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 1,015,022 C→T 28.0% E349E (GAG→GAA)  fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,015,0220CT28.0% 125.8 / 51.8 82E349E (GAG→GAA) fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base C (32/27);  new base T (10/13);  total (42/40)
Fisher's exact test for biased strand distribution p-value = 4.64e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

TGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCT  >  minE/1014953‑1015089
                                                                     |                                                                   
tgCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGct                                                                    >  1:2447807/1‑71 (MQ=255)
tgCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGc                                                                     <  1:4014522/70‑1 (MQ=255)
  cGAGGATCTCTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGttct                                                                  <  1:5311474/71‑1 (MQ=255)
   gAGGATCTCTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCtt                                                                 <  1:2465297/71‑1 (MQ=255)
   gAGGATCTCTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCtt                                                                 >  1:4719536/1‑71 (MQ=255)
     ggATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTcc                                                               <  1:3887002/71‑1 (MQ=255)
      gATCTCTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCttgtg                                                              <  1:3068296/71‑4 (MQ=255)
      gATCTCTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCttgtg                                                              <  1:4259137/71‑4 (MQ=255)
        tctcTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGttct                                                                  >  1:2940352/1‑65 (MQ=255)
        tctcTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGttct                                                                  >  1:2350452/1‑65 (MQ=255)
            tttCATCGGACGGTTAAGGTCAACGCGCACCTCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCgg                                                             <  1:2311441/66‑1 (MQ=255)
            tttCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCgg                                                             <  1:3736445/66‑1 (MQ=255)
            tttCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCgg                                                             <  1:1159007/66‑1 (MQ=255)
            tttCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGata                                                         >  1:4984110/1‑70 (MQ=255)
             ttCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGatata                                                       >  1:2253598/1‑71 (MQ=255)
              tCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGatat                                                        <  1:580646/69‑1 (MQ=255)
               cATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGatatat                                                      <  1:5345646/70‑1 (MQ=255)
                aTCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGttc                                                                   >  1:191617/1‑56 (MQ=255)
                     gcGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTg                                               <  1:1535543/70‑1 (MQ=255)
                      cGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGata                                                         >  1:1666905/1‑60 (MQ=255)
                      cGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGata                                                         >  1:604235/1‑60 (MQ=255)
                      cGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGata                                                         >  1:278606/1‑60 (MQ=255)
                       ggTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTg                                               <  1:3973303/69‑1 (MQ=255)
                        gTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGatata                                                       <  1:1932995/60‑1 (MQ=255)
                         ttAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTgggt                                            >  1:3086546/1‑68 (MQ=255)
                         ttAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGc                                                  >  1:994112/1‑64 (MQ=255)
                         ttAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGc                                                  >  1:4762380/1‑64 (MQ=255)
                         ttAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGAt                                            >  1:1242021/1‑70 (MQ=255)
                          tAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCttgt                                                               >  1:3407854/1‑48 (MQ=12)
                          tAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCttgt                                                               >  1:4421043/1‑48 (MQ=12)
                          tAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTGGGttg                                          >  1:515249/1‑70 (MQ=255)
                          tAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTGGGttg                                          >  1:4670912/1‑70 (MQ=255)
                          tAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGatata                                                       >  1:4125810/1‑58 (MQ=255)
                          tAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGatata                                                       >  1:3206924/1‑58 (MQ=255)
                          tAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGatata                                                       >  1:3200222/1‑58 (MQ=255)
                          tAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGatata                                                       >  1:4132302/1‑58 (MQ=255)
                          tAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTa                                          >  1:4273965/1‑71 (MQ=255)
                           aaGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTGGGttgt                                         >  1:836348/1‑69 (MQ=255)
                           aaGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGct                                                                    >  1:5376067/1‑44 (MQ=255)
                           aaGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTAt                                         >  1:3408586/1‑71 (MQ=255)
                                 aaCGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTc                                                                >  1:4955736/1‑42 (MQ=255)
                                 aaCGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTc                                                                >  1:835567/1‑42 (MQ=255)
                                 aaCGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCg                                                              >  1:2314612/1‑44 (MQ=255)
                                 aaCGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTc                                     >  1:4136100/1‑69 (MQ=255)
