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 1,271,105 A→G 28.6% V384V (GTT→GTC)  yedQ ← predicted diguanylate cyclase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,271,1050AG28.6% 115.3 / 51.8 115V384V (GTT→GTC) yedQpredicted diguanylate cyclase
Reads supporting (aligned to +/- strand):  ref base A (63/19);  new base G (10/23);  total (73/42)
Fisher's exact test for biased strand distribution p-value = 4.76e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.94e-01

Only 100 of 115 total aligned reads displayed.

TAAACGCGTTAAGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACATGGTGGTAAAGAGCGCCCAC  >  minE/1271039‑1271162
                                                                  |                                                         
taAACGCGTTAAGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAAc                                                         >  1:944004/1‑69 (MQ=255)
taAACGCGTTAAGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAAc                                                         >  1:1889794/1‑69 (MQ=255)
taAACGCGTTAAGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAAc                                                         >  1:1372282/1‑69 (MQ=255)
taAACGCGTTAAGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAAc                                                         >  1:771654/1‑69 (MQ=255)
taAACGCGTTAAGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAAc                                                         >  1:854334/1‑69 (MQ=255)
  aaCGCGTTAAGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCa                                                       >  1:1104200/1‑69 (MQ=255)
  aaCGCGTTAAGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCa                                                       >  1:653030/1‑69 (MQ=255)
  aaCGCGTTAAGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCa                                                       >  1:1305773/1‑69 (MQ=255)
  aaCGCGTTAAGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCa                                                       >  1:2402432/1‑69 (MQ=255)
  aaCGCGTTAAGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCa                                                       >  1:408403/1‑69 (MQ=255)
  aaCGCGTTAAGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCa                                                       >  1:2423509/1‑69 (MQ=255)
  aaCGCGTTAAGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCa                                                       >  1:1722906/1‑69 (MQ=255)
  aaCGCGTTAAGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCa                                                       >  1:1547033/1‑69 (MQ=255)
  aaCGCGTTAAGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCa                                                       >  1:1632488/1‑69 (MQ=255)
  aaCGCGTTAAGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCa                                                       >  1:2735333/1‑69 (MQ=255)
  aaCGCGTTAAGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAACCa                                                       <  1:2883224/69‑1 (MQ=255)
    cgcgTTAAGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAACCATc                                                     >  1:3184318/1‑69 (MQ=255)
    cgcgTTAAGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAACCATc                                                     >  1:3126148/1‑69 (MQ=255)
    cgcgTTAAGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAACCATc                                                     >  1:2735730/1‑69 (MQ=255)
        ttAAGGTGTCGTGCCACGCCTGTCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCgg                                                  >  1:1267838/1‑68 (MQ=255)
         tAAGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCg                                                <  1:2413024/69‑1 (MQ=255)
          aaGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGcta                                               >  1:3144339/1‑67 (MQ=255)
          aaGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGa                                               >  1:2699370/1‑69 (MQ=255)
          aaGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGa                                               >  1:2817086/1‑69 (MQ=255)
          aaGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGa                                               >  1:2642817/1‑69 (MQ=255)
          aaGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGa                                               >  1:537440/1‑69 (MQ=255)
          aaGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGa                                               >  1:1970629/1‑69 (MQ=255)
          aaGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGa                                               >  1:107007/1‑69 (MQ=255)
          aaGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGa                                               >  1:1342935/1‑69 (MQ=255)
          aaGGTGTCGTGCCACGACTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGa                                               >  1:2592559/1‑69 (MQ=255)
              tgtCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATca                                           <  1:1387870/69‑1 (MQ=255)
                tCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATcaca                                         <  1:1854971/69‑1 (MQ=255)
                tCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATcaca                                         <  1:156099/69‑1 (MQ=255)
                tCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATcaca                                         <  1:1823407/69‑1 (MQ=255)
                  gTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATcaca                                         >  1:2285915/1‑67 (MQ=255)
                  gTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATCACAt                                        >  1:2759285/1‑68 (MQ=255)
                                aCTGGAACGAGCTTTGCAGAACATACATGTTGCTGACCATCCGGCGAATCACATACCaggagaggag                           <  1:255303/67‑1 (MQ=255)
                                aCTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCATCCGGCGAATCACATACCaggagaggag                           <  1:425659/67‑1 (MQ=255)
                                aCTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCATCCGGCGAATCACATACCaggagaggag                           <  1:3171514/67‑1 (MQ=255)
                                aCTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCATCCGGCGAATCACATACCaggagaggag                           <  1:142782/67‑1 (MQ=255)
                                aCTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCATCCGGCGAATCACATACCaggagaggag                           <  1:1867210/67‑1 (MQ=255)
                                aCTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCATCCGGCGAATCACATACCaggagaggag                           <  1:582026/67‑1 (MQ=255)
                                aCTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCATCCGGCGAATCACATACCaggagaggag                           <  1:3401830/67‑1 (MQ=255)
                                aCTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCATCCGGCGAATCACATACCaggagaggag                           <  1:1526332/67‑1 (MQ=255)
                                aCTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCATCCGGCGAATCACATACCaggagaggag                           <  1:3435775/67‑1 (MQ=255)
                                aCTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCATCCGGCGAATCACATACCaggagaggag                           <  1:1681465/67‑1 (MQ=255)
                                aCTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCATCCGGCGAATCACATACCaggagaggag                           <  1:661271/67‑1 (MQ=255)
                                aCTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCATCCGGCGAATCACATACCaggagaggag                           <  1:739736/67‑1 (MQ=255)
                                aCTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCATCCGGCGAATCACATACCaggagaggag                           <  1:404006/67‑1 (MQ=255)
                                aCTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCATCCGGCGAATCACATACCaggagaggag                           <  1:2596701/67‑1 (MQ=255)
                                aCTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCATCCGGCGAATCACATACCaggagaggag                           <  1:2404894/67‑1 (MQ=255)
                                aCTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCATCCGGCGAATCACATACCaggagaggag                           <  1:1820502/67‑1 (MQ=255)
                                aCTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCATCCGGCGAATCACATACCaggagaggag                           <  1:2424454/67‑1 (MQ=255)
                                aCTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCATCCGGCGAATCACATACCaggagaggag                           <  1:1079283/67‑1 (MQ=255)
                                aCTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCATCCGGCGAATCACATACCaggagaggag                           <  1:2478865/67‑1 (MQ=255)
                                aCTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCATCCGGCGAATCACATACCaggagaggag                           <  1:2508756/67‑1 (MQ=255)
                                aCTGCAACGAGCTTTGCAGAACATACATGTTGCTGACCATCCGGCGAATCACATACCaggagaggag                           <  1:1824080/67‑1 (MQ=255)
                                   gCAACGAGCTTTGCAGAACATACATGTTGCTAATCATCCGGCGAATCACATACCAGGAGATGAGTAACa                      >  1:3427024/1‑69 (MQ=255)
                                   gCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGga                                 <  1:1507802/58‑1 (MQ=255)
                                   gCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGga                                 <  1:849515/58‑1 (MQ=255)
                                   gCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACa                      >  1:319243/1‑69 (MQ=255)
                                   gCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACa                      >  1:1404849/1‑69 (MQ=255)
                                   gCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACa                      >  1:350364/1‑69 (MQ=255)
                                   gCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACa                      >  1:2216208/1‑69 (MQ=255)
                                   gCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACa                      >  1:2259258/1‑69 (MQ=255)
                                   gCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACa                      >  1:745354/1‑69 (MQ=255)
                                   gCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACa                      >  1:3096920/1‑69 (MQ=255)
