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 1,028,197 C→T 29.6% F384F (TTC→TTT)  malX → fused maltose and glucose‑specific PTS enzyme IIBC components

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,028,1970CT29.6% 122.7 / 55.7 121F384F (TTC→TTT) malXfused maltose and glucose‑specific PTS enzyme IIBC components
Reads supporting (aligned to +/- strand):  ref base C (49/36);  new base T (24/12);  total (73/48)
Fisher's exact test for biased strand distribution p-value = 4.19e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.39e-01

Only 100 of 121 total aligned reads displayed.

CACCGTCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGCCAGTGGTGGCGGCAATC  >  minE/1028137‑1028263
                                                            |                                                                  
cACTGTCATGTCTGTGCTCGGCGTCACCTTCGGTAATACCGACGGCAATATCATCGACTTTGTGGTGtt                                                            >  1:3297615/1‑69 (MQ=255)
cACTGTCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGATGGCAATATCATCGACTTTGTGGTGtt                                                            >  1:2565498/1‑69 (MQ=255)
cACTGTCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTTGTGGTGtt                                                            >  1:984651/1‑69 (MQ=255)
cACTGTCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTTGTGGTGtt                                                            >  1:95705/1‑69 (MQ=255)
cACTGTCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTTGTGGTGtt                                                            >  1:695149/1‑69 (MQ=255)
cACTGTCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTTGTGGTGtt                                                            >  1:351801/1‑69 (MQ=255)
cACTGTCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTTGTGGTGtt                                                            >  1:3095928/1‑69 (MQ=255)
cACTGTCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTTGTGGTGtt                                                            >  1:2981558/1‑69 (MQ=255)
cACTGTCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTTGTGGTGtt                                                            >  1:2564989/1‑69 (MQ=255)
cACTGTCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTTGTGGTGtt                                                            >  1:1751394/1‑69 (MQ=255)
cACTGTCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTTGTGGTGtt                                                            >  1:1673088/1‑69 (MQ=255)
cACTGTCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTTGTGGTGtt                                                            >  1:1553174/1‑69 (MQ=255)
     tCATGTCTGTGCTCTGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTa                                                       <  1:1086820/69‑1 (MQ=255)
     tCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTa                                                       <  1:959362/69‑1 (MQ=255)
     tCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTa                                                       <  1:2195556/69‑1 (MQ=255)
     tCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTa                                                       <  1:2161344/69‑1 (MQ=255)
     tCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTa                                                       <  1:2148551/69‑1 (MQ=255)
     tCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTa                                                       <  1:1218135/69‑1 (MQ=255)
     tCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTa                                                       <  1:1984462/69‑1 (MQ=255)
     tCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTa                                                       <  1:1208042/69‑1 (MQ=255)
     tCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTa                                                       <  1:2687551/69‑1 (MQ=255)
     tCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTa                                                       <  1:2734884/69‑1 (MQ=255)
     tCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTa                                                       <  1:1871576/69‑1 (MQ=255)
     tCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTa                                                       <  1:281624/69‑1 (MQ=255)
     tCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTa                                                       <  1:1692862/69‑1 (MQ=255)
     tCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTa                                                       <  1:814516/69‑1 (MQ=255)
         gTCTGTGGTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTTGTGGTGTTCGGTAttt                                                    >  1:2066738/1‑68 (MQ=255)
         gTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTTGTGGTGTTCGGTAttt                                                    >  1:3223340/1‑68 (MQ=255)
         gTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTTGTGGTGTTCGGTAttt                                                    >  1:169493/1‑68 (MQ=255)
         gTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTTGTGGTGTTCGGTAttt                                                    >  1:725510/1‑68 (MQ=255)
         gTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTTGTGGTGTTCGGTAttt                                                    >  1:2242764/1‑68 (MQ=255)
         gTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTTGTGGTGTTCGGTAttt                                                    >  1:748439/1‑68 (MQ=255)
         gTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTCTGTGGTGTTCGGTAttt                                                    >  1:584024/1‑68 (MQ=255)
          tCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTg                                                  >  1:1020145/1‑69 (MQ=255)
          tCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTg                                                  >  1:952376/1‑69 (MQ=255)
          tCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTg                                                  >  1:895506/1‑69 (MQ=255)
          tCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTg                                                  >  1:2444247/1‑69 (MQ=255)
          tCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTg                                                  >  1:871104/1‑69 (MQ=255)
          tCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTg                                                  >  1:737365/1‑69 (MQ=255)
          tCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTg                                                  >  1:2688087/1‑69 (MQ=255)
          tCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTg                                                  >  1:2973001/1‑69 (MQ=255)
          tCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTg                                                  >  1:696626/1‑69 (MQ=255)
          tCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTg                                                  >  1:1781628/1‑69 (MQ=255)
          tCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTg                                                  >  1:1297177/1‑69 (MQ=255)
          tCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTg                                                  >  1:1756574/1‑69 (MQ=255)
          tCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTg                                                  <  1:206940/69‑1 (MQ=255)
          tCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTg                                                  >  1:145154/1‑69 (MQ=255)
          tCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTg                                                  >  1:1949851/1‑69 (MQ=255)
                         aCCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCgg                                                         >  1:2165844/1‑47 (MQ=255)
