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 1,653,633 C→A 30.8% intergenic (‑75/‑250) upp ← / → purM uracil phosphoribosyltransferase/phosphoribosylaminoimidazole synthetase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,653,6330CA30.8% 146.0 / 64.6 110intergenic (‑75/‑250)upp/purMuracil phosphoribosyltransferase/phosphoribosylaminoimidazole synthetase
Reads supporting (aligned to +/- strand):  ref base C (42/34);  new base A (16/18);  total (58/52)
Fisher's exact test for biased strand distribution p-value = 5.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 110 total aligned reads displayed.

CCTTTGAGGGGCAGCCACAAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTAT  >  minE/1653568‑1653699
                                                                 |                                                                  
ccTTTGCGGGGCAGCCACAAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCtt                                                                  <  1:2190779/68‑1 (MQ=255)
ccTTTGAGGGGCAGCCACAAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCtt                                                                  <  1:1202595/68‑1 (MQ=255)
ccTTTGAGGGGCAGCCACAAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCtt                                                                  <  1:2483682/68‑1 (MQ=255)
ccTTTGAGGGGCAGCCACAAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCtt                                                                  <  1:290421/68‑1 (MQ=255)
ccTTTGAGGGGCAGCCACAAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCtt                                                                  <  1:1975352/68‑1 (MQ=255)
ccTTTGAGGGGCAGCCACAAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCtt                                                                  <  1:1009228/68‑1 (MQ=255)
ccTTTGAGGAGCAGCCACAAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCtt                                                                  <  1:1124414/68‑1 (MQ=255)
 cTTTGAGGGGCAGCCACAAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCtt                                                                  <  1:807952/67‑1 (MQ=255)
      aGGGGCAGCCACAAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTg                                                           >  1:510049/1‑69 (MQ=255)
      aGGGGCAGCCACAAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTg                                                           >  1:794637/1‑69 (MQ=255)
       ggggCAGCCACAAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTg                                                           <  1:1719433/68‑1 (MQ=255)
       ggggCAGCCACAAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTg                                                           <  1:2717581/68‑1 (MQ=255)
       ggggCAGCCACAAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTg                                                           <  1:2591074/68‑1 (MQ=255)
         ggCAGCCACAAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGAc                                                         >  1:1547240/1‑68 (MQ=255)
          gCAGCCACAAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACtt                                                       <  1:695760/69‑1 (MQ=255)
           cAGCCACAAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACtt                                                       <  1:1286527/68‑1 (MQ=255)
             gCCACAAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCtt                                                                  <  1:1760322/55‑1 (MQ=255)
                acaAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTATTTTCGTTGACTTTAGTCa                                                 <  1:1697165/69‑1 (MQ=255)
                acaAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTATTTTCGTTGACTTTAGTCa                                                 <  1:175607/69‑1 (MQ=255)
                acaAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTATTTTCGTTGACTTTAGTCa                                                 <  1:1564859/69‑1 (MQ=255)
                acaAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTATTTTCGTTGACTTTAGTCa                                                 <  1:1492196/69‑1 (MQ=255)
                acaAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTATTTTCGTTGACTTTAGTCa                                                 <  1:1242634/69‑1 (MQ=255)
                acaAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTATTTTCGTTGACTTTAGTCa                                                 <  1:397905/69‑1 (MQ=255)
                acaAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTATTTTCGTTGACTTTAGTCa                                                 <  1:1139216/69‑1 (MQ=255)
                 caAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTATTTTCGTTGACTTTAGTCa                                                 <  1:2318899/68‑1 (MQ=255)
                 caAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTATTTTCGTTGACTTTAGTCa                                                 <  1:2305837/68‑1 (MQ=255)
                 caAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTATTTTCGTTGACTTTAGTCa                                                 <  1:2859567/68‑1 (MQ=255)
                 caAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTATTTTCGTTGACTTTAGTCa                                                 <  1:3001463/68‑1 (MQ=255)
                 caAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTATTTTCGTTGACTTTAGTCa                                                 <  1:39309/68‑1 (MQ=255)
