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 843,576 G→A 41.4% L147L (TTG→TTA)  galU → glucose‑1‑phosphate uridylyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE843,5760GA41.4% 43.4 / 75.8 106L147L (TTG→TTA) galUglucose‑1‑phosphate uridylyltransferase
Reads supporting (aligned to +/- strand):  ref base G (31/31);  new base A (28/16);  total (59/47)
Fisher's exact test for biased strand distribution p-value = 1.73e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.41e-01

Only 100 of 106 total aligned reads displayed.

TAGTGGGTGATGAACCGGTAGCTGTTATTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATAGCCAGATCAT  >  minE/843509‑843638
                                                                   |                                                              
tAGTGGGTGATGAACCGGTAGCTGTTATTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGt                                                               >  1:852489/1‑69 (MQ=255)
tAGTGGGTGATGAACCGGTAGCTGTTATTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGt                                                               >  1:3148640/1‑69 (MQ=255)
tAGTGGGTGATGAACCGGTAGCTGTTATTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGt                                                               >  1:1837288/1‑69 (MQ=255)
tAGTGGGTGATGAACCGGTAGCTGTTATTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGt                                                               >  1:2309615/1‑69 (MQ=255)
     ggTGATGAACCGGTAGCTGTTATTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGTCACAg                                                          >  1:2043149/1‑69 (MQ=255)
     ggTGATGAACCGGTAGCTGTTATTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGTCACAg                                                          >  1:424521/1‑69 (MQ=255)
         atgaACCGGTAGCTGTTATTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGTCACAGGATa                                                      <  1:211833/69‑1 (MQ=255)
         atgaACCGGTAGCTGTTATTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGTCACAGGATa                                                      <  1:2076643/69‑1 (MQ=255)
         atgaACCGGTAGCTGTTATTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGTCACAGGATa                                                      <  1:3419877/69‑1 (MQ=255)
         atgaACCGGTAGCTGTTATTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGTCACAGGATa                                                      <  1:866821/69‑1 (MQ=255)
         atgaACCGGTAGCTGTTATTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGTCACAGGATa                                                      <  1:839200/69‑1 (MQ=255)
         atgaACCGGTAGCTGTTATTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGTCACAGGATa                                                      <  1:2715308/69‑1 (MQ=255)
          tgaACCGGTAGCTGTTATTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGTCACAGGATa                                                      <  1:3283317/68‑1 (MQ=255)
           gaACCGGTAGCTGTTATTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGTCACAGGATaa                                                     <  1:3360500/68‑1 (MQ=255)
           gaACCGGTAGCTGTTATTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGTCACAGGATaa                                                     <  1:437408/68‑1 (MQ=255)
           gaACCGGTAGCTGTTATTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGTCACAGGATaa                                                     <  1:375218/68‑1 (MQ=255)
           gaACCGGTAGCTGTTATTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGTCACAGGATaa                                                     <  1:620776/68‑1 (MQ=255)
            aaCCGGTAGCTGTTATTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGTCACAGGATaa                                                     <  1:3425126/67‑1 (MQ=255)
                    gCTGTTATTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGTCACAGGATAACCTGGCagag                                           >  1:563691/1‑69 (MQ=255)
                    gCTGTTATTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGTCACAGGATAACCTGGCagag                                           >  1:2113858/1‑69 (MQ=255)
                       gTTATTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGTCACAGGATAACCTGGCAGAgatg                                        >  1:1134399/1‑69 (MQ=255)
                       gTTATTTTGCCTGACGTTATTCTGGATGAATATGAATCCGATTTGTCACAGGATAACCTGGCAGAgatg                                        >  1:261417/1‑69 (MQ=255)
                       gTTATTTTGCCTGACGTTATTCTGGATGAATATGAATCCGATTTATc                                                              >  1:1430798/1‑47 (MQ=255)
                       gTTATTTTGCCTGACGTTATTCTGGATGAATATGAATCCGATTTATCACAGGATaa                                                     >  1:1919693/1‑56 (MQ=255)
                       gTTATTTTGCCTGACGTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAgatg                                        >  1:2698015/1‑69 (MQ=255)
                       gTTATTTTGCCTGACGTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAgatg                                        >  1:2596275/1‑69 (MQ=255)
                       gTTATTTTGCCTGACGTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAgatg                                        >  1:2783329/1‑69 (MQ=255)
                       gTTATTTTGCCTGACGTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAgatg                                        >  1:3035063/1‑69 (MQ=255)
                       gTTATTTTGCCTGACGTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAgatg                                        >  1:2252101/1‑69 (MQ=255)
                       gTTATTTTGCCTGACGTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAgatg                                        >  1:3319015/1‑69 (MQ=255)
                       gTTATTTTGCCTGACGTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAgatg                                        >  1:2183235/1‑69 (MQ=255)
                       gTTATTTTGCCTGACGTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAgatg                                        >  1:1106835/1‑69 (MQ=255)
                       gTTATTTTGCCTGACGTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAgatg                                        >  1:2169359/1‑69 (MQ=255)
                       gTTATTTTGCCTGACGTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAgatg                                        >  1:106960/1‑69 (MQ=255)
                       gTTATTTTGCCTGACGTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAgatg                                        >  1:1710724/1‑69 (MQ=255)
                       gTTATTTTGCCTGACGTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAgatg                                        >  1:1389171/1‑69 (MQ=255)
                       gTTATTTTGCCTGACGTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAgatg                                        >  1:1520856/1‑69 (MQ=255)
                       gTTATTTTGCCTGACGTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAgatg                                        >  1:162958/1‑69 (MQ=255)
                       gTTATTTTGCCTGACGTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACATGGCAGAgatg                                        >  1:2677236/1‑69 (MQ=255)
                          aTTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGTCACAGGATAACCTGGCAGAgatga                                       <  1:2822806/67‑1 (MQ=255)
                                      gTTATTCTGTATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAGATGATCCGGCGCTTtgat                         <  1:459797/69‑1 (MQ=255)
                                      gTTATTCTGGATTAATATGAATCCGATTTATCACAGGATAACCTGGCAGAGATGATCGGCCGCTTtgat                         <  1:3407745/69‑1 (MQ=255)
                                      gTTATTCTGGATGAATATGAATCCGATTTGTCACAGGATAACCTGGCaga                                            >  1:1331381/1‑50 (MQ=255)
                                      gTTATTCTGGATGAATATGAATCCGATTTGTCACAGGATAACCTGGCaga                                            >  1:2570050/1‑50 (MQ=255)
                                      gTTATTCTGGATGAATATGAATCCGATTTGTCACAGGATAACCTGGCaga                                            >  1:728784/1‑50 (MQ=255)
                                      gTTATTCTGGATGAATATGAATCCGATTTGTAACAGGATAACCTGGCaga                                            >  1:749426/1‑50 (MQ=255)
                                      gTTATTCTGGATGAATATGAATCCGATTTATCACATGATAACCTGGCAGAGATGATCCGCCGCTTtgat                         <  1:59417/69‑1 (MQ=255)
                                      gTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAGATGATCCGCCGCTTtgat                         <  1:2104415/69‑1 (MQ=255)
                                      gTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAGATGATCCGCCGCTTtgat                         <  1:3230498/69‑1 (MQ=255)
                                      gTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAGATGATCCGCCGCTTtgat                         <  1:285050/69‑1 (MQ=255)
                                      gTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAGATGATCCGCCGCTTtgat                         <  1:3302125/69‑1 (MQ=255)
                                      gTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAGATGATCCGCCGCTTtgat                         <  1:1773909/69‑1 (MQ=255)
                                      gTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAGATGATCCGCCGCTTtgat                         <  1:1138445/69‑1 (MQ=255)
                                      gTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAGATGATCCGCCGCTTtgat                         <  1:2421030/69‑1 (MQ=255)
                                      gTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAGATGATCCGCCGCTTtgat                         <  1:355468/69‑1 (MQ=255)
                                      gTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAGATGATCCGCCGCTTtgat                         <  1:1629913/69‑1 (MQ=255)
                                      gTTATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAGATGATCCGCCGCTTtgat                         <  1:3413296/69‑1 (MQ=255)
                                       ttATTCTGGATGAATATGAATCCGATTTATCACAGGATAACCTGGCAGAGATGATCCGCCGCTTtgat                         <  1:356973/68‑1 (MQ=255)
                                        tATTCTGGATGAATATGAATCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTtgatga                       >  1:2449596/1‑69 (MQ=255)
                                         aTTCTGGATGTATATGAATCCGATTTATCACAGGATAACCTGGCAGAGATGATCCGCCGCTTtgat                         <  1:3299957/66‑1 (MQ=255)
                                         aTTCTGGATGAATATGAATCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTtgatga                       <  1:2431758/68‑1 (MQ=255)
                                         aTTCTGGATGAATATGAATCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTtgatga                       <  1:746695/68‑1 (MQ=255)
                                         aTTCTGGATGAATATGAATCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTtgatga                       <  1:2993425/68‑1 (MQ=255)
                                            cTGGATGAATATGAATCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGaaa                     >  1:2357317/1‑67 (MQ=255)
                                            cTGGATGAATATGAATCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACg                   <  1:2845001/69‑1 (MQ=255)
                                            cTGGATGAATATGAATCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACg                   >  1:1286606/1‑69 (MQ=255)
                                            cTGGATGAATATGAATCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACg                   >  1:2828535/1‑69 (MQ=255)
                                            cTGGATGAATATGAATCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACg                   >  1:2383791/1‑69 (MQ=255)
                                            cTGGATGAATATGAATCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACg                   <  1:2474764/69‑1 (MQ=255)
                                            cTGGATGAATATGAATCCGATTTGTAACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACg                   >  1:1665108/1‑69 (MQ=255)
                                              ggATGAATATGAATCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACgg                  <  1:504206/68‑1 (MQ=255)
                                              ggATGAATATGAATCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACgg                  <  1:938294/68‑1 (MQ=255)
                                              ggATGAATATGAATCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACgg                  <  1:2924689/68‑1 (MQ=255)
                                              ggATGAATATGAATCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACgg                  <  1:1981850/68‑1 (MQ=255)
                                                      atgaatCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATa            >  1:1346621/1‑66 (MQ=255)
                                                      atgaatCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATa            >  1:2675941/1‑66 (MQ=255)
                                                      atgaatCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATa            >  1:3399055/1‑66 (MQ=255)
                                                       tgaatCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCttt                            >  1:865732/1‑49 (MQ=255)
                                                       tgaatCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATa            >  1:3330781/1‑65 (MQ=255)
                                                       tgaatCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATa            >  1:659180/1‑65 (MQ=255)
                                                       tgaatCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATa            >  1:560375/1‑65 (MQ=255)
                                                       tgaatCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATa            >  1:2300935/1‑65 (MQ=255)
                                                       tgaatCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATa            >  1:2494922/1‑65 (MQ=255)
                                                       tgaatCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATa            >  1:2568542/1‑65 (MQ=255)
                                                       tgaatCCGATTTATCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATa            >  1:446214/1‑65 (MQ=255)
                                                       tgaatCCGATTTATCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATa            >  1:2344849/1‑65 (MQ=255)
                                                       tgaatCCGATTTATCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATa            >  1:555349/1‑65 (MQ=255)
                                                       tgaatCCGATTTATCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATa            >  1:432413/1‑65 (MQ=255)
                                                       tgaatCCGATTTATCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATa            >  1:1219197/1‑65 (MQ=255)
                                                       tgaatCCGATTTATCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATa            >  1:1627505/1‑65 (MQ=255)
                                                       tgaatCCGATTTATCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATa            >  1:640914/1‑65 (MQ=255)
                                                       tgaatCCGATTTATCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATa            >  1:1435163/1‑65 (MQ=255)
                                                       tgaatCCGATTTATCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATa            >  1:1236632/1‑65 (MQ=255)
                                                       agaatCCGATTTATCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATa            >  1:1476854/2‑65 (MQ=255)
                                                                  tGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATAGCCAGATCAt  <  1:1144085/64‑1 (MQ=255)
                                                                  tGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATAGCCAGATCAt  <  1:1245614/64‑1 (MQ=255)
                                                                  tGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATAGCCAGATCAt  <  1:1342964/64‑1 (MQ=255)
                                                                  tGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATAGCCAGATCAt  <  1:658722/64‑1 (MQ=255)
                                                                  tGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATAGCCAGATCAt  <  1:1815657/64‑1 (MQ=255)
                                                                  tGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATAGCCAGATCAt  <  1:2520706/64‑1 (MQ=255)
                                                                   |                                                              
TAGTGGGTGATGAACCGGTAGCTGTTATTTTGCCTGATGTTATTCTGGATGAATATGAATCCGATTTGTCACAGGATAACCTGGCAGAGATGATCCGCCGCTTTGATGAAACGGGTCATAGCCAGATCAT  >  minE/843509‑843638

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