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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,635,184 G→A 44.4% V107V (GTG→GTA)  ugpB → glycerol‑3‑phosphate transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,635,1840GA44.4% 25.2 / 77.4 99V107V (GTG→GTA) ugpBglycerol‑3‑phosphate transporter subunit
Reads supporting (aligned to +/- strand):  ref base G (47/8);  new base A (27/17);  total (74/25)
Fisher's exact test for biased strand distribution p-value = 9.75e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.65e-01

Only 100 of 113 total aligned reads displayed.

GGTTTATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGTTTCAGGTTACTACTC  >  minE/2635121‑2635249
                                                               |                                                                 
ggTTTATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTAtt                                                                 >  1:104145/1‑66 (MQ=255)
ggTTTATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTAtt                                                                 >  1:2151874/1‑66 (MQ=255)
ggTTTATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTAtt                                                                 >  1:2136162/1‑66 (MQ=255)
ggTTTATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTAtt                                                                 >  1:2099145/1‑66 (MQ=255)
ggTTTATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTAtt                                                                 >  1:2739162/1‑66 (MQ=255)
ggTTTATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTAtt                                                                 >  1:2029618/1‑66 (MQ=255)
ggTTTATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTAtt                                                                 >  1:2771076/1‑66 (MQ=255)
ggTTTATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTAtt                                                                 >  1:3123791/1‑66 (MQ=255)
ggTTTATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTAtt                                                                 >  1:3307282/1‑66 (MQ=255)
ggTTTATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTAtt                                                                 >  1:3370298/1‑66 (MQ=255)
ggTTTATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTAtt                                                                 >  1:519834/1‑66 (MQ=255)
ggTTTATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTAtt                                                                 >  1:1551207/1‑66 (MQ=255)
ggTTTATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTAtt                                                                 >  1:1431797/1‑66 (MQ=255)
ggTTTATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTAtt                                                                 >  1:720270/1‑66 (MQ=255)
ggTTTATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTAtt                                                                 >  1:823394/1‑66 (MQ=255)
   ttATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTATTTAAaga                                                           >  1:1689890/1‑69 (MQ=255)
   ttATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTATTTAAaga                                                           >  1:1043289/1‑69 (MQ=255)
   ttATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTATTTAAaga                                                           >  1:851261/1‑69 (MQ=255)
   ttATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTATTTAAaga                                                           >  1:1874246/1‑69 (MQ=255)
   ttATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTATTTAAaga                                                           >  1:3038099/1‑69 (MQ=255)
   ttATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTATTTAAaga                                                           >  1:3124682/1‑69 (MQ=255)
   ttATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTATTTAAaga                                                           >  1:164440/1‑69 (MQ=255)
   ttATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTATTTAAaga                                                           >  1:2195986/1‑69 (MQ=255)
   ttATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTATTTAAaga                                                           >  1:1271684/1‑69 (MQ=255)
   ttATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTATTTAAaga                                                           >  1:550158/1‑69 (MQ=255)
           ttGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGa                                                   >  1:797050/1‑69 (MQ=255)
                   gacaccaTGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTc                                           >  1:2526991/3‑69 (MQ=255)
                   gCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTc                                           <  1:2303653/69‑1 (MQ=255)
                   gCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTc                                           >  1:2485409/1‑69 (MQ=255)
                   gCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTc                                           >  1:2497750/1‑69 (MQ=255)
