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 2,572,705 C→T 38.3% intergenic (+1473/‑306) yibH → / → ysaB hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,572,7050CT38.3% 139.8 / 165.1 167intergenic (+1473/‑306)yibH/ysaBhypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (58/45);  new base T (40/24);  total (98/69)
Fisher's exact test for biased strand distribution p-value = 5.18e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.80e-01

Only 100 of 177 total aligned reads displayed.

TAAACAGGTGGCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGT  >  minE/2572635‑2572775
                                                                      |                                                                      
  aaCAGGTGGCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCacct                                                                      <  1:3974861/71‑1 (MQ=255)
  aaCAGGTGGCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCacc                                                                       >  1:171268/1‑70 (MQ=255)
       gTGGCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCtt                                                                 >  1:2416482/1‑71 (MQ=255)
          gCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTc                                                                >  1:4964614/1‑69 (MQ=255)
            tAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGc                                                            >  1:2094602/1‑71 (MQ=255)
             aaTCCCAAGGGGATCGATTGCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGcc                                                           >  1:2985563/1‑71 (MQ=255)
              aTCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGcc                                                           <  1:3723592/70‑1 (MQ=255)
               tCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGccc                                                          >  1:137772/1‑70 (MQ=255)
               tCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCa                                                         <  1:2969901/71‑1 (MQ=255)
                cccAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCaa                                                        >  1:4792942/1‑71 (MQ=255)
                 ccAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAAt                                                       >  1:1848093/1‑71 (MQ=255)
                  cAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTc                                                                <  1:3296740/61‑1 (MQ=255)
                  cAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTc                                                                <  1:1032664/61‑1 (MQ=255)
                  cAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATc                                                      >  1:5319246/1‑71 (MQ=255)
                  cAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATc                                                      >  1:73009/1‑71 (MQ=255)
                  cAAGGGGATCGATTCCAGAAATAGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAAt                                                       >  1:55964/1‑70 (MQ=255)
                   aaGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTc                                                                <  1:917203/60‑1 (MQ=255)
                        gATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGcc                                                >  1:1086747/1‑71 (MQ=255)
                             aTTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCaccta                                                                     <  1:3775956/45‑1 (MQ=255)
                                ccAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCa                                                              >  1:1602066/1‑49 (MQ=255)
                                ccAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCa                                                              >  1:5590047/1‑49 (MQ=255)
                                 cAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTta                                       <  1:4871295/71‑1 (MQ=255)
                                 cAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTta                                       <  1:2017498/71‑1 (MQ=255)
                                   gagaTCGGATTCAACGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGatat                                      <  1:1170903/67‑1 (MQ=255)
                                   gagaTCGGATTCAACGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGatat                                      <  1:3519381/67‑1 (MQ=255)
                                   gAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCa                                                         <  1:2400665/51‑1 (MQ=255)
                                   gAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgtg                                          <  1:3999812/66‑1 (MQ=255)
                                   gAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTtata                                     <  1:1731037/71‑1 (MQ=255)
                                    aaaTCGGGTTCAACGGATACTGATAAAAATTCCacctacct                                                                  >  1:300929/1‑41 (MQ=255)
                                    aaaTCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGccc                                               >  1:5141368/1‑59 (MQ=255)
                                    aaaTCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTg                                              >  1:2153154/1‑61 (MQ=255)
                                      aTCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCg                                  <  1:1734648/71‑1 (MQ=255)
                                       tCGGATTCAACGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAATCGGatc                                                 <  1:2424029/55‑3 (MQ=255)
                                       ccGGATTCAACGGATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGc                                 >  1:1231848/2‑71 (MQ=255)
                                       ccGGATTCAACGGATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGc                                 >  1:1660448/2‑71 (MQ=255)
                                          ggTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGcccc                              <  1:2673676/71‑1 (MQ=255)
                                           attCAGCGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCgg                                                    <  1:5664344/47‑1 (MQ=255)
                                           attCAGCGGATACGCATACAGACTCCATCCCCCCTCCAGCCCTATCGGGTCCTGAGTGATATACCGCCCct                             <  1:2205840/70‑1 (MQ=255)
                                           attCAACGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGat                                                  >  1:320179/2‑49 (MQ=255)
                                            ttCAGCGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCTCCCctg                            >  1:4336450/1‑71 (MQ=255)
                                            ttCAACGGATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAgt                                           <  1:5182467/56‑1 (MQ=255)
                                            ttCAACGGATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGccccag                            >  1:1136220/1‑69 (MQ=255)
                                            ttCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCaa                                                        <  1:1049083/43‑1 (MQ=255)
