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 1,646,236 T→A 40.0% I21I (ATT→ATA)  gcvR → DNA‑binding transcriptional repressor, regulatory protein accessory to GcvA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,646,2360TA40.0% 67.2 / 111.8 115I21I (ATT→ATA) gcvRDNA‑binding transcriptional repressor, regulatory protein accessory to GcvA
Reads supporting (aligned to +/- strand):  ref base T (36/33);  new base A (5/41);  total (41/74)
Fisher's exact test for biased strand distribution p-value = 3.72e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

Only 100 of 121 total aligned reads displayed.

AGTTTGACACTGTCATCGCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAATATTGAAGACAGTCGCCTGGCGAT  >  minE/1646171‑1646301
                                                                 |                                                                 
aGTTTGACACTGTCATCGCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATtgtg                                                                <  1:3412527/69‑1 (MQ=255)
aGTTTGACACTGTCATCGCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATtgtg                                                                <  1:3270127/69‑1 (MQ=255)
aGTTTGACACTGTCATCGCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATtgtg                                                                <  1:741978/69‑1 (MQ=255)
aGTTTGACACTGTCATCGCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATtgtg                                                                <  1:1940638/69‑1 (MQ=255)
 gTTTGACACTGTCATCGCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATtgtg                                                                <  1:2189805/68‑1 (MQ=255)
  tttGACACTGTCATCGCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGaa                                                              <  1:604845/69‑1 (MQ=255)
  tttGACACTGTCATCGCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGaa                                                              <  1:825286/69‑1 (MQ=255)
  tttGACACTGTCATCGCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGaa                                                              <  1:1188122/69‑1 (MQ=255)
  tttGACACTGTCATCGCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGaa                                                              <  1:1283396/69‑1 (MQ=255)
  tttGACACTGTCATCGCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGaa                                                              <  1:1851683/69‑1 (MQ=255)
  tttGACACTGTCATCGCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGaa                                                              <  1:157811/69‑1 (MQ=255)
   ttGACACTGTCATCGCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATtg                                                                  >  1:2075461/1‑64 (MQ=255)
   ttGACACTGTCATCGCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGaa                                                              <  1:452372/68‑1 (MQ=255)
   ttGACACTGTCATCGCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGAac                                                             >  1:3061093/1‑69 (MQ=255)
   ttGACACTGTCATCGCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGAac                                                             >  1:1960870/1‑69 (MQ=255)
          tGTCATCGCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGAACACCATCa                                                      <  1:1758846/69‑1 (MQ=255)
              aTCGCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGAACACCATCAccc                                                   >  1:1945786/1‑68 (MQ=255)
                 gCAACATTATCTGGTGATCACTGCGTTGTGTGCCGATCGCCCTGGAATTGTGAacac                                                           >  1:2568068/1‑57 (MQ=255)
                 gCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGAacac                                                           >  1:1421205/1‑57 (MQ=255)
                 gCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGAacac                                                           >  1:988449/1‑57 (MQ=255)
                 gCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGAacac                                                           >  1:3388220/1‑57 (MQ=255)
                 gCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGAacac                                                           >  1:3122236/1‑57 (MQ=255)
                 gCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGAacac                                                           >  1:2828110/1‑57 (MQ=255)
                 gCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGAacac                                                           >  1:2759829/1‑57 (MQ=255)
                 gCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGAacac                                                           >  1:2397979/1‑57 (MQ=255)
                 gCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGAacac                                                           >  1:2348683/1‑57 (MQ=255)
                 gCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGAacac                                                           >  1:2042738/1‑57 (MQ=255)
                 gCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGAacac                                                           >  1:1155075/1‑57 (MQ=255)
                 gCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGAacac                                                           >  1:1318289/1‑57 (MQ=255)
                 gCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGAacac                                                           >  1:917117/1‑57 (MQ=255)
