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 2,082,252 C→T 48.9% G133G (GGC→GGT)  exuR → DNA‑binding transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,082,2520CT48.9% 1.5 / 86.7 96G133G (GGC→GGT) exuRDNA‑binding transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base C (27/22);  new base T (21/26);  total (48/48)
Fisher's exact test for biased strand distribution p-value = 4.14e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.41e-01

Only 100 of 137 total aligned reads displayed.

GCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCACATTCAGGTCGCTCTGGCGACGCAGAA  >  minE/2082190‑2082320
                                                              |                                                                    
gCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACaa                                                                <  1:1056754/69‑1 (MQ=255)
                    ggACATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAAc                                                                  <  1:2984865/47‑1 (MQ=255)
                     gACATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTgg                                           <  1:1596046/69‑1 (MQ=255)
                     gACATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTgg                                           <  1:2830627/69‑1 (MQ=255)
                     gACATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTgg                                           <  1:419140/69‑1 (MQ=255)
                     gACATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTgg                                           <  1:1129305/69‑1 (MQ=255)
                      aCATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTggg                                          <  1:2163157/69‑1 (MQ=255)
                      aCATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTggg                                          <  1:581400/69‑1 (MQ=255)
                      aCATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTggg                                          <  1:615664/69‑1 (MQ=255)
                       catcatGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTggta                                         >  1:2619483/1‑67 (MQ=255)
                       catcatGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGa                                         >  1:493148/1‑69 (MQ=255)
                       catcatGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGa                                         >  1:327215/1‑69 (MQ=255)
                       catcatGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGa                                         >  1:2909708/1‑69 (MQ=255)
                       catcatGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGa                                         >  1:1077441/1‑69 (MQ=255)
                           atGAAACTGATGTCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCg                                                <  1:897093/58‑1 (MQ=255)
                           atGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCg                                                <  1:2809872/58‑1 (MQ=255)
                           atGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCg                                                <  1:1525427/58‑1 (MQ=255)
                           atGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCg                                                <  1:2632173/58‑1 (MQ=255)
                             gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGAt                                                    >  1:1862770/1‑52 (MQ=255)
                             gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                                          >  1:2654411/1‑62 (MQ=255)
                             gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                                          >  1:540224/1‑62 (MQ=255)
                             gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                                          >  1:2501974/1‑62 (MQ=255)
                             gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                                          >  1:2242124/1‑62 (MQ=255)
                             gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                                          >  1:965862/1‑62 (MQ=255)
                             gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                                          >  1:2148985/1‑62 (MQ=255)
                             gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                                          >  1:1943679/1‑62 (MQ=255)
                             gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                                          >  1:2724999/1‑62 (MQ=255)
                             gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                                          >  1:1096950/1‑62 (MQ=255)
                             gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                                          >  1:1343991/1‑62 (MQ=255)
                             gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                                          >  1:1327047/1‑62 (MQ=255)
                             gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                                          >  1:1674247/1‑62 (MQ=255)
                             gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                                          >  1:1257925/1‑62 (MQ=255)
                             gAAATTGATGGCCATTCAGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTggg                                          >  1:119525/1‑62 (MQ=255)
                             gAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGc                                    <  1:10966/68‑1 (MQ=255)
                             gAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                                   >  1:1350977/1‑69 (MQ=255)
                                   gATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCca                             <  1:958035/69‑1 (MQ=255)
                                   gATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCca                             <  1:365944/69‑1 (MQ=255)
                                   gATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCca                             >  1:803949/1‑69 (MQ=255)
                                   gATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCca                             <  1:2099290/69‑1 (MQ=255)
                                   gATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCca                             >  1:426725/1‑69 (MQ=255)
                                    aTGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGt                                                       >  1:2524044/1‑42 (MQ=255)
                                       gCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGc                                    >  1:2955808/1‑58 (MQ=255)
                                         cATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCACATTc                        <  1:1780448/68‑1 (MQ=255)
                                              aGGAGCTGGCACGCGGTGAACAATGCTTCCTTGATTCCGAGTGGGATTTGCa                                   <  1:1991855/52‑1 (MQ=255)
                                              aGGAGCAGGCACGCGGTTAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                                   <  1:421154/52‑1 (MQ=255)
                                              aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                                   <  1:3013347/52‑1 (MQ=255)
                                              aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                                   <  1:658570/52‑1 (MQ=255)
                                              aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                                   <  1:1275907/52‑1 (MQ=255)
                                              aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                                   <  1:3076281/52‑1 (MQ=255)
                                              aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                                   <  1:2875035/52‑1 (MQ=255)
                                              aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                                   <  1:1113778/52‑1 (MQ=255)