                                            ttCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCaa                                                        <  1:2808058/43‑1 (MQ=255)
                                            ttCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTta                                       <  1:1139060/60‑1 (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                                                       >  1:4909787/1‑42 (MQ=255)
                                              aaaCGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgtgt                                         >  1:711242/2‑56 (MQ=255)
                                               aaCGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGATATATCGCCCctgcag                         >  1:1521892/1‑69 (MQ=255)
                                               aaCGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCg                                                     >  1:2630580/1‑43 (MQ=255)
                                               aaCGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCg                                                     >  1:3729997/1‑43 (MQ=255)
                                               aaCGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCctgctg                         >  1:3513883/1‑71 (MQ=255)
                                                aCGGATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCcagcag                         >  1:3815513/1‑68 (MQ=255)
                                                 cGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGATATATCGCCCCTGCAGCg                       <  1:4503678/71‑1 (MQ=255)
                                                 cGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCGCCCCTGCAGCg                       <  1:3995756/71‑1 (MQ=255)
                                                 cGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCg                       >  1:5666993/1‑71 (MQ=255)
                                                  ggATACTGATAAAAATTCCATCCCCCTT‑CAGCCCAATCGGATCCTGAGTGATATACCTCCCCTGCAGCggg                     >  1:2878568/1‑70 (MQ=255)
                                                  ggATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCGCCCCTGCAGCgg                      >  1:5171066/1‑71 (MQ=255)
                                                  ggATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgtgt                                         <  1:241324/52‑1 (MQ=255)
                                                  ggATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgtgt                                         <  1:1911403/52‑1 (MQ=255)
                                                  ggATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATAc                                    >  1:666565/1‑57 (MQ=255)
                                                  ggATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATAc                                    >  1:1156018/1‑57 (MQ=255)
                                                   gATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCCAGCAGCgg                      >  1:5212955/1‑70 (MQ=255)
                                                   gATACTGATAAAAATTCCACCTACCTTCCAGCCCAATc                                                      >  1:428937/1‑38 (MQ=255)
                                                   gATACTGATAAAAATTCCACCTACCTTCCAGCCCAATc                                                      >  1:4998431/1‑38 (MQ=255)
                                                   gATACTGATAAAAATTCCACCTACCTTCCAGCCCAATc                                                      >  1:4633215/1‑38 (MQ=255)
                                                   gATACTGATAAAAATTCCACCTACCTTCCAGCCCAATc                                                      >  1:4480579/1‑38 (MQ=255)
                                                    aTACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGa                                                   >  1:3232991/1‑40 (MQ=255)
                                                    aTACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGt                     >  1:2729850/1‑70 (MQ=255)
                                                     tACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAg                                            >  1:2754358/1‑46 (MQ=255)
                                                     tACTGATAAAAATTCCACCTACCTTCCAGCCCAAt                                                       <  1:5058875/35‑1 (MQ=255)
                                                     tACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGa                                                   <  1:1103184/39‑1 (MQ=255)
                                                       cTGATAAAAATTCCATCCCCCCTTCAGCCCAATCg                                                     <  1:2042505/35‑1 (MQ=16)
                                                       cTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGa                                             >  1:1606250/1‑43 (MQ=255)
                                                       cTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTta                                       >  1:76943/1‑49 (MQ=255)
                                                       cTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGccc                               >  1:4294827/1‑57 (MQ=255)
                                                        tGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCt                                               <  1:2519766/40‑1 (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)
                                                         gATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCt                                               <  1:5332975/39‑1 (MQ=16)
                                                         gATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCt                                               <  1:1263718/39‑1 (MQ=16)
                                                          aTAAAAATTCCATCCCGCTTTCAGCCCAATCGGATCCTGAGTGAtatat                                    >  1:3379299/1‑48 (MQ=255)
                                                          aTAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGAta                                       >  1:2750914/1‑46 (MQ=255)
                                                          aTAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATAc                                    >  1:4383217/1‑49 (MQ=255)
                                                          aTAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGtt              <  1:1445588/71‑1 (MQ=255)
                                                           tAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCCagcagc                        <  1:1807372/60‑1 (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)
                                                                   ccACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGataa      >  1:4211728/1‑70 (MQ=255)
                                                                    cACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGataat     <  1:967637/70‑1 (MQ=255)
                                                                     acctacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCtgctgc                        <  1:309814/50‑1 (MQ=255)
                                                                      cctacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGt  <  1:2116581/71‑1 (MQ=255)
                                                                      |                                                                      
TAAACAGGTGGCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGT  >  minE/2572635‑2572775

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