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 2,082,240 A→G 42.0% E129E (GAA→GAG)  exuR → DNA‑binding transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,082,2400AG42.0% 32.1 / 85.4 112E129E (GAA→GAG) exuRDNA‑binding transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base A (40/25);  new base G (21/26);  total (61/51)
Fisher's exact test for biased strand distribution p-value = 8.68e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.10e-01

Only 100 of 119 total aligned reads displayed.

ATATTGCCGAATTCGCGGCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCACATTCAGGTCGCTCT  >  minE/2082173‑2082308
                                                                   |                                                                    
atatTGCCGAATTCGCGGCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAAc                                                                     >  1:1252138/1‑69 (MQ=255)
atatTGCCGAATTCGCGGCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAAc                                                                     >  1:3261901/1‑69 (MQ=255)
atatTGCCGAATTCGCGGCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAAc                                                                     >  1:1419982/1‑69 (MQ=255)
atatTGCCGAATTCGCGGCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAAc                                                                     >  1:351267/1‑69 (MQ=255)
atatTGCCGAATTCGCGGCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAAc                                                                     >  1:2147959/1‑69 (MQ=255)
atatTGCCGAATTCGCGGCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAAc                                                                     >  1:453347/1‑69 (MQ=255)
atatTGCCGAATTCGCGGCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAAc                                                                     >  1:2834629/1‑69 (MQ=255)
atatTGCCGAATTCGCGGCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAAc                                                                     >  1:2400860/1‑69 (MQ=255)
atatTGCCGAATTCGCGGCAACTCAGGTAAAGAAACAGGACATCATGAAACTGATGGCCATTCAGGAAc                                                                     >  1:221414/1‑69 (MQ=255)
   ttGCCGAATTCGCGGCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAACAgg                                                                  >  1:1173371/1‑69 (MQ=255)
   ttGCCGAATTCGCGGCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAACAgg                                                                  >  1:521724/1‑69 (MQ=255)
   ttGCCGAATTCGCGGCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAACAgg                                                                  >  1:2767975/1‑69 (MQ=255)
   ttGCCGAATTCGCGGCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAACAgg                                                                  >  1:730412/1‑69 (MQ=255)
   ttGCCGAATTCGCGGCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAACAgg                                                                  >  1:3350617/1‑69 (MQ=255)
   ttGCCGAATTCGCGGCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAACAg                                                                   >  1:1124555/1‑68 (MQ=255)
   ttGCCGAATTCGCGGCAACTCAGGTAACGAAACAGGACATCACGAAACTGATGGCCATTCAGGAACAgg                                                                  >  1:3370400/1‑69 (MQ=255)
     gCCGAATTCGCGGCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAACAGgcg                                                                >  1:3247941/1‑69 (MQ=255)
     gCCGAATTCGCGGCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAACAGgcg                                                                >  1:3110826/1‑69 (MQ=255)
     gCCGAATTCGCGGCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAACAGgcg                                                                <  1:1558291/69‑1 (MQ=255)
     gCCGAATTCGCGGCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAACAGgcg                                                                <  1:1460437/69‑1 (MQ=255)
                 gCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACaa                                                    <  1:1056754/69‑1 (MQ=255)
                 gCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACaa                                                    <  1:2664441/69‑1 (MQ=255)
                               gAAACAGGACATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGAtt                                       >  1:1084624/1‑68 (MQ=255)
                               gAAACAGGACATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGAtt                                       >  1:26002/1‑68 (MQ=255)
                                     ggACATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAAc                                                      <  1:2984865/47‑1 (MQ=255)
                                      gACATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTgg                               <  1:1596046/69‑1 (MQ=255)
                                      gACATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTgg                               <  1:2830627/69‑1 (MQ=255)
                                      gACATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTgg                               <  1:1129305/69‑1 (MQ=255)
                                      gACATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTgg                               <  1:419140/69‑1 (MQ=255)
                                       aCATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTggg                              <  1:615664/69‑1 (MQ=255)
                                       aCATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTggg                              <  1:2163157/69‑1 (MQ=255)
                                       aCATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTggg                              <  1:581400/69‑1 (MQ=255)
                                        catcatGAAACTGATGGCCATTCAGGAACAGGcgcgcg                                                            >  1:310430/1‑38 (MQ=255)
                                        catcatGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTggta                             >  1:2619483/1‑67 (MQ=255)
                                        catcatGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGa                             >  1:2909708/1‑69 (MQ=255)
                                        catcatGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGa                             >  1:1077441/1‑69 (MQ=255)
                                        catcatGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGa                             >  1:2571508/1‑69 (MQ=255)
                                        catcatGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGa                             >  1:78802/1‑69 (MQ=255)
                                        catcatGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGa                             >  1:327215/1‑69 (MQ=255)
                                        catcatGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGa                             >  1:493148/1‑69 (MQ=255)
                                        catcatGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGa                             >  1:2975300/1‑69 (MQ=255)
                                        catcatGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGa                             >  1:1425123/1‑69 (MQ=255)
                                            atGAAACTGATGTCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCg                                    <  1:897093/58‑1 (MQ=255)
                                              gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGAt                                        >  1:1862770/1‑52 (MQ=255)
                                              gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                              >  1:2860156/1‑62 (MQ=255)
                                              gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                              >  1:965862/1‑62 (MQ=255)
                                              gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                              >  1:2724999/1‑62 (MQ=255)
                                              gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                              >  1:3174008/1‑62 (MQ=255)
                                              gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                              >  1:3310644/1‑62 (MQ=255)
