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 2,572,713 C→T 34.9% intergenic (+1481/‑298) yibH → / → ysaB hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,572,7130CT34.9% 190.8 / 157.5 178intergenic (+1481/‑298)yibH/ysaBhypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (62/53);  new base T (39/23);  total (102/76)
Fisher's exact test for biased strand distribution p-value = 2.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 189 total aligned reads displayed.

TGGCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTA  >  minE/2572643‑2572782
                                                                      |                                                                     
  gCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTc                                                                       >  1:1142815/1‑69 (MQ=255)
  gCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTc                                                                       >  1:4964614/1‑69 (MQ=255)
  gCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCa                                                                     <  1:1422235/71‑1 (MQ=255)
       tCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGccc                                                                 >  1:137772/1‑70 (MQ=255)
       tCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCa                                                                <  1:2969901/71‑1 (MQ=255)
        cccAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCaa                                                               >  1:4792942/1‑71 (MQ=255)
         ccAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACATACCTTCCAGCCCaa                                                               >  1:2296532/1‑70 (MQ=255)
          cAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTc                                                                       <  1:1032664/61‑1 (MQ=255)
          cAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTc                                                                       <  1:3296740/61‑1 (MQ=255)
          cAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTc                                                                       <  1:2106058/61‑1 (MQ=255)
          cAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATc                                                             <  1:2416703/71‑1 (MQ=255)
          cAAGGGGATCGATTCCAGAAATAGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAAt                                                              >  1:55964/1‑70 (MQ=255)
           aaGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTc                                                                       <  1:917203/60‑1 (MQ=255)
           aaGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCg                                                            >  1:1465919/1‑71 (MQ=255)
             ggggATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCgaa                                                          <  1:724763/71‑3 (MQ=255)
             ggggATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCg                                                            >  1:2091529/1‑69 (MQ=255)
                gATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCa                                                                <  1:2036989/62‑1 (MQ=255)
                gATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGcc                                                       >  1:1086747/1‑71 (MQ=255)
                        ccAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCa                                                                     >  1:4658891/1‑49 (MQ=255)
                        ccAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCa                                                                     >  1:1602066/1‑49 (MQ=255)
                        ccAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgtgt                                                <  1:1882051/70‑1 (MQ=255)
                         cAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTta                                              <  1:4871295/71‑1 (MQ=255)
                           gagaTCGGATTCAACGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGatat                                             <  1:3519381/67‑1 (MQ=255)
                           gAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgtg                                                 <  1:3999812/66‑1 (MQ=255)
                            aaaTCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTg                                                     >  1:2153154/1‑61 (MQ=255)
                              aTCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCg                                         <  1:1734648/71‑1 (MQ=255)
                               ccGGATTCAGCGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAgtga                                                <  1:4494340/62‑2 (MQ=255)
                                cGGATTCAACGGATACTGATAAAAATTCCATCCCCCTTTCAg                                                                    <  1:171590/42‑1 (MQ=255)
                                  ggTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGcccc                                     <  1:2673676/71‑1 (MQ=255)
                                   attCAGCGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCgg                                                           <  1:5664344/47‑1 (MQ=255)
                                   attCAACGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGat                                                         >  1:320179/2‑49 (MQ=255)
                                    ttCAGCGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCTCCCctg                                   >  1:4336450/1‑71 (MQ=255)
                                    ttCAACGGATACTGATACATATTCCATCCACCTCTCAACCCAATCGGGTCCGGGGTGATATAcc                                          >  1:1843433/1‑64 (MQ=255)
                                    ttCAACGGATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAgt                                                  <  1:5182467/56‑1 (MQ=255)
                                    ttCAACGGATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGccccag                                   >  1:1136220/1‑69 (MQ=255)
                                    ttCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCaa                                                               <  1:1049083/43‑1 (MQ=255)
                                    ttCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCaa                                                               <  1:2808058/43‑1 (MQ=255)
                                     tCAACGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCGCCCct                                    >  1:4019555/1‑69 (MQ=255)
                                      cAACGGATACTGATACATATTCCATCCACCTCTCAACCCAATCGGGTCCGGGGTGATATACCGCCCctgc                                  <  1:5249456/70‑1 (MQ=255)
                                      cAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAAt                                                              >  1:4909787/1‑42 (MQ=255)
                                      cAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAAt                                                              >  1:3854995/1‑42 (MQ=255)
                                      cAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTta                                              >  1:1947126/1‑58 (MQ=255)
                                       aaCGGATACTGATAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTg                                                     >  1:3002682/1‑50 (MQ=255)
                                       aaCGGATACTGATAAAAATTCCATCCCCCCTTCAGTCCAAt                                                              >  1:4998908/1‑41 (MQ=255)
                                       aaCGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCGCCCctgcag                                <  1:2167400/71‑3 (MQ=255)
