑46 (MQ=255)
                                            cAACGGATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGccccag                              >  1:3173499/1‑67 (MQ=255)
                                            cAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAAt                                                         >  1:3854995/1‑42 (MQ=255)
                                            cAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAAt                                                         >  1:4909787/1‑42 (MQ=255)
                                            aaaCGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgtgt                                           >  1:711242/2‑56 (MQ=255)
                                             aaCGGATACTGATACATATTCCATCCACCTCTCAACCCAATCGGGTCCGGGGTGATATACCGCCCctgcaa                           >  1:5397850/1‑69 (MQ=255)
                                             aaCGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTg                                                >  1:3002682/1‑50 (MQ=255)
                                             aaCGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGATATATCGCCCctgcag                           >  1:1521892/1‑69 (MQ=255)
                                             aaCGGATACTGATAAAAATTCCATCCCCCCTTCAGTCCAAt                                                         >  1:4998908/1‑41 (MQ=255)
                                             aaCGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCg                                                       >  1:3729997/1‑43 (MQ=255)
                                             aaCGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCg                                                       >  1:671114/1‑43 (MQ=255)
                                             aaCGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCctgctg                           >  1:3513883/1‑71 (MQ=255)
                                              aCGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATAc                                      >  1:610003/1‑59 (MQ=255)
                                               cGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGATATATCGCCCCTGCAGCg                         <  1:4503678/71‑1 (MQ=255)
                                               cGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCGCCCCTGCAGCg                         <  1:3995756/71‑1 (MQ=255)
                                               cGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgtgt                                           <  1:1588314/53‑1 (MQ=255)
                                                ggATACTGATAAAAATTCCATCCCCCTT‑CAGCCCAATCGGATCCTGAGTGATATACCTCCCCTGCAGCggg                       >  1:2878568/1‑70 (MQ=255)
                                                ggATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgtgt                                           <  1:241324/52‑1 (MQ=255)
                                                ggATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATAc                                      >  1:3432235/1‑57 (MQ=255)
                                                ggATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATAc                                      >  1:1156018/1‑57 (MQ=255)
                                                 gATACTGATACATATTCCATCCACCTCTCAACCCAATCGGGTCCGGGGTGATATACCGccc                                 <  1:175360/61‑1 (MQ=255)
                                                 gATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCCAGCAGCgg                        >  1:5212955/1‑70 (MQ=255)
                                                 gATACTGATAAAAATTCCACCTACCTTCCAGCCCAATc                                                        >  1:4480579/1‑38 (MQ=255)
                                                 gATACTGATAAAAATTCCACCTACCTTCCAGCCCAATc                                                        >  1:4633215/1‑38 (MQ=255)
                                                  aTACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGt                       >  1:2729850/1‑70 (MQ=255)
                                                   tACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCcagcag                           <  1:329436/65‑3 (MQ=255)
                                                   tACTGATAAAAATTCCACCTACCTTCCAGCCCAAt                                                         <  1:4293725/35‑1 (MQ=255)
                                                   tACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGa                                                     <  1:1103184/39‑1 (MQ=255)
                                                    aCTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGa                                               >  1:240013/1‑44 (MQ=255)
                                                     cTGATAAAAATTCCATCCCCCCTTCAGCCCAATCg                                                       <  1:2042505/35‑1 (MQ=16)
                                                     cTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGa                                               >  1:1606250/1‑43 (MQ=255)
                                                      tGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCt                                                 <  1:2534791/40‑1 (MQ=255)
                                                      tGATAAAAATTCCACCTACCTCCCAGCCCAATCGGAGCCt                                                 <  1:432037/40‑1 (MQ=255)
                                                       gATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCCAGCAGCgg                        >  1:4979797/1‑64 (MQ=255)
                                                       gATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCCAGCAGCgg                        >  1:1934447/1‑64 (MQ=255)
                                                        aTAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGAtatat                                      >  1:2503737/1‑48 (MQ=255)
                                                        aTAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGAta                                         >  1:2750914/1‑46 (MQ=255)
                                                        aTAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATAc                                      >  1:4383217/1‑49 (MQ=255)
                                                         tAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCtgctgc                          <  1:2339800/60‑1 (MQ=255)
                                                          aaaaaTTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGatat                                        >  1:4746828/1‑45 (MQ=255)
                                                           aaaaTTCCATCACCCCTTCAGCCCAATCGGATCCTGAGTGAtata                                       >  1:5468939/1‑45 (MQ=255)
                                                           aaaaTTCCACCTACCTTCCAGCCCAATCGGAGCATGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTAcc             >  1:4425874/1‑71 (MQ=255)
                                                             aaTTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATAcctc                                   <  1:4132582/47‑3 (MQ=255)
                                                               ttCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGat          >  1:3171790/1‑70 (MQ=255)
                                                                 ccACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGataa        <  1:5065269/70‑1 (MQ=255)
                                                                 ccACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGataa        >  1:4211728/1‑70 (MQ=255)
                                                                  cACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGataat       <  1:967637/70‑1 (MQ=255)
                                                                   acctacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCtgctgc                          <  1:514564/50‑1 (MQ=255)
                                                                     ctacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCgg                        >  1:2143794/1‑50 (MQ=255)
                                                                     ctacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGt    >  1:2631853/1‑70 (MQ=255)
                                                                      tacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCctgc                             <  1:3548074/44‑1 (MQ=255)
                                                                      tacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCctgc                             <  1:5145287/44‑1 (MQ=255)
                                                                      |                                                                      
AACAGGTGGCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTA  >  minE/2572637‑2572777

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A