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 975,534 C→T 35.0% V27V (GTG→GTA)  ydeH ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE975,5340CT35.0% 83.4 / 62.5 111V27V (GTG→GTA) ydeHconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (51/21);  new base T (22/17);  total (73/38)
Fisher's exact test for biased strand distribution p-value = 1.46e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 111 total aligned reads displayed.

AGAATGGTTATCCGTTATTTCTGGCTTACTGGCATCTCTCGCGACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTCCGTT  >  minE/975471‑975600
                                                               |                                                                  
aGAATGGTTATCCGTTATTTCTGGCTTACTGGCATCTCTCGCGACCACGCTGTGAAACATACTCAcc                                                                 >  1:3121903/1‑67 (MQ=255)
aGAATGGTTATCCGTTATTTCTGGCTTACTGGCATCTCTCGCGACCACGCTGTGAAACATACTCACCa                                                                >  1:2040065/1‑68 (MQ=255)
aGAATGGTTATCCGTTATTTCTGGCTTACTGGCATCTCTCGCGACCACGCTGTGAAACATACTCACCa                                                                >  1:620745/1‑68 (MQ=255)
aGAATGGTTATCCGTTATTTCTGGCTTACTGGCATCTCTCGCGACCACGCTGTGAAACATACTCACCa                                                                >  1:2679419/1‑68 (MQ=255)
aGAATGGTTATCCGTTATTTCTGGCTTACTGGCATCTCTCGCGACCACGCTGTGAAACATACTCACCa                                                                >  1:3004731/1‑68 (MQ=255)
aGAATGGTTATCCGTTATTTCTGGCTTACTGGCATCTCTCGCGACCACGCTGTGAAACATACTCACCa                                                                >  1:1221856/1‑68 (MQ=255)
      gTTATCCGTTATTTCTGGCTTACTGGCATCTCTCGCGACCACGCTGTGAAACATACTCACCAGCCACt                                                          >  1:2627959/1‑68 (MQ=255)
      gTTATCCGTTATTTCTGGCTTACTGGCATCTCTCGCGACCACGCTGTGAAACATACTCACCAGCCACt                                                          >  1:1979414/1‑68 (MQ=255)
        tATCCGTTATTTCTGGCTTACTGGCATCTCTCGCGACCACGCTGTGAAACATACTCACCAGCCACTGGt                                                       <  1:620449/69‑1 (MQ=255)
        tATCCGTTATTTCTGGCTTACTGGCATCTCTCGCGACCACGCTGTGAAACATACTCACCAGCCACTGGt                                                       <  1:2124409/69‑1 (MQ=255)
        tATCCGTTATTTCTGGCTTACTGGCATCTCTCGCGACCACGCTGTGAAACATACTCACCAGCCACTGGt                                                       <  1:1148763/69‑1 (MQ=255)
               tATTTCTGGCTTACTGGCATCTCTCGCGACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGc                                                <  1:2544601/69‑1 (MQ=255)
               tATTTCTGGCTTACTGGCATCTCTCGCGACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGc                                                <  1:3179641/69‑1 (MQ=255)
               tATTTCTGGCTTACTGGCATCTCTCGCGACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGc                                                <  1:602080/69‑1 (MQ=255)
                         ttACTGGCATCTCTCGCGACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGc                                       <  1:1723505/68‑1 (MQ=255)
                          tACTGGCATCTCTCGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:391906/69‑1 (MQ=255)
                          tACTGGCATCTCTCGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:1859257/69‑1 (MQ=255)
                          tACTGGCATCTCTCGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:2282896/69‑1 (MQ=255)
                          tACTGGCATCTCTCGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:1110532/69‑1 (MQ=255)
                          tACTGGCATCTCTCGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:2295678/69‑1 (MQ=255)
                          tACTGGCATCTCTCGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:2555390/69‑1 (MQ=255)
                          tACTGGCATCTCTCGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:2593419/69‑1 (MQ=255)
                          tACTGGCATCTCTCGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:2615665/69‑1 (MQ=255)
                          tACTGGCATCTCTCGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:641739/69‑1 (MQ=255)
                          tACTGGCATCTCTCGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:1186881/69‑1 (MQ=255)
                          tACTGGCATCTCTCGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:1428924/69‑1 (MQ=255)
                          tACTGGCATCTCTCGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:1454752/69‑1 (MQ=255)
                          tACTGGCATCTCTCGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:1513669/69‑1 (MQ=255)
                          tACTGGCATCTCTCGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:732261/69‑1 (MQ=255)
                           aCTGGCATCTCTCGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:2705280/68‑1 (MQ=255)
                           aCTGGCATCTCTCGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:609071/68‑1 (MQ=255)
                                cATCTCTCGCGACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGc                                                <  1:2511629/52‑1 (MQ=255)
                                   ctctcGGGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTgaga                             >  1:3012473/1‑68 (MQ=255)
                                   ctctcGCGACCACGCTGTGAAACATACTTACCAGCCACTgg                                                        >  1:471256/1‑41 (MQ=255)
                                   ctctcGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCa                                               >  1:632335/1‑50 (MQ=255)
                                   ctctcGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGa                                           >  1:447853/1‑54 (MQ=255)
                                   ctctcGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTgaga                             >  1:755972/1‑68 (MQ=255)
                                   ctctcGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTgaga                             >  1:644451/1‑68 (MQ=255)
                                   ctctcGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTgaga                             >  1:1731584/1‑68 (MQ=255)
