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 2,677,561 G→A 24.8% Y123Y (TAC→TAT)  yhgA ← predicted transposase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,677,5610GA24.8% 104.1 / 28.1 84Y123Y (TAC→TAT) yhgApredicted transposase
Reads supporting (aligned to +/- strand):  ref base G (42/21);  new base A (13/8);  total (55/29)
Fisher's exact test for biased strand distribution p-value = 7.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.31e-01

TGGGATCGGCGAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGCGGC  >  minE/2677500‑2677629
                                                             |                                                                    
tGGGATCGGCGAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAaaca                                                               <  1:2656435/69‑1 (MQ=255)
   gATCGGCGAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAaacaac                                                             <  1:1181620/68‑1 (MQ=255)
   gATCGGCGAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAaacaac                                                             <  1:2791742/68‑1 (MQ=255)
   gATCGGCGAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAaacaac                                                             <  1:2202842/68‑1 (MQ=255)
       ggCGAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGATAAAACAACAATgg                                                        <  1:3056752/69‑1 (MQ=255)
         cGAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGATAAAACAACAATGGc                                                       <  1:107092/68‑1 (MQ=255)
         cGAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGATAAAACAACAATGGc                                                       <  1:327068/68‑1 (MQ=255)
         cGAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGATAAAACAACAATGGc                                                       <  1:3326128/68‑1 (MQ=255)
         cGAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGATAAAACAACAATGGc                                                       <  1:2832388/68‑1 (MQ=255)
         cGAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGATAAAACAACAATGGc                                                       <  1:1870963/68‑1 (MQ=255)
         cGAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGATAAAACAACAATGGc                                                       <  1:182406/68‑1 (MQ=255)
         cGAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGATAAAACAACAATGGc                                                       <  1:876281/68‑1 (MQ=255)
          gAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGATAAAACAACAATgg                                                        >  1:639395/1‑66 (MQ=255)
          gAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGATAAAACAACAATGGcac                                                     >  1:2297393/1‑69 (MQ=255)
          gAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGATAAAACAACAATGGcac                                                     >  1:1530141/1‑69 (MQ=255)
          gAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGATAAAACAACAATGGcac                                                     >  1:2222608/1‑69 (MQ=255)
          gAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGATAAAACAACAATGGcac                                                     >  1:24369/1‑69 (MQ=255)
          gAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGATAAAACAACAATGGcac                                                     >  1:1198805/1‑69 (MQ=255)
          gAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGATAAAACAACAATGGcac                                                     >  1:279027/1‑69 (MQ=255)
          gAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGATAAAACAACAATGGcac                                                     >  1:681280/1‑69 (MQ=255)
          gAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGATAAAACAACAATGGcac                                                     >  1:780541/1‑69 (MQ=255)
          gAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGATAAAACAACAATGGcac                                                     >  1:48660/1‑69 (MQ=255)
          gAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGATAAAACAACAATGGcac                                                     >  1:3136161/1‑69 (MQ=255)
          gAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGATAAAACAACAATGGcac                                                     >  1:2786813/1‑69 (MQ=255)
          gAAACAATCCAGCCAACACAGCGAATAGGAATAGGGGCTTTCAATACCGTGATAAAACAACAATGGcac                                                     >  1:663010/1‑69 (MQ=255)
           aaaCAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGcacc                                                    <  1:3372904/69‑1 (MQ=255)
           aaaCAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGcacc                                                    <  1:1700981/69‑1 (MQ=255)
             aCAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGcaccac                                                  >  1:1753795/1‑69 (MQ=255)
             aCAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGcaccac                                                  >  1:3078290/1‑69 (MQ=255)
             aCAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGcaccac                                                  >  1:2422638/1‑69 (MQ=255)
             aCAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGcacca                                                   >  1:2306899/1‑68 (MQ=255)
                  ccAGCCAACAGAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATc                                              >  1:114456/1‑68 (MQ=255)
                  ccAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATc                                              >  1:1862614/1‑68 (MQ=255)
                  ccAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATc                                              >  1:1248316/1‑68 (MQ=255)
                  ccAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATc                                              >  1:343445/1‑68 (MQ=255)
                  ccAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATc                                              >  1:3116783/1‑68 (MQ=255)
                  ccAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATc                                              >  1:239000/1‑68 (MQ=255)
                  ccAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATc                                              >  1:1386184/1‑68 (MQ=255)
                       cAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATCGGCAAc                                        >  1:822048/1‑69 (MQ=255)
                       cAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATCGGCAAc                                        >  1:2879657/1‑69 (MQ=255)
                       cAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATCGGCAAc                                        >  1:2971591/1‑69 (MQ=255)
                       cAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATCGGCAAc                                        >  1:1489474/1‑69 (MQ=255)
                       cAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATCGGCAAc                                        >  1:1087800/1‑69 (MQ=255)
                       cAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATCGGCAAc                                        >  1:1796570/1‑69 (MQ=255)
                       cAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATCGGCAAc                                        >  1:1888818/1‑69 (MQ=255)
                           acaGCGAATAGGGATAGGGGCTTTCAATAGCGTGGTAAAACAACAATGGCACCACCATCGGCAACGtt                                     >  1:1596671/1‑68 (MQ=255)