                                    gcgcACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGtt                                >  1:1228562/1‑71 (MQ=255)
                                     ttcACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTGGGTTGTGTTCCAGttt                               >  1:3514730/3‑71 (MQ=255)
                                      tcACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTGGGTTGTGTTCCAGttt                               <  1:2587755/69‑1 (MQ=255)
                                      tcACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTGGGTTGTGTTCCAGttt                               <  1:3939654/69‑1 (MQ=255)
                                      gcACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGtttt                              <  1:1686862/71‑1 (MQ=255)
                                       cACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGtttt                              <  1:2858984/70‑1 (MQ=255)
                                         ccGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATAttt                                                    <  1:3619840/46‑1 (MQ=255)
                                          cGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGa                          >  1:5163860/1‑71 (MQ=255)
                                          cGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGa                          >  1:788805/1‑71 (MQ=255)
                                          cGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGa                          >  1:189977/1‑71 (MQ=255)
                                          cGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGa                          >  1:2906151/1‑71 (MQ=255)
                                           gCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGAt                         >  1:5046768/1‑71 (MQ=255)
                                           gCTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTGGGTTGTGTTCCAGTTTTTCGAt                         <  1:3122600/71‑1 (MQ=255)
                                            cTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATc                        <  1:3000213/71‑1 (MQ=255)
                                            cTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATc                        <  1:4133638/71‑1 (MQ=255)
                                            cTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTGGGTTGTGTTCCAGTTTTTCGATc                        <  1:4118388/71‑1 (MQ=255)
                                               cGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTGGGTTGTGTTCCAGTTTTTCGATCCa                      <  1:1328439/70‑1 (MQ=255)
                                               cGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTGGGTTGTGTTCCAGTTTTTCGATCCa                      <  1:290012/70‑1 (MQ=255)
                                                gCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAg                     <  1:2193112/70‑1 (MQ=255)
                                                gCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAg                     <  1:2727331/70‑1 (MQ=255)
                                                gCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAg                     <  1:3180425/70‑1 (MQ=255)
                                                gCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAg                     <  1:5063043/70‑1 (MQ=255)
                                                 ccTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGAt                   <  1:2532187/71‑1 (MQ=255)
                                                   ttCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGa                                             >  1:5271891/1‑43 (MQ=255)
                                                   ttCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGAt                                            <  1:1672559/44‑1 (MQ=255)
                                                   ttCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTa                                          >  1:3055530/1‑46 (MQ=255)
                                                   ttCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTAGATTATGTTCCAGTTTTTCGATc                        <  1:796523/64‑1 (MQ=255)
                                                    tctcCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATccc                >  1:376745/1‑71 (MQ=255)
                                                     ctcCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATcccc               >  1:2551854/1‑71 (MQ=255)
                                                        ccGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCt              <  1:323718/69‑1 (MQ=255)
                                                           cTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATg                                        <  1:3716480/40‑1 (MQ=255)
                                                           cTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATg                                        <  1:5297305/40‑1 (MQ=255)
                                                           cTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACgg         <  1:139382/71‑1 (MQ=255)
                                                           cTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACgg         >  1:1005824/1‑71 (MQ=255)
                                                           cTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACgg         <  1:3582069/71‑1 (MQ=255)
                                                           cTTTGCGCAGCTCTTCAGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACgg         >  1:5533592/1‑71 (MQ=255)
                                                            tttGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGAt                   >  1:2850554/1‑60 (MQ=255)
                                                             tggcgcAGTTCTTGTGGAATGTACTGGCCTGGGTTGTGTTCCAGTTTTTCGATCCAGATACCTTCGCGGtt       >  1:3669571/3‑71 (MQ=255)
                                                              tGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGtt       >  1:1342141/1‑70 (MQ=255)
                                                               gcgcAGTTCTTGTGGAATGTACTGGCCTGGGTTGTGTTCCAGTTTTTCGATCCa                      <  1:2989331/54‑1 (MQ=255)
                                                                cgcAGTTCTTGTGGAATGTACTGGCCTGGGTTGTGTTCCAGTTTTTCGATCCAGATACCTTCGCGGTTGa     >  1:2236303/1‑70 (MQ=255)
                                                                cgcAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGa     <  1:4711421/70‑1 (MQ=255)
                                                                 tctgCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGa     <  1:1433269/66‑1 (MQ=255)
                                                                 gcAGTTCTTGTGGAATGTACTGGCCTGGGTTGTGTTCCAGTTTTTCGATCCAGATACCTTCGCGGTTGAtt   <  1:458306/71‑2 (MQ=255)
                                                                  cAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCt  <  1:2214529/71‑1 (MQ=255)
                                                                     ctctTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCt  >  1:748674/1‑68 (MQ=255)
                                                                     |                                                                   
TGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCT  >  minE/1014953‑1015089

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A