                                              gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                              >  1:2654411/1‑62 (MQ=255)
                                              gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                              >  1:1943679/1‑62 (MQ=255)
                                              gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                              >  1:1674247/1‑62 (MQ=255)
                                              gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                              >  1:1343991/1‑62 (MQ=255)
                                              gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                              >  1:2148985/1‑62 (MQ=255)
                                              gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                              >  1:1257925/1‑62 (MQ=255)
                                              gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                              >  1:2242124/1‑62 (MQ=255)
                                              gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                              >  1:2349996/1‑62 (MQ=255)
                                              gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                              >  1:119525/1‑62 (MQ=255)
                                              gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                              >  1:1096950/1‑62 (MQ=255)
                                              gAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGc                        <  1:10966/68‑1 (MQ=255)
                                              gAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                       >  1:1350977/1‑69 (MQ=255)
                                                    gATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCca                 >  1:803949/1‑69 (MQ=255)
                                                    gATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCca                 >  1:808419/1‑69 (MQ=255)
                                                    gATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCca                 <  1:2099290/69‑1 (MQ=255)
                                                    gATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCca                 >  1:426725/1‑69 (MQ=255)
                                                    gATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCca                 <  1:365944/69‑1 (MQ=255)
                                                    gATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCca                 <  1:958035/69‑1 (MQ=255)
                                                    gATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCca                 >  1:3244571/1‑69 (MQ=255)
                                                     aTGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGt                                           >  1:2524044/1‑42 (MQ=255)
                                                        gCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGc                        >  1:2955808/1‑58 (MQ=255)
                                                          cATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCACATTc            <  1:1780448/68‑1 (MQ=255)
                                                          cATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCACATTc            <  1:648908/68‑1 (MQ=255)
                                                               aGGAGCTGGCACGCGGTGAACAATGCTTCCTTGATTCCGAGTGGGATTTGCa                       <  1:1991855/52‑1 (MQ=255)
                                                               aGGAGCAGGCACGCGGTTAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                       <  1:421154/52‑1 (MQ=255)
                                                               aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                       <  1:1237763/52‑1 (MQ=255)
                                                               aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                       <  1:2750433/52‑1 (MQ=255)
                                                               aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                       <  1:250911/52‑1 (MQ=255)
                                                               aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                       <  1:933599/52‑1 (MQ=255)
                                                               aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                       <  1:923124/52‑1 (MQ=255)
                                                               aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                       <  1:82005/52‑1 (MQ=255)
                                                               aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                       <  1:24151/52‑1 (MQ=255)
                                                               aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                       <  1:1113778/52‑1 (MQ=255)
                                                               aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                       <  1:658570/52‑1 (MQ=255)
                                                               aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                       <  1:1150740/52‑1 (MQ=255)
                                                               aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                       <  1:1275907/52‑1 (MQ=255)
                                                               aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                       <  1:3013347/52‑1 (MQ=255)
                                                               aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                       <  1:1336637/52‑1 (MQ=255)
                                                               aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                       <  1:3076281/52‑1 (MQ=255)
                                                               aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                       <  1:2032147/52‑1 (MQ=255)
                                                               aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                       <  1:1556659/52‑1 (MQ=255)
                                                               aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                       <  1:3171680/52‑1 (MQ=255)
                                                               aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                       <  1:1836814/52‑1 (MQ=255)
                                                               aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTCGCa                       <  1:2814354/52‑1 (MQ=255)
                                                                ggAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                       <  1:3366081/51‑1 (MQ=255)
                                                                  aaCAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTg                         >  1:569257/1‑47 (MQ=255)
                                                                  aaCAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTg                         >  1:2849703/1‑47 (MQ=255)
                                                                  aaCAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTg                         >  1:1131892/1‑47 (MQ=255)
                                                                  aaCAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTg                         >  1:2362827/1‑47 (MQ=255)
                                                                  aaCAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTg                         >  1:1679382/1‑47 (MQ=255)
                                                                   aCAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCACATTCAGGTCGctct  >  1:3197294/1‑69 (MQ=255)
                                                                   |                                                                    
ATATTGCCGAATTCGCGGCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCACATTCAGGTCGCTCT  >  minE/2082173‑2082308

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