                                       aaCGGATACTGATAAAAATTCCACCTACCTTCCAg                                                                    >  1:1215970/1‑35 (MQ=255)
                                       aaCGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCg                                                            >  1:2630580/1‑43 (MQ=255)
                                       aaCGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCg                                                            >  1:3729997/1‑43 (MQ=255)
                                       aaCGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCg                                                            >  1:671114/1‑43 (MQ=255)
                                        aCGGATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCcagcag                                >  1:554642/1‑68 (MQ=255)
                                        aCGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATAc                                           >  1:610003/1‑59 (MQ=255)
                                         cGGATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAGTGATATACCGCCCCTGCAGCg                              <  1:3995756/71‑1 (MQ=255)
                                          ggATACTGATAAAAATTCCATCCCCCTT‑CAGCCCAATCGGATCCTGAGTGATATACCTCCCCTGCAGCggg                            >  1:2878568/1‑70 (MQ=255)
                                          ggATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAgtgt                                                <  1:241324/52‑1 (MQ=255)
                                          ggATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATAc                                           >  1:3432235/1‑57 (MQ=255)
                                           gATACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCCAGCAGCgg                             >  1:5212955/1‑70 (MQ=255)
                                           gATACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAgtgat                                               >  1:1654182/1‑50 (MQ=255)
                                           gATACTGATAAAAATTCCACCTACCTTCCAGCCCAATc                                                             >  1:428937/1‑38 (MQ=255)
                                            aTACTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGa                                                          >  1:3232991/1‑40 (MQ=255)
                                            aTACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGt                            >  1:2729850/1‑70 (MQ=255)
                                             tACTGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCTGAg                                                   >  1:2754358/1‑46 (MQ=255)
                                             tACTGATAAAAATTCCATCCCCACTTCAGCCCAATCGGATCCTGAg                                                   >  1:4576623/1‑46 (MQ=255)
                                             tACTGATAAAAATTCCACCTACCTTCCAGCCCAAt                                                              <  1:5058875/35‑1 (MQ=255)
                                             tACTGATAAAAATTCCACCTACCTTCCAGCCCAAt                                                              <  1:4293725/35‑1 (MQ=255)
                                             tACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGa                                                          <  1:1103184/39‑1 (MQ=255)
                                              aCTGATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGa                                                    >  1:240013/1‑44 (MQ=255)
                                               cTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTta                                              >  1:76943/1‑49 (MQ=255)
                                                tGATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCt                                                      <  1:3630668/40‑1 (MQ=255)
                                                tGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCt                                                      <  1:2534791/40‑1 (MQ=255)
                                                tGATAAAAATTCCACCTACCTCCCAGCCCAATCGGAGCCt                                                      <  1:432037/40‑1 (MQ=255)
                                                 gATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCCAGCAGCgg                             >  1:1934447/1‑64 (MQ=255)
                                                 gATAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCCAGCAGCgg                             >  1:4979797/1‑64 (MQ=255)
                                                 gATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCt                                                      <  1:5332975/39‑1 (MQ=16)
                                                 gATAAAAATTCCATCCCCCCTTCAGCCCAATCGGATCCt                                                      <  1:1263718/39‑1 (MQ=16)
                                                  aTAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGAtatat                                           >  1:5594015/1‑48 (MQ=255)
                                                  aTAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGAtatat                                           >  1:2503737/1‑48 (MQ=255)
                                                  aTAAAAATTCCATCCCCCTTTCAGCCCAATCGGATCCTGAGTGAtata                                            >  1:3729263/1‑48 (MQ=255)
                                                  aTAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATAc                                           >  1:4383217/1‑49 (MQ=255)
                                                   tAAAAATTCCATCCCCCCTTCAGTCCAATCGGATCCTGAGTGATATACCGCCCCagcagc                               <  1:1807372/60‑1 (MQ=255)
                                                    aaaaaTTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTAc                   >  1:1167399/1‑71 (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             >  1:4211728/1‑70 (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                                  <  1:5145287/44‑1 (MQ=255)
                                                                tacctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCctgc                                  <  1:158107/44‑1 (MQ=255)
                                                                tacctTCCAGCCCAATCGGAGCCTGAGAGTTATACCGCCCCAGCTGCGGTTAAAGTTACCGAAAATAGAta       >  1:2432791/1‑71 (MQ=255)
                                                                  cctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTTCGGTTAATGTTACCGATAATAGTta       <  1:3063471/69‑1 (MQ=255)
                                                                  cctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGa                <  1:3796863/60‑1 (MQ=255)
                                                                  cctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTta       <  1:5310379/69‑1 (MQ=255)
                                                                  cctTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTta       <  1:4763221/69‑1 (MQ=255)
                                                                    ttCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTa                    >  1:815782/1‑54 (MQ=255)
                                                                     tCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAg    >  1:1695969/1‑69 (MQ=255)
                                                                      ccAGCCCAATCGGAGCCTGAGTGTTATACCGCCCctgc                                  >  1:274979/1‑38 (MQ=255)
                                                                      ccAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTTCTGCGGTTAATGTTACCGATAATAGTTATAGt   <  1:5113808/69‑1 (MQ=255)
                                                                      |                                                                     
TGGCTAATCCCAAGGGGATCGATTCCAGAAATCGGGTTCAACGGATACTGATAAAAATTCCACCTACCTTCCAGCCCAATCGGAGCCTGAGTGTTATACCGCCCCTGCTGCGGTTAATGTTACCGATAATAGTTATAGTA  >  minE/2572643‑2572782

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