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 619,623 C→T 33.5% D310D (GAC→GAT)  rpsA → 30S ribosomal subunit protein S1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE619,6230CT33.5% 84.0 / 55.3 104D310D (GAC→GAT) rpsA30S ribosomal subunit protein S1
Reads supporting (aligned to +/- strand):  ref base C (25/44);  new base T (21/14);  total (46/58)
Fisher's exact test for biased strand distribution p-value = 2.37e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.60e-01

Only 100 of 104 total aligned reads displayed.

ACGGCTGCTTCGTTGAAATCGAAGAAGGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGAAGTTAT  >  minE/619562‑619685
                                                             |                                                               
aCGGCTGCTTCGTTGAAATCGAAGAAGGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACca                                                          <  1:3106191/69‑1 (MQ=255)
aCGGCTGCTTCGTTGAAATCGAAGAAGGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACca                                                          <  1:1683428/69‑1 (MQ=255)
aCGGCTGCTTCGTTGAAATCGAAGAAGGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACca                                                          <  1:722298/69‑1 (MQ=255)
aCGGCTGCTTCGTTGAAATCGAAGAAGGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACca                                                          <  1:1734729/69‑1 (MQ=255)
aCGGCTGCTTCGTTGAAATCGAAGAAGGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACca                                                          <  1:1762622/69‑1 (MQ=255)
aCGGCTGCTTCGTTGAAATCGAAGAAGGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACca                                                          <  1:1220991/69‑1 (MQ=255)
aCGGCTGCTTCGTTGAAATCGAAGAAGGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACca                                                          <  1:3330946/69‑1 (MQ=255)
         tCGTTGAAATCGAAGAAGGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACa                                                <  1:791737/69‑1 (MQ=255)
         tCGTTGAAATCGAAGAAGGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACa                                                <  1:1920388/69‑1 (MQ=255)
         tCGTTGAAATCGAAGAAGGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACa                                                <  1:1355821/69‑1 (MQ=255)
         tCGTTGAAATCGAAGAAGGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACa                                                <  1:1287759/69‑1 (MQ=255)
            ttGAAATCGAAGAAGGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATc                                              <  1:2364068/68‑1 (MQ=255)
                    gaagaaGGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTc                                      >  1:1569119/1‑68 (MQ=255)
                    gaagaaGGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTc                                      >  1:2913264/1‑68 (MQ=255)
                    gaagaaGGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTc                                      >  1:2832194/1‑68 (MQ=255)
                    gaagaaGGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTc                                      >  1:80842/1‑68 (MQ=255)
                         agGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAgt                                <  1:1790287/69‑1 (MQ=255)
                         agGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAgt                                <  1:2828783/69‑1 (MQ=255)
                         agGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAgt                                <  1:2896119/69‑1 (MQ=255)
                         agGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAgt                                <  1:1960879/69‑1 (MQ=255)
                         agGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAgt                                <  1:2811421/69‑1 (MQ=255)
                         agGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAgt                                <  1:2621213/69‑1 (MQ=255)
                         agGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAgt                                <  1:1699691/69‑1 (MQ=255)
                         agGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAgt                                <  1:1078085/69‑1 (MQ=255)
                         agGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAgt                                <  1:3358301/69‑1 (MQ=255)
                          ggCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAgtt                               <  1:381374/69‑1 (MQ=255)
                          ggCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAgtt                               <  1:2733966/69‑1 (MQ=255)
                          ggCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAgtt                               <  1:1047562/69‑1 (MQ=255)
                          ggCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAgt                                <  1:2768416/68‑1 (MQ=255)
                           gCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAgtt                               <  1:1489398/68‑1 (MQ=255)
                               tGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTaa                          <  1:13755/69‑1 (MQ=255)
                               tGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTaa                          <  1:201672/69‑1 (MQ=255)
                                       tGGTACACGTTTCCGAAATGGACTGGACCAACAAAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGc                   <  1:175185/69‑1 (MQ=255)
                                          tACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTcc                                     >  1:691798/1‑47 (MQ=255)
                                          tACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGa                 >  1:3152822/1‑67 (MQ=255)
                                          tACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGa                 >  1:2497134/1‑67 (MQ=255)
                                          tACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGa                 >  1:175493/1‑67 (MQ=255)
                                           acacGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAAc                         <  1:2446840/58‑1 (MQ=255)
                                           acacGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAAc                         <  1:311987/58‑1 (MQ=255)
                                           acacGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAAc                         <  1:2755882/58‑1 (MQ=255)
                                           acacGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAAc                         <  1:86358/58‑1 (MQ=255)
                                           acacGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAAc                         <  1:2042197/58‑1 (MQ=255)
                                           acacGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAAc                         <  1:2015725/58‑1 (MQ=255)
                                           acacGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAAc                         <  1:2895823/58‑1 (MQ=255)
                                           acacGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAAc                         <  1:1276147/58‑1 (MQ=255)
                                           acacGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGAt                <  1:3377888/67‑1 (MQ=255)
                                           acacGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGt              <  1:3136531/69‑1 (MQ=255)
                                           acacGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGt              <  1:891071/69‑1 (MQ=255)