                 caAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTATTTTCGTTGACTTTAGTCa                                                 <  1:759746/68‑1 (MQ=255)
                  aaaaaaaaTCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTATTTTCGTTGACTTTAGTCa                                                 <  1:2744108/67‑1 (MQ=255)
                                          cctTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGtt                       >  1:101069/1‑69 (MQ=255)
                                           ctTTCTTCAAGGCGGCAATATTCTTTTCGTTTACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTa                      >  1:1339990/1‑69 (MQ=255)
                                           ctTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGAt                             >  1:3255500/1‑62 (MQ=255)
                                           ctTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTa                      >  1:864304/1‑69 (MQ=255)
                                           ctTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTa                      >  1:1113871/1‑69 (MQ=255)
                                           ctTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTATAGTCAAAATGATAACGGTTTgaga                              >  1:1238421/1‑61 (MQ=255)
                                                      gcggcAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCa           <  1:249093/69‑1 (MQ=255)
                                                      gcggcAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCa           <  1:2014099/69‑1 (MQ=255)
                                                      gcggcAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCa           <  1:761375/69‑1 (MQ=255)
                                                       cggcAATATTATTTTCGTTGACTTTAGTCAAAACGATaa                                        >  1:1127467/1‑39 (MQ=37)
                                                       cggcAATATTATTTTCGTTGACTTTAGTCAAAACGATaa                                        >  1:630634/1‑39 (MQ=37)
                                                       cggcAATATTATTTTCGTTGACTTTAGTCAAAACGATaa                                        >  1:489813/1‑39 (MQ=37)
                                                       cggcAATATTATTTTCGTTGACTTTAGTCAAAACGATaa                                        >  1:782434/1‑39 (MQ=37)
                                                       cggcAATATTATTTTCGTTGACTTTAGTCAAAACGATaa                                        >  1:3202717/1‑39 (MQ=37)
                                                       cggcAATATTATTTTCGTTGACTTTAGTCAAAACGATaa                                        >  1:3015076/1‑39 (MQ=37)
                                                       cggcAATATTATTTTCGTTGACTTTAGTCAAAACGATaa                                        >  1:2895547/1‑39 (MQ=37)
                                                       cggcAATATTATTTTCGTTGACTTTAGTCAAAACGATaa                                        >  1:2845901/1‑39 (MQ=37)
                                                       cggcAATATTATTTTCGTTGACTTTAGTCAAAACGATaa                                        >  1:1105345/1‑39 (MQ=37)
                                                       cggcAATATTATTTTCGTTGACTTTAGTCAAAACGATaa                                        >  1:1809610/1‑39 (MQ=37)
                                                       cggcAATATTATTTTCGTTGACTTTAGTCAAAACGATaa                                        >  1:2266857/1‑39 (MQ=37)
                                                       cggcAATATTATTTTCGTTGACTTTAGTCAAAACGATaa                                        >  1:1672685/1‑39 (MQ=37)
                                                       cggcAATATTATTTTCGTTGACTTTAGTCAAAACGATaa                                        >  1:1826198/1‑39 (MQ=37)
                                                       cggcAATATTATTTTCGTTGACTTTAGTCAAAACGATaa                                        >  1:191409/1‑39 (MQ=37)
                                                       cggcAATATTATTTTCGTTGACTTTAGTCAAAACGATaa                                        >  1:1497514/1‑39 (MQ=37)
                                                       cggcAATATTATTTTCGTTGACTTTAGTCAAAACGATaa                                        >  1:2300309/1‑39 (MQ=37)
                                                          cAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATg       <  1:200320/69‑1 (MQ=255)
                                                          cAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATg       <  1:72351/69‑1 (MQ=255)
                                                          cAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATg       <  1:338167/69‑1 (MQ=255)
                                                          cAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATg       <  1:2281219/69‑1 (MQ=255)
                                                            atatTCTTTTCGTTGACTTTAGTCGAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGt     >  1:283682/1‑69 (MQ=255)
                                                            atatTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGt     >  1:2736954/1‑69 (MQ=255)
                                                            atatTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGt     >  1:2486730/1‑69 (MQ=255)
                                                            atatTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGt     >  1:1820058/1‑69 (MQ=255)
                                                            atatTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGt     >  1:79889/1‑69 (MQ=255)