                         aCCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCgg                                                         >  1:117186/1‑47 (MQ=255)
                         aCCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCgg                                                         >  1:250578/1‑47 (MQ=255)
                         aCCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCgg                                                         >  1:2939476/1‑47 (MQ=255)
                           cATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCa                                  <  1:3216199/68‑1 (MQ=255)
                                 tAATACCGAGGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTa                           <  1:2568070/69‑1 (MQ=255)
                                 tAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTa                           <  1:2433703/69‑1 (MQ=255)
                                  aaTACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTa                           <  1:1023794/68‑1 (MQ=255)
                                  aaTACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTa                           <  1:2591872/68‑1 (MQ=255)
                                  aaTACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTa                           <  1:1507896/68‑1 (MQ=255)
                                  aaTACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTa                           <  1:3171983/68‑1 (MQ=255)
                                  aaTACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTa                           <  1:3285150/68‑1 (MQ=255)
                                  aaTACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTa                           <  1:3093313/68‑1 (MQ=255)
                                   aTACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTa                           <  1:829367/67‑1 (MQ=255)
                                     aCCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATg                       >  1:1029560/1‑69 (MQ=255)
                                     aCCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATg                       >  1:2775825/1‑69 (MQ=255)
                                     aCCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATg                       >  1:1843109/1‑69 (MQ=255)
                                      ccGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATgg                      >  1:756574/1‑69 (MQ=255)
                                      ccGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATgg                      >  1:2611575/1‑69 (MQ=255)
                                          cGGCAATATCATCGACTTTGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGcc                  <  1:74808/69‑1 (MQ=255)
                                          cGGCAATATCATCGACTTTGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGcc                  <  1:1637646/69‑1 (MQ=255)
                                          cGGCAATATCATCGACTTTGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGcc                  <  1:1698088/69‑1 (MQ=255)
                                          cGGCAATATCATCGACTTTGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGcc                  <  1:587729/69‑1 (MQ=255)
                                          cGGCAATATCATCGACTTTGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGcc                  <  1:3392734/69‑1 (MQ=255)
                                          cGGCAATATCATCGACTTTGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGcc                  <  1:48388/69‑1 (MQ=255)
                                          cGGCAATATCATCGACTTTGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGcc                  <  1:3191246/69‑1 (MQ=255)
                                          cGGCAATATCATCGACTTTGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGcc                  <  1:2970021/69‑1 (MQ=255)
                                          cGGCAATATCATCGACTTTGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGcc                  <  1:2560536/69‑1 (MQ=255)
                                           ggCAATATCATCGACTTTGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGcc                  <  1:1137769/68‑1 (MQ=255)
                                           ggCAATATCATCGACTTTGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGcc                  <  1:1821025/68‑1 (MQ=255)
                                                    atcGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGCCAgtggtg           >  1:238883/1‑66 (MQ=255)
                                                    atcGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGCCAGTGGTggc         >  1:3213998/1‑68 (MQ=255)
                                                    atcGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGCCAGTGGTggc         >  1:1933844/1‑68 (MQ=255)
                                                    atcGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGCCAGTGGTggc         >  1:2643646/1‑68 (MQ=255)
                                                    atcGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGCCAGTGGTggc         >  1:1322673/1‑68 (MQ=255)
                                                    atcGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGCCAGTGGTggc         >  1:1602728/1‑68 (MQ=255)
                                                    atcGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGCCAGTGGTggc         >  1:1025244/1‑68 (MQ=255)
                                                    atcGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGCCAGTGGTggc         >  1:2084470/1‑68 (MQ=255)
                                                    atcGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGCCAGTGGTggc         >  1:1282363/1‑68 (MQ=255)
                                                       gACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACAt                        <  1:903852/50‑1 (MQ=255)
                                                       gACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACAt                        <  1:2153354/50‑1 (MQ=255)
                                                       gACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACAt                        <  1:383021/50‑1 (MQ=255)
                                                          ttCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGCCAGTGGTGGCGGCAATc  >  1:1271845/1‑69 (MQ=255)
                                                          ttCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGCCAGTGGTGGCGGCAATc  >  1:160156/1‑69 (MQ=255)
                                                          ttCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGCCAGTGGTGGCGGCAATc  >  1:3407869/1‑69 (MQ=255)
                                                          ttCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGCCAGTGGTGGCGGCAATc  >  1:3006373/1‑69 (MQ=255)
                                                          ttCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGCCAGTGGTGGCGGCAATc  >  1:2911660/1‑69 (MQ=255)
                                                          ttCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGCCAGTGGTGGCGGCAATc  >  1:2745334/1‑69 (MQ=255)
                                                          ttCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGCCAGTGGTGGCGGCAATc  >  1:19049/1‑69 (MQ=255)
                                                          ttCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGCCAGTGGTGGCGGCAATc  >  1:2683795/1‑69 (MQ=255)
                                                          ttCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGCCAGTGGTGGCGGCAATc  >  1:1950326/1‑69 (MQ=255)
                                                          ttCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGCCAGTGGTGGCGGCAATc  >  1:1304653/1‑69 (MQ=255)
                                                            |                                                                  
CACCGTCATGTCTGTGCTCGGCGTCACCATCGGTAATACCGACGGCAATATCATCGACTTCGTGGTGTTCGGTATTTTGCATGGTCTGTCAACCAAGTGGTACATGGTGCCAGTGGTGGCGGCAATC  >  minE/1028137‑1028263

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