                                           acacGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGt              <  1:1006147/69‑1 (MQ=255)
                                            cacGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAAc                         <  1:108249/57‑1 (MQ=255)
                                             acGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAAc                         <  1:650437/56‑1 (MQ=255)
                                               gattCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGt           >  1:2416216/3‑68 (MQ=255)
                                               gTTTCCGAAATGGATTGGACCAAC‑AAAAACATCCCCCCGTCCAAAGTTGTTAACGTTGGCGATGTAGt           >  1:688381/1‑68 (MQ=255)
                                               gTTTCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAg            >  1:1090313/1‑67 (MQ=255)
                                               gTTTCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAg            >  1:336151/1‑67 (MQ=255)
                                               gTTTCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAg            >  1:547139/1‑67 (MQ=255)
                                               gTTTCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGt           >  1:605368/1‑68 (MQ=255)
                                               gTTTCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGt           >  1:3311853/1‑68 (MQ=255)
                                               gTTTCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGt           >  1:1425131/1‑68 (MQ=255)
                                               gTTTCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGt           >  1:3410936/1‑68 (MQ=255)
                                               gTTTCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGt           >  1:1494801/1‑68 (MQ=255)
                                               gTTTCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGt           >  1:2983842/1‑68 (MQ=255)
                                               gTTTCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGt           >  1:739392/1‑68 (MQ=255)
                                               gTTTCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGt           >  1:2069752/1‑68 (MQ=255)
                                               gTTTCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGt           >  1:1043807/1‑68 (MQ=255)
                                               gTTTCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGt           >  1:708052/1‑68 (MQ=255)
                                               gTTTCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGt           >  1:1909778/1‑68 (MQ=255)
                                               gTTTCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGt           >  1:1914971/1‑68 (MQ=255)
                                               gTTTCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGt           >  1:1047941/1‑68 (MQ=255)
                                                 ttCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGa        <  1:663287/69‑1 (MQ=255)
                                                 ttCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGa        <  1:1330020/69‑1 (MQ=255)
                                                 ttCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGa        <  1:824069/69‑1 (MQ=255)
                                                 ttCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGa        <  1:397431/69‑1 (MQ=255)
                                                 ttCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGa        <  1:841211/69‑1 (MQ=255)
                                                 ttCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGa        <  1:3248633/69‑1 (MQ=255)
                                                 ttCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGa        <  1:2210183/69‑1 (MQ=255)
                                                 ttCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGa        <  1:2766791/69‑1 (MQ=255)
                                                 ttCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGa        <  1:1995208/69‑1 (MQ=255)
                                                 ttCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGa        <  1:2847089/69‑1 (MQ=255)
                                                 ttCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGa        <  1:1714858/69‑1 (MQ=255)
                                                 ttCCGAAATGGATTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTAAACGTTGGCGATGTAGTGGa        <  1:2926389/69‑1 (MQ=255)
                                                 ttCCGAAATGGATTGGACCAAC‑AAAAACATCCACACGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGa        <  1:2107174/69‑1 (MQ=255)
                                                  tCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGaa       >  1:1000355/1‑69 (MQ=255)
                                                  tCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGaa       >  1:2324692/1‑69 (MQ=255)
                                                  tCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGaa       >  1:618827/1‑69 (MQ=255)
                                                  tCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGGTGGCGATGTAGTGGaa       >  1:1756442/1‑69 (MQ=255)
                                                        aTGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAAc                         >  1:1159990/1‑45 (MQ=255)
                                                        aTGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAAc                         <  1:1221901/45‑1 (MQ=255)
                                                        aTGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCg                  >  1:1887466/1‑52 (MQ=255)
                                                        aTGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGAAGTTAt  >  1:1553103/1‑68 (MQ=255)
                                                        aTGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGAAGTTAt  >  1:2402777/1‑68 (MQ=255)
                                                        aTGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGAAGTTAt  >  1:2858082/1‑68 (MQ=255)
                                                        aTGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGAAGTTAt  >  1:475575/1‑68 (MQ=255)
                                                        aTGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGAAGTTAt  >  1:432902/1‑68 (MQ=255)
                                                        aTGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGAAGTTAt  >  1:2041528/1‑68 (MQ=255)
                                                        aTGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGAAGTTAt  >  1:75569/1‑68 (MQ=255)
                                                        aTGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGAAGTTAt  >  1:3106572/1‑68 (MQ=255)
                                                        aTGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGAAGTTAt  >  1:2045451/1‑68 (MQ=255)
                                                        aTGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGAAGTTAt  >  1:1473362/1‑68 (MQ=255)
                                                        aTGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGAAGTTAt  >  1:120995/1‑68 (MQ=255)
                                                             |                                                               
ACGGCTGCTTCGTTGAAATCGAAGAAGGCGTTGAAGGCCTGGTACACGTTTCCGAAATGGACTGGACCAAC‑AAAAACATCCACCCGTCCAAAGTTGTTAACGTTGGCGATGTAGTGGAAGTTAT  >  minE/619562‑619685

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