                                   gCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACa                      >  1:3010803/1‑69 (MQ=255)
                                   gCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACa                      >  1:2768340/1‑69 (MQ=255)
                                   gCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACa                      >  1:2764492/1‑69 (MQ=255)
                                   gCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACa                      >  1:1146338/1‑69 (MQ=255)
                                   gCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACa                      >  1:2723162/1‑69 (MQ=255)
                                   gCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACa                      >  1:627892/1‑69 (MQ=255)
                                   gCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACa                      >  1:687808/1‑69 (MQ=255)
                                   gCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACa                      >  1:2603883/1‑69 (MQ=255)
                                   gCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGG‑GAATCACATACCAGGAGATGAGTAACa                      >  1:2633746/1‑68 (MQ=255)
                                   gCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGG‑GAATCACATACCAGGAGATGAGTAACAt                     >  1:2207659/1‑69 (MQ=255)
                                             ttGCAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACATGGTGGTa              <  1:897840/67‑1 (MQ=255)
                                                cAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTaa                        >  1:567267/1‑54 (MQ=255)
                                                cAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTaa                        >  1:881010/1‑54 (MQ=255)
                                                cAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACAAGGTGGTAAag           <  1:1012131/67‑1 (MQ=255)
                                                cAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGGACATGAGTaa                        >  1:2715607/1‑54 (MQ=255)
                                                    acatacatGTTGCTAACCATCCGGCGAATCACATACCAGga                                 <  1:1885339/41‑1 (MQ=255)
                                                    acatacatGTTGCTAACCATCCGGCGAATCACATACCAGga                                 <  1:318065/41‑1 (MQ=255)
                                                    acatacatGTTGCTAACCATCCGGCGAATCACATACCAGga                                 <  1:2997979/41‑1 (MQ=255)
                                                    acatacatGTTGCTAACCATCCGGCGAATCACATACCAGga                                 <  1:367869/41‑1 (MQ=255)
                                                    acatacatGTTGCTAACCATCCGGCGAATCACATACCAGga                                 <  1:1748335/41‑1 (MQ=255)
                                                    acatacatGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACATGGTGGTAAAGAGCGcc     <  1:1270566/69‑1 (MQ=255)
                                                    acatacatGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACATGGTGGTAAAGAGCGcc     <  1:2308697/69‑1 (MQ=255)
                                                    acatacatGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACATGGTGGTAAAGAGCGcc     <  1:778421/69‑1 (MQ=255)
                                                    acatacatGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACATGGTGGTAAAGAGCGcc     <  1:1757603/69‑1 (MQ=255)
                                                     catacatGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACATGGTGGTAAAGAgcgc      >  1:1981596/1‑67 (MQ=255)
                                                     catacatGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACATGGTGGTAAAGAGCGcc     >  1:711453/1‑68 (MQ=255)
                                                     catacatGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACATGGTGGTAAAGAGCGcc     >  1:193791/1‑68 (MQ=255)
                                                     catacatGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACATGGTGGTAAAGAGCGcc     >  1:2598609/1‑68 (MQ=255)
                                                     catacatGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACATGGTGGTAAAGAGCGcc     >  1:2688143/1‑68 (MQ=255)
                                                     catacatGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACATGGTGGTAAAGAGCGcc     >  1:3400854/1‑68 (MQ=255)
                                                     catacatGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACATGATGGTAAAGAGCGcc     >  1:2056348/1‑68 (MQ=255)
                                                         catGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACATGGTGGTAAAGAGCGCCcac  >  1:1409144/1‑67 (MQ=255)
                                                         catGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACATGGTGGTAAAGAGCGCCca   >  1:169667/1‑66 (MQ=255)
                                                                  |                                                         
TAAACGCGTTAAGGTGTCGTGCCACGCCTGCCACTGCAACGAGCTTTGCAGAACATACATGTTGCTAACCATCCGGCGAATCACATACCAGGAGATGAGTAACATGGTGGTAAAGAGCGCCCAC  >  minE/1271039‑1271162

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