                           acaGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATCGGCAACGttt                                    >  1:442254/1‑69 (MQ=255)
                           acaGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATCGGCAACGttt                                    >  1:1563480/1‑69 (MQ=255)
                           acaGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATCGGCAACGttt                                    >  1:1640555/1‑69 (MQ=255)
                           acaGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATCGGCAACGttt                                    >  1:25887/1‑69 (MQ=255)
                           acaGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATCGGCAACGttt                                    >  1:2533380/1‑69 (MQ=255)
                           acaGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATCGGCAACGttt                                    >  1:2487347/1‑69 (MQ=255)
                           acaGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATCGGCAACGttt                                    >  1:1956215/1‑69 (MQ=255)
                           acaGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATCGGCAACGttt                                    >  1:1213775/1‑69 (MQ=255)
                                    agggatagggGCTTTCAATACCGTGGTAAAACAACAATGGCTCCACCATCGGc                                           <  1:3029017/53‑1 (MQ=255)
                                    agggatagggGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATCGGc                                           <  1:195474/53‑1 (MQ=255)
                                    agggatagggGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATCGGc                                           <  1:732924/53‑1 (MQ=255)
                                    agggatagggGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATCGGc                                           <  1:2307448/53‑1 (MQ=255)
                                                     aTACCGTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTg           <  1:2323126/68‑1 (MQ=255)
                                                     aTACCGTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTg           <  1:3345851/68‑1 (MQ=255)
                                                     aTACCGTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTg           <  1:3044302/68‑1 (MQ=255)
                                                     aTACCGTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTg           <  1:2970697/68‑1 (MQ=255)
                                                     aTACCGTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTg           <  1:341245/68‑1 (MQ=255)
                                                     aTACCGTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTg           <  1:2226543/68‑1 (MQ=255)
                                                     aTACCGTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTg           <  1:2195970/68‑1 (MQ=255)
                                                     aTACCGTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTg           <  1:2062678/68‑1 (MQ=255)
                                                     aTACCGTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTg           <  1:464241/68‑1 (MQ=255)
                                                     aTACCGTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTg           <  1:635354/68‑1 (MQ=255)
                                                     aTACCGTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTg           <  1:72413/68‑1 (MQ=255)
                                                          gTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGAt               >  1:3228086/1‑59 (MQ=255)
                                                          gTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGc     >  1:3377629/1‑69 (MQ=255)
                                                          gTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGc     >  1:462357/1‑69 (MQ=255)
                                                          gTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGc     >  1:3288122/1‑69 (MQ=255)
                                                          gTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGc     >  1:881710/1‑69 (MQ=255)
                                                          gTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGc     >  1:1641209/1‑69 (MQ=255)
                                                          gTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGc     >  1:1647084/1‑69 (MQ=255)
                                                          gTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGc     >  1:289403/1‑69 (MQ=255)
                                                          gTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGc     >  1:2727277/1‑69 (MQ=255)
                                                          gTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGc     >  1:2654908/1‑69 (MQ=255)
                                                          gTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGc     >  1:1197977/1‑69 (MQ=255)
                                                          gTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGc     >  1:2044198/1‑69 (MQ=255)
                                                          gTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGc     >  1:1259466/1‑69 (MQ=255)
                                                          gTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGc     >  1:3239825/1‑69 (MQ=255)
                                                          gTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGc     >  1:1755558/1‑69 (MQ=255)
                                                             gTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCAt        >  1:2824855/1‑63 (MQ=255)
                                                             gTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGCgg   >  1:1071245/1‑68 (MQ=255)
                                                             gTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGCgg   >  1:1677182/1‑68 (MQ=255)
                                                             gTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGCgg   >  1:3032676/1‑68 (MQ=255)
                                                             gTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGCGGc  >  1:1197433/1‑69 (MQ=255)
                                                             gTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGCGGc  >  1:498139/1‑69 (MQ=255)
                                                             gTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGCGGc  >  1:1544800/1‑69 (MQ=255)
                                                             gTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGCGGc  >  1:1616701/1‑69 (MQ=255)
                                                             gTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGCGGc  >  1:1823277/1‑69 (MQ=255)
                                                             gTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGCGGc  >  1:2413567/1‑69 (MQ=255)
                                                             gTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGCGGc  >  1:2890372/1‑69 (MQ=255)
                                                             gTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGCGGc  >  1:319826/1‑69 (MQ=255)
                                                             |                                                                    
TGGGATCGGCGAAACAATCCAGCCAACACAGCGAATAGGGATAGGGGCTTTCAATACCGTGGTAAAACAACAATGGCACCACCATCGGCAACGTTTTGTATCCAGCATCAAGGTGATTTTGCATTGCGGC  >  minE/2677500‑2677629

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A