                                                            atatTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGt     <  1:2444915/69‑1 (MQ=255)
                                                            atatTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGt     >  1:1366351/1‑69 (MQ=255)
                                                            atatTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGt     >  1:54584/1‑69 (MQ=255)
                                                            atatTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGt     >  1:499320/1‑69 (MQ=255)
                                                            atatTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGt     >  1:1159613/1‑69 (MQ=255)
                                                            atatTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGt     <  1:3242882/69‑1 (MQ=255)
                                                            atatTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGt     >  1:3241585/1‑69 (MQ=255)
                                                            atatTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGt     >  1:3154730/1‑69 (MQ=255)
                                                            atatTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGt     >  1:2821409/1‑69 (MQ=255)
                                                            atatTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGt     >  1:3013455/1‑69 (MQ=255)
                                                            atatTCTTTTCCTTGACTTTAGTCAAAATGATAACGTTTTGAGATAAAGTTATTTTATATTCAGATGGt     >  1:2701196/1‑69 (MQ=255)
                                                            atatTCTTTTAGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGt     >  1:2052928/1‑69 (MQ=255)
                                                             tatTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGt     <  1:3265840/68‑1 (MQ=255)
                                                              atTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCa           <  1:1316041/61‑1 (MQ=255)
                                                              atTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCa           <  1:2142294/61‑1 (MQ=255)
                                                              atTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGt     <  1:2349568/67‑1 (MQ=255)
                                                              atTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGt     <  1:3203523/67‑1 (MQ=255)
                                                              atTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGt     <  1:149701/67‑1 (MQ=255)
                                                              atTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGt     <  1:510445/67‑1 (MQ=255)
                                                              atTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGt     <  1:447016/67‑1 (MQ=255)
                                                               ttCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCa           >  1:501350/1‑60 (MQ=255)
                                                               ttCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCa           >  1:1247557/1‑60 (MQ=255)
                                                               ttCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCa           >  1:1241903/1‑60 (MQ=255)
                                                               ttCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCa           >  1:795923/1‑60 (MQ=255)
                                                               ttCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGAt        >  1:1151831/1‑63 (MQ=255)
                                                               ttCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTa   >  1:2961867/1‑68 (MQ=255)
                                                               ttCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTa   >  1:1145078/1‑68 (MQ=255)
                                                               ttCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTa   >  1:2594922/1‑68 (MQ=255)
                                                               ttCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTa   >  1:1571938/1‑68 (MQ=255)
                                                               ttCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTa   >  1:1485515/1‑68 (MQ=255)
                                                               ttCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTa   >  1:3341624/1‑68 (MQ=255)
                                                               ttCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTa   >  1:277088/1‑68 (MQ=255)
                                                               ttCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTa   >  1:3314571/1‑68 (MQ=255)
                                                               ttCTTTTCGTTGACTTT‑GTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTAt  >  1:1311385/1‑68 (MQ=255)
                                                               ttCTTTTAGTTGACTTTAGTCAAAATGATAACGGTTTgaga                              >  1:1452500/1‑41 (MQ=255)
                                                                 |                                                                  
CCTTTGAGGGGCAGCCACAAAAAAAATCGACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGACTTTAGTCAAAATGATAACGGTTTGAGATAAAGTTATTTTATATTCAGATGGTTAT  >  minE/1653568‑1653699

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