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 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,015,100 A→G 23.2% N323N (AAT→AAC)  fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,015,1000AG23.2% 124.8 / 37.1 69N323N (AAT→AAC) fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base A (30/23);  new base G (8/8);  total (38/31)
Fisher's exact test for biased strand distribution p-value = 7.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.39e-01

ATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTCAGCAGAGCAGGAGACGCCCATACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAATCA  >  minE/1015034‑1015170
                                                                  |                                                                      
atatTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTAc                                                                    >  1:614520/1‑71 (MQ=255)
     tGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTc                                                                <  1:3580333/70‑1 (MQ=255)
       ccTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTcag                                                              <  1:1789955/70‑1 (MQ=255)
         tGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTcag                                                              >  1:2800083/1‑68 (MQ=255)
         tGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTcag                                                              >  1:834441/1‑68 (MQ=255)
         tGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTc                                                                <  1:2398348/66‑1 (MQ=255)
         tGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTc                                                                <  1:155690/66‑1 (MQ=255)
          ggATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTcagca                                                            >  1:2212769/1‑69 (MQ=255)
           gATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGata                                                                        >  1:266991/1‑56 (MQ=255)
           gATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTcagcag                                                           <  1:1247317/69‑1 (MQ=255)
           gATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTCagcagag                                                         <  1:1056671/71‑1 (MQ=255)
            aTTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTcagcag                                                           <  1:1669408/68‑1 (MQ=255)
              tATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTa                                                                     >  1:1125117/1‑56 (MQ=255)
              tATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTCagcagagcag                                                      >  1:2973981/1‑71 (MQ=255)
              tATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTCagcagagc                                                        <  1:1669752/69‑1 (MQ=255)
               gtGTTCCAGTTTTTCGATCCAGATACCTTCGCGGTTGATTTTCGCTTTAATGTTACGGTCagcggagcag                                                      <  1:721844/69‑1 (MQ=255)
                tGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTCAGCAGAGCAgg                                                     <  1:3892848/70‑1 (MQ=255)
                 gTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTCagcagag                                                         >  1:392659/1‑65 (MQ=255)
                 gTTCCAGTTTTTCGATCCAGATACCTTCGCGGTTGATTTTCGCTTTAATGTTACGGTca                                                               >  1:1812360/1‑59 (MQ=255)
                  ttCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTcagca                                                            <  1:2643762/61‑1 (MQ=255)
                  ttCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTCAGCAGAGCAGgaga                                                  <  1:3764014/71‑1 (MQ=255)
                  ttCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTCAGCAGAGCAGgaga                                                  >  1:607970/1‑71 (MQ=255)
                     cAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTCAGCAGAGCAGGAGACGc                                               >  1:78816/1‑71 (MQ=255)
                      aGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTAGATATTACGGTCagcagag                                                         <  1:2524783/60‑1 (MQ=255)
                        tttttCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGt                                                                 <  1:1312897/50‑1 (MQ=255)
                        tttttCGATCCAGATACCTTCGCGGTTGATTTTCGCTTTAATGTTACGGTCAGCGGAGCAGGAGACGccc                                             <  1:793432/70‑1 (MQ=255)
                          tttCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTcagca                                                            >  1:2012158/1‑53 (MQ=255)
                          tttCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTCAGCAGAGCAGga                                                    >  1:2102585/1‑61 (MQ=255)
                          tttCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTCAGCAGAGCAGGAGACGc                                               >  1:2842329/1‑66 (MQ=255)
                          tttCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTCAGCAGAGCAGGAGACGCCCATa                                          >  1:2452796/1‑71 (MQ=255)
                          tttCGATCCAGATACCTTCGCGGTTGATTTTCGCTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCAtg                                          >  1:3208825/1‑70 (MQ=255)
                          tttCGATCCAGATACCTTCGCGGTTGATTTTCGCTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCAtg                                          >  1:3156853/1‑70 (MQ=255)
                            tCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGata                                                                        >  1:961996/1‑39 (MQ=255)
                            tCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTCAGCAGAGCAGga                                                    <  1:2499349/59‑1 (MQ=255)
                            tCGATCCAGATACCTTCGCGGTTGATTTTCGCTTTAATGTTACGGTCAGCGGAGCAgg                                                     >  1:3667360/1‑58 (MQ=255)
                            tCGATCCAGATACCTTCGCGGTTGATTTTCGCTTTAATGTTACGGTCAGCGGAGCAgg                                                     >  1:2734118/1‑58 (MQ=255)