                   gCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTc                                           >  1:561479/1‑69 (MQ=255)
                   gCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTc                                           >  1:937175/1‑69 (MQ=255)
                   gCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTc                                           >  1:2677607/1‑69 (MQ=255)
                   gCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTc                                           >  1:907316/1‑69 (MQ=255)
                   gCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTc                                           >  1:2767083/1‑69 (MQ=255)
                   gCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTc                                           >  1:763614/1‑69 (MQ=255)
                   gCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTc                                           >  1:751544/1‑69 (MQ=255)
                   gCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTc                                           >  1:661506/1‑69 (MQ=255)
                   gCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTc                                           >  1:1862444/1‑69 (MQ=255)
                   gCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTc                                           >  1:2036731/1‑69 (MQ=255)
                   gCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTc                                           <  1:1623346/69‑1 (MQ=255)
                   gCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTc                                           >  1:139946/1‑69 (MQ=255)
                   gCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTc                                           >  1:1382443/1‑69 (MQ=255)
                   gCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTc                                           >  1:122910/1‑69 (MQ=255)
                   gCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTc                                           >  1:2234223/1‑69 (MQ=255)
                            atgGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGt                                    >  1:508321/1‑67 (MQ=255)
                            atgGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGt                                    >  1:2421911/1‑67 (MQ=255)
                            atgGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGt                                    >  1:2425892/1‑67 (MQ=255)
                            atgGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGt                                    >  1:647711/1‑67 (MQ=255)
                            atgGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGt                                    >  1:1004753/1‑67 (MQ=255)
                            atgGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGt                                    >  1:1462410/1‑67 (MQ=255)
                              ggCGTCGAAAGCCATTAAACCGTTGTATGACGTATTTAAAGAGGCAGGGATTCAATTCGATGAGTCGCa                                <  1:2159109/69‑1 (MQ=255)
                              ggCGTCGAAAGCCATTAAACCGGTGTATGACGTATTTAAAGAGGCAGGGATTCAATTCGATGAGTCGCa                                <  1:919307/69‑1 (MQ=255)
                              ggCGTCGAAAGCCATTAAACCGGTGTATGACGTATTTAAAGAGGCAGGGATTCAATTCGATGAGTCGCa                                <  1:3077734/69‑1 (MQ=255)
                              ggCGTCGAAAGCCATTAAACCGGTGTATGACGTATTTAAAGAGGCAGGGATTCAATTCGATGAGTCGCa                                <  1:309979/69‑1 (MQ=255)
                              ggCGTCGAAAGCCATTAAACCGGTGTATGACGTATTTAAAGAGGCAGGGATTCAATTCGATGAGTCGCa                                <  1:3133454/69‑1 (MQ=255)
                              ggCGTCGAAAGCCATTAAACCGGTGTATGACGTATTTAAAGAGGCAGGGATTCAATTCGATGAGTCGCa                                <  1:1772519/69‑1 (MQ=255)
                              ggCGTCGAAAGCCATTAAACCGGTGTATGACGTATTTAAAGAGGCAGGGATTCAATTCGATGAGTCGCa                                <  1:2600202/69‑1 (MQ=255)
                              ggCGTCGAAAGCCATTAAACCGGTGTATGACGTATTTAAAGAGGCAGGGATTCAATTCGATGAGTCGCa                                <  1:3313988/69‑1 (MQ=255)
                              ggCGTCGAAAGCCATTAAACCGGTGTATGACGTATTTAAAGAGGCAGGGATTCAATTCGATGAGTCGCa                                <  1:2351371/69‑1 (MQ=255)
                              ggCGTCGAAAGCCATTAAACCGGTGTATGACGTATTTAAAGAGGCAGGGATTCAATTCGATGAGTCGCa                                <  1:1118328/69‑1 (MQ=255)
                              ggCGTCGAAAGCCATTAAACCGGTGTATGACGTATTTAAAGAGGCAGGGATTCAATTCGATGAGTCGCa                                <  1:333016/69‑1 (MQ=255)
                              ggCGTCCAAAGCCATTAAACCGGTGTATGACGTATTTAAAGAGGCAGGGATTCAATTCGATGAGTCGCa                                <  1:2476355/69‑1 (MQ=255)
                               gCGTCGAAAGCCATTAAACCGGTGTATGACGTATTTAAAGAGGCAGGGATTCAATTCGATGAGTCGCa                                <  1:983880/68‑1 (MQ=255)
                               gCGTCGAAAGCCATTAAACCGGTGTATGACGTATTTAAAGAGGCAGGGATTCAATTCGATGAGTCGCa                                <  1:2214973/68‑1 (MQ=255)
                                          cATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCg                      >  1:2746105/1‑67 (MQ=255)
                                          cATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGAc                    >  1:1147054/1‑69 (MQ=255)