                                              aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                                   <  1:3171680/52‑1 (MQ=255)
                                              aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                                   <  1:1150740/52‑1 (MQ=255)
                                              aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                                   <  1:2750433/52‑1 (MQ=255)
                                              aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                                   <  1:1836814/52‑1 (MQ=255)
                                              aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                                   <  1:2032147/52‑1 (MQ=255)
                                              aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                                   <  1:2170298/52‑1 (MQ=255)
                                              aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                                   <  1:933599/52‑1 (MQ=255)
                                              aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                                   <  1:923124/52‑1 (MQ=255)
                                              aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                                   <  1:24151/52‑1 (MQ=255)
                                              aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                                   <  1:250911/52‑1 (MQ=255)
                                              aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                                   <  1:876035/52‑1 (MQ=255)
                                              aGGAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                                   <  1:82005/52‑1 (MQ=255)
                                               ggAGCAGGCACGCGGTGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCa                                   <  1:3366081/51‑1 (MQ=255)
                                                 aaCAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTg                                     >  1:1679382/1‑47 (MQ=255)
                                                 aaCAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTg                                     >  1:2849703/1‑47 (MQ=255)
                                                 aaCAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTg                                     >  1:1131892/1‑47 (MQ=255)
                                                 aaCAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTg                                     >  1:3238933/1‑47 (MQ=255)
                                                 aaCAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTg                                     >  1:569257/1‑47 (MQ=255)
                                                 aaCAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTg                                     >  1:2362827/1‑47 (MQ=255)
                                                  aCAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCACATTCAGGTCGctct              >  1:3197294/1‑69 (MQ=255)
                                                           cggtgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCATATTCAGGTATCCCTGGCGACGCa     <  1:3322728/69‑1 (MQ=255)
                                                           cggtgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCATATTCAGGTAGCCCTGGCGACGCa     <  1:1127537/69‑1 (MQ=255)
                                                           cggtgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCATATTCAGGTAGCCCTGGCGACGCa     <  1:823430/69‑1 (MQ=255)
                                                           cggtgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCATATTCAGGTAGCCCTGGCGACGCa     <  1:1057119/69‑1 (MQ=255)
                                                           cggtgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCATATTCAGGTAGCCCTGGCGACGCa     <  1:683920/69‑1 (MQ=255)
                                                           cggtgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCATATTCAGGTAGCCCTGGCGACGCa     <  1:1805016/69‑1 (MQ=255)
                                                           cggtgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCATATTCAGGTAGCCCTGGCGACGCa     <  1:1778253/69‑1 (MQ=255)
                                                           cggtgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCATATTCAGGTAGCCCTGGCGACGCa     <  1:2581202/69‑1 (MQ=255)
                                                           cggtgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCATATTCAGGTAGCCCTGGCGACGCa     <  1:2420203/69‑1 (MQ=255)
                                                           cggtgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCATATTCAGGTAGCCCTGGCGACGCa     <  1:1534861/69‑1 (MQ=255)
                                                           cggtgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCATATTCAGGTAGCCCTGGCGACGCa     <  1:2679548/69‑1 (MQ=255)
                                                           cggtgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCATATTCAGGTAGCCCTGGCGACGCa     <  1:3416159/69‑1 (MQ=255)
                                                           cggtgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCATATTCAGGTAGCCCTGGCGACGCa     <  1:2783634/69‑1 (MQ=255)
                                                           cggtgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCATATTCAGGTAGCCCTGGCGACGCa     <  1:3216775/69‑1 (MQ=255)
                                                           cggtgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCATATTCAGGTAGCCCTGGCGACGCa     <  1:2175871/69‑1 (MQ=255)
                                                           cggtgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCATATTCAGGTAGCCCTGGCGACGCa     <  1:32909/69‑1 (MQ=255)
                                                           cggtgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCATATTCAGGTAGCCCTGGCGACGCa     <  1:3308590/69‑1 (MQ=255)
                                                           cggtgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCATATCCAGGTAGCCCTGGCGACGCa     <  1:3127360/69‑1 (MQ=255)
                                                            ggcgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCACATTCAGGTCGCTCTGGCGACGCAg    <  1:501167/69‑1 (MQ=255)
                                                            ggcgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCACATTCAGGTCGCTCTGGCGACGCAg    <  1:793969/69‑1 (MQ=255)
                                                            ggcgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCACATTCAGGTCGCTCTGGCGACGCAg    <  1:1374434/69‑1 (MQ=255)
                                                            ggcgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCACATTCAGGTCGCTCTGGCGACGCAg    <  1:498968/69‑1 (MQ=255)
                                                            ggcgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCACATTCAGGTCGCTCTGGCGACGCAg    <  1:1793970/69‑1 (MQ=255)
                                                              cgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCACATTCAGGTCGCTCTGGCGACGCAGaa  <  1:665164/69‑1 (MQ=255)
                                                              cgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCACATTCAGGTCGCTCTGGCGACGCAGaa  <  1:2584101/69‑1 (MQ=255)
                                                              cgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCACATTCAGGTCGCTCTGGCGACGCAGaa  <  1:2793465/69‑1 (MQ=255)
                                                              cgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCACATTCAGGTCGCTCTGGCGACGCAGaa  <  1:562389/69‑1 (MQ=255)
                                                              cgAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCACATTCAGGTCGCTCTGGCGACGCAGaa  <  1:3313315/69‑1 (MQ=255)
                                                              cgAACAATGCTTCCGTAATTCCGAGTGGGATTTGCAGTTCCACATTCAGGTCGCTCTGGCGACGCAGaa  <  1:2347959/69‑1 (MQ=255)
                                                              |                                                                    
GCAACTCAGGTAACGAAACAGGACATCATGAAACTGATGGCCATTCAGGAACAGGCGCGCGGCGAACAATGCTTCCGTGATTCCGAGTGGGATTTGCAGTTCCACATTCAGGTCGCTCTGGCGACGCAGAA  >  minE/2082190‑2082320

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