                                 ccAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTCAGCAGAGCAGGAGACGCCCATaccgaccg                                   >  1:3135370/1‑71 (MQ=255)
                                  cAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTCAGCAGAGCAGGAGACGCCCATACCGACCgg                                  >  1:1743945/1‑71 (MQ=255)
                                    gATCCCCTGACTGTTTATCTTCGCTTTGATATTACGGTCAGCAGAGCAGGAGACGCCCATACCGACCggg                                 <  1:3775032/70‑1 (MQ=255)
                                     aTCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTCAGCAGAGCAGGAGACGccc                                             >  1:2886572/1‑57 (MQ=255)
                                     aTCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTCAGCAGAGCAGGAGACGccc                                             >  1:2632534/1‑57 (MQ=255)
                                      tCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTCAGCAGAGCAGGAGACGCCCa                                            >  1:2387389/1‑57 (MQ=255)
                                        cccTGACGGTTGATCTTCGCTTTGATATTACGGTCAGCAGAGCAGGAGACGCCCATACCGACCGGGCAgg                             <  1:241152/70‑1 (MQ=255)
                                        cccTGACGGTTGATCTTCGCTTTGATATTACGGTCAGCAGAGCAGGAGACGCCCATACCGACCGGGCAGGa                            >  1:3128745/1‑71 (MQ=255)
                                        cccTGACGGTTGATCTTCGCTTTGATATTACGGTCAGCAGAGCAGGAGACGCCCATACCGACCGGGCAGGa                            >  1:2455545/1‑71 (MQ=255)
                                         ccTGACGGTTGATCTTCGCTTTGATATTACGGTCAGCAGAGCAGGAGACGCCCATACCGACCGGGCAGGAt                           <  1:2456632/71‑1 (MQ=255)
                                            gACGGTTGATCTTCGCTTTGATATTACGGTCAGCAGAGCAGgaga                                                  >  1:215618/1‑45 (MQ=255)
                                            gACGGTTGATCTTCGCTTTGATATTACGGTCAGCAGAGCAGga                                                    <  1:2911233/43‑1 (MQ=255)
                                            gACGGTTGATCTTCGCTTTGATATTACGGTCAGCAGAGCAGGAGACGCCCATaccgac                                     >  1:1989042/1‑58 (MQ=255)
                                            cgcGGTTGATTTTCGCTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATgc                         >  1:1496659/3‑70 (MQ=255)
                                             gcGGTTGATTTTAGCTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCAt                                           >  1:1824979/2‑51 (MQ=255)
                                             aCGGTTGATCTTCGCTTTGATATTACGGTCAGCAGAGCAGGAGACGCCCATACCGACCGGGCAGGATgcgc                       <  1:3068290/71‑1 (MQ=255)
                                                 ttGATTTTCGCTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGa                            <  1:1931279/62‑1 (MQ=255)
                                                 ttGATTTTCGCTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGcc                      <  1:1287592/68‑1 (MQ=255)
                                                 ttGATCTTCGCTTTGATATTACGGTCAGCAGATCAGGAGACGCCCATACCGACCGGGCAGGATGCGCCGt                    >  1:353839/1‑70 (MQ=255)
                                                  tGATTTTCGCTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGa                            <  1:1551877/61‑1 (MQ=255)
                                                  tGATCTTCGCTTTGATATTACGGTCAGCAGAGCAGGAGACGCCCa                                            >  1:821960/1‑45 (MQ=255)
                                                   gATTTTCGCTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCATgccgaccg                                   >  1:1015337/1‑53 (MQ=255)
                                                   gATCTTCGCTTTGATATTACGGTCAGCAGAGCAGGAGACGCCCATa                                          >  1:3037636/1‑46 (MQ=255)
                                                       ttCGCTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTg              <  1:3726174/70‑1 (MQ=255)
                                                        tCGCTTTGATATTACGGTCAGCAGAGCAGGAGACGCCCATACCGACCGGGCAGGATGCGCCGTGACGTgg             >  1:996414/1‑70 (MQ=255)
                                                        tCGCTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTgg             <  1:3781144/70‑1 (MQ=255)
                                                         cGCTTTGATATTACGGTCAGCAGAGCAGGAGACGCCCATACCGACCGGGCAGGATGCGCCGTGACGTg              <  1:287031/68‑1 (MQ=255)
                                                          gCTTTGATATTACGGTCAGCAGAGCAGGAGACGCCCa                                            >  1:2516929/1‑37 (MQ=255)
                                                          gCTTTGATATTACGGTCAGCAGAGCAGGAGACGCCCa                                            >  1:587563/1‑37 (MQ=255)
                                                          gCTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCa           <  1:3384544/70‑1 (MQ=255)
                                                           cTTTGATATTACGGTCAGCAGAGCAGGAGACGCCCATa                                          >  1:3394296/1‑38 (MQ=255)
                                                            tttGATATTACGGTCAGCAGAGCAGGAGACGCCCATACCGACCGGGCAGGATGCGCCGTGACg                <  1:1846925/63‑1 (MQ=255)
                                                             ttGATATTACGGTCAGCAGAGCAGGAGACGCCCATACCGACCgg                                  >  1:759547/1‑44 (MQ=255)
                                                             ttGATATTACGGTCAGCAGAGCAGGAGACGCCCATACCGACCgg                                  <  1:2159129/44‑1 (MQ=255)
                                                              tGATATTACGGTCAGCAGAGCAGGAGACGCCCATACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGc        <  1:903527/69‑1 (MQ=255)
                                                                atatTACGGTCAGCAGAGCAGGAGACGCCCATACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAAt    <  1:3508987/71‑1 (MQ=255)
                                                                  atTACGGTCAGCAGAGCAGGAGACGCCCATACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAATCa  >  1:683627/1‑71 (MQ=255)
                                                                  atTACGGTCAGCAGAGCAGGAGACGCCCATACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAATCa  >  1:2950878/1‑71 (MQ=255)
                                                                  |                                                                      
ATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTTGATATTACGGTCAGCAGAGCAGGAGACGCCCATACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAATCA  >  minE/1015034‑1015170

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