                                          cATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGAc                    >  1:486633/1‑69 (MQ=255)
                                          cATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGAc                    <  1:1647453/69‑1 (MQ=255)
                                          cATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGAc                    <  1:426181/69‑1 (MQ=255)
                                          cATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGAc                    <  1:3428570/69‑1 (MQ=255)
                                          cATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGAc                    <  1:2062684/69‑1 (MQ=255)
                                          cATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGAc                    <  1:856060/69‑1 (MQ=255)
                                             tAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGt                 <  1:1317922/69‑1 (MQ=255)
                                              aaaCCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGt                 >  1:1168138/1‑68 (MQ=255)
                                              aaaCCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGt                 >  1:3381885/1‑68 (MQ=255)
                                              aaaCCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGt                 >  1:3170744/1‑68 (MQ=255)
                                              aaaCCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGt                 >  1:2842127/1‑68 (MQ=255)
                                              aaaCCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGt                 >  1:1109374/1‑68 (MQ=255)
                                                         tGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCg                      >  1:2311581/1‑52 (MQ=255)
                                                         tGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCg                      >  1:2510052/1‑52 (MQ=255)
                                                         tGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGTTTCAGGTtacta     >  1:917856/1‑69 (MQ=255)
                                                         tGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGTTTCAGGTtacta     >  1:2344087/1‑69 (MQ=255)
                                                         tGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGTTTCAGGTtacta     >  1:704481/1‑69 (MQ=255)
                                                         tGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGTTTCAGGTtacta     >  1:2494965/1‑69 (MQ=255)
                                                         tGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGTTTCAGGTtacta     >  1:556582/1‑69 (MQ=255)
                                                         tGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGTTTCAGGTtacta     >  1:493824/1‑69 (MQ=255)
                                                         tGAAGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGTTTCAGGTtacta     >  1:1742981/1‑69 (MQ=255)
                                                             gtgtTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGTTTCAGGTTACTACTc  >  1:2552232/1‑68 (MQ=255)
                                                              tgtTTAAAGAGGCAGTGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGTTTCAGGt          <  1:2364938/59‑1 (MQ=255)
                                                              tgtTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGTTTCAGGt          <  1:1150676/59‑1 (MQ=255)
                                                              tgtTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGTTTCAGGt          <  1:3177983/59‑1 (MQ=255)
                                                              tgtTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGTTTCAGGt          <  1:1370138/59‑1 (MQ=255)
                                                              tgtTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGTTTCAGGt          <  1:1590306/59‑1 (MQ=255)
                                                              tgtTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGTTTCAGGt          <  1:1595643/59‑1 (MQ=255)
                                                              tgtTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGTTTCAGGt          <  1:3318518/59‑1 (MQ=255)
                                                              tgtTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGTTTCAGGt          <  1:223557/59‑1 (MQ=255)
                                                              tgtTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGTTTCAGGt          <  1:2823938/59‑1 (MQ=255)
                                                              tgtTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGTTTCAGGt          <  1:1993187/59‑1 (MQ=255)
                                                              tgtTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGTTTCAGGt          <  1:2242220/59‑1 (MQ=255)
                                                               |                                                                 
GGTTTATGAAGTTGGCACCGCCACCATGATGGCGTCGAAAGCCATTAAACCGGTGTATGACGTGTTTAAAGAGGCAGGGATTCAGTTCGATGAGTCGCAGTTTGTGCCGACGGTTTCAGGTTACTACTC  >  minE/2635121‑2635249

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