                       ttATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATAGTGAACACCATCAGCCGTCTTGTCag                                         <  1:440564/69‑1 (MQ=255)
                       ttATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCag                                         <  1:949148/69‑1 (MQ=255)
                       ttATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCag                                         <  1:415839/69‑1 (MQ=255)
                       ttATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCag                                         <  1:3412681/69‑1 (MQ=255)
                       ttATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCag                                         <  1:1393151/69‑1 (MQ=255)
                       ttATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCag                                         <  1:459487/69‑1 (MQ=255)
                       ttATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCag                                         <  1:9545/69‑1 (MQ=255)
                       ttATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCag                                         <  1:1541572/69‑1 (MQ=255)
                       ttATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCag                                         <  1:505230/69‑1 (MQ=255)
                       ttATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCag                                         <  1:590648/69‑1 (MQ=255)
                       ttATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCag                                         <  1:2701785/69‑1 (MQ=255)
                       ttATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCag                                         <  1:2607912/69‑1 (MQ=255)
                       ttATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCag                                         <  1:647272/69‑1 (MQ=255)
                       ttATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCag                                         <  1:171483/69‑1 (MQ=255)
                       ttATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCag                                         <  1:1916405/69‑1 (MQ=255)
                       ttATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCag                                         <  1:911826/69‑1 (MQ=255)
                       ttATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCag                                         <  1:2328594/69‑1 (MQ=255)
                       ttATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCag                                         <  1:2325926/69‑1 (MQ=255)
                       ttATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCag                                         <  1:1126840/69‑1 (MQ=255)
                       ttATCTGGTGATCACTGCGTTGGGGGCCGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCag                                         <  1:3211794/69‑1 (MQ=255)
                         aTCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGAACACCATCACCCGTCATGTCagta                                       <  1:832335/69‑1 (MQ=255)
                         aTCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGAACACCATCACCCGTCATGTCagta                                       <  1:1303263/69‑1 (MQ=255)
                         aTCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGAACACCATCACCCGTCATGTCagta                                       <  1:1786031/69‑1 (MQ=255)
                                   cACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCt                              >  1:349042/1‑68 (MQ=255)
                                    aCTGCGTTGGGTGCCGATCGCCCTGGAATTGTGaa                                                              <  1:2774238/35‑1 (MQ=255)
                                       gCGTTGGGTGCCGATCGCCCTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTaa                          >  1:2892448/1‑68 (MQ=255)
                                       gCGTTGGGTGCCGATCGCCCTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTaa                          >  1:540842/1‑68 (MQ=255)
                                       gCGTTGGGTGCCGATCGCCCTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTaa                          >  1:3237447/1‑68 (MQ=255)
                                       gCGTTGGGTGCCGATCGCCCTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTaa                          >  1:2376773/1‑68 (MQ=255)
                                       gCGTTGGGTGCCGATCGCCCTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAat                         >  1:2899168/1‑69 (MQ=255)
                                       gCGTTGGGTGCCGATCGCCCTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAat                         >  1:2377245/1‑69 (MQ=255)
                                       gCGTTGGGTGCCGATCGCCCTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAat                         >  1:1004369/1‑69 (MQ=255)
                                          ttGGGTGCCGATCGCCCTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAatat                       <  1:2163244/68‑1 (MQ=255)
                                          ttGGGTGCCGATCGCCCTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAatat                       <  1:2374290/68‑1 (MQ=255)
                                          ttGGGTGCCGATCGCCCTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAatat                       <  1:1970147/68‑1 (MQ=255)
                                          ttGGGTGCCGATCGCCCTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAatat                       <  1:15469/68‑1 (MQ=255)
                                          ttGGGTGCCGATCGCCCTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAatat                       <  1:1116312/68‑1 (MQ=255)
                                              gTGCCGATCGCCCTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAATATTGaa                   <  1:2783354/68‑1 (MQ=255)
                                                 ccGATCGGCCTGGAATTGTGAACACCATCACCCGTCCTGGCAGTAGTTGCGGCTGTAATATTGaa                   <  1:2708692/65‑1 (MQ=255)
                                                  cGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAATATTGAAGa                 >  1:1605232/1‑66 (MQ=255)
                                                  cGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAATATTGAAGa                 >  1:463483/1‑66 (MQ=255)
                                                  cGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAATATTGAAGa                 >  1:1063911/1‑66 (MQ=255)
                                                  cGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAATATTGAAGa                 >  1:869036/1‑66 (MQ=255)
                                                  cGATCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAATATTGAAGa                 >  1:44883/1‑66 (MQ=255)
                                                    aTCTCCCTGGAATAGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAata                        <  1:1059915/57‑1 (MQ=255)
                                                    aTCGCCCTGGAATAGTGAACTCCATCACCCGTCATGTCAGTAGTTGCGGCTGTAata                        <  1:866473/57‑1 (MQ=255)
                                                    aTCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAata                        <  1:920301/57‑1 (MQ=255)
                                                    aTCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAata                        <  1:623374/57‑1 (MQ=255)
                                                    aTCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAata                        <  1:2524938/57‑1 (MQ=255)
                                                    aTCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAata                        <  1:1004899/57‑1 (MQ=255)
                                                    aTCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAata                        <  1:1668265/57‑1 (MQ=255)
                                                    aTCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAata                        <  1:2516020/57‑1 (MQ=255)
                                                    aTCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAata                        <  1:1878877/57‑1 (MQ=255)
                                                    aTCGCCCTGGAATAGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTCTAata                        <  1:951003/57‑1 (MQ=255)
                                                      cGCCCTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAATATTGAAGACAGTCGc          >  1:1991860/1‑69 (MQ=255)
                                                      cGCCCTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAATATTGAAGACAGTCGc          >  1:1025578/1‑69 (MQ=255)
                                                      cGCCCTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAATATTGAAGACAGTCGc          >  1:792322/1‑69 (MQ=255)
                                                      cGCCCTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAATATTGAAGACAGTCGc          >  1:2406738/1‑69 (MQ=255)
                                                      cGCCCTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAATATTGAAGACAGTCGc          >  1:2885919/1‑69 (MQ=255)
                                                         ccTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAATATTGAAGACAGTCGCCTg       <  1:2110244/69‑1 (MQ=255)
                                                         ccTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAATATTGAAGACAGTCGCCTg       <  1:1932914/69‑1 (MQ=255)
                                                         ccTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAATATTGAAGACAGTCGCCTg       <  1:2473368/69‑1 (MQ=255)
                                                         ccTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAATATTGAAGACAGTCGCCTg       <  1:172790/69‑1 (MQ=255)
                                                         ccTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAATATTGAAGACAGTCGCCTg       <  1:1449004/69‑1 (MQ=255)
                                                         ccTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAATATTGAAGACAGTCGCCTg       <  1:1291183/69‑1 (MQ=255)
                                                         ccTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAATATTGAAGACAGTCGCCTg       <  1:3039185/69‑1 (MQ=255)
                                                         ccTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAATATTGAAGACAGTCGCCTg       <  1:3130811/69‑1 (MQ=255)
                                                              aaTAGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAtta                        <  1:336502/47‑1 (MQ=255)
                                                               aTTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAATATTGAAGACAGTCGCCTGGCGAt  <  1:1968519/68‑1 (MQ=255)
                                                               aTTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAATATTGAAGACAGTCGCCTGGCGAt  <  1:3083714/68‑1 (MQ=255)
                                                                 |                                                                 
AGTTTGACACTGTCATCGCAACATTATCTGGTGATCACTGCGTTGGGTGCCGATCGCCCTGGAATTGTGAACACCATCACCCGTCATGTCAGTAGTTGCGGCTGTAATATTGAAGACAGTCGCCTGGCGAT  >  minE/1646171‑1646301

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