                                   ctctcGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTgaga                             >  1:2825186/1‑68 (MQ=255)
                                   ctctcGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTgaga                             >  1:2934410/1‑68 (MQ=255)
                                   ctctcGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTgaga                             >  1:1119948/1‑68 (MQ=255)
                                   ctctcGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTgaga                             >  1:2618422/1‑68 (MQ=255)
                                   ctctcGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTgaga                             >  1:2286836/1‑68 (MQ=255)
                                   ctctcGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTgaga                             >  1:3035012/1‑68 (MQ=255)
                                   ctctcGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTgaga                             >  1:2207157/1‑68 (MQ=255)
                                   ctctcGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTgaga                             >  1:1475240/1‑68 (MQ=255)
                                   ctctcGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTgaga                             >  1:355359/1‑68 (MQ=255)
                                   ctctcGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTgaga                             >  1:1562731/1‑68 (MQ=255)
                                   ctctcGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTgaga                             >  1:1602338/1‑68 (MQ=255)
                                   ctctcGCGACCACGCTGTGAAACATACTTACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTgaga                             >  1:587070/1‑68 (MQ=255)
                                   ctctcGCGACCACGCTGTGAAACATACTTACCAGCAACTGGTAGTGGGCATCGATAGCCTTATTgaga                             >  1:3319959/1‑68 (MQ=255)
                                    tctcGCGACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGAt                            >  1:1845008/1‑68 (MQ=255)
                                        gcgACCACGCTGTGAAACTTACTCACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:2286511/55‑1 (MQ=255)
                                        gcgACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAg                                        >  1:888975/1‑52 (MQ=255)
                                        gcgACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:3319844/55‑1 (MQ=255)
                                        gcgACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:892883/55‑1 (MQ=255)
                                        gcgACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:2540398/55‑1 (MQ=255)
                                        gcgACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:2587098/55‑1 (MQ=255)
                                        gcgACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:2535072/55‑1 (MQ=255)
                                        gcgACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:1147779/55‑1 (MQ=255)
                                        gcgACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:1682186/55‑1 (MQ=255)
                                        gcgACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCt                                     <  1:1911297/55‑1 (MQ=255)
                                        gcgACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGAttt                          >  1:2266485/1‑66 (MQ=255)
                                        gcgACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTaa                        >  1:3063210/1‑68 (MQ=255)
                                        gcgACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTa                         >  1:621324/1‑67 (MQ=255)
                                        gcgACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTa                         >  1:2058349/1‑67 (MQ=255)
                                        gcgACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTa                         >  1:371194/1‑67 (MQ=255)
                                        gcgACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTa                         >  1:1710675/1‑67 (MQ=255)
                                        gcgACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTa                         >  1:3430499/1‑67 (MQ=255)
                                        gcgACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTa                         >  1:664507/1‑67 (MQ=255)
                                        gcgACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTa                         >  1:1121798/1‑67 (MQ=255)
                                        gcgACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTa                         >  1:1117675/1‑67 (MQ=255)
                                        gcgACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTa                         >  1:1064229/1‑67 (MQ=255)
                                        gcgACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAAc                       >  1:3005683/1‑69 (MQ=255)
                                          gACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACaa                     <  1:2127862/69‑1 (MQ=255)
                                                      aaaCATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACaa                     <  1:3235811/57‑1 (MQ=255)
                                                      aaaCATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACaa                     <  1:3346198/57‑1 (MQ=255)
                                                           tACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTcc     >  1:3098935/1‑68 (MQ=255)
                                                           tACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTcc     >  1:1901362/1‑68 (MQ=255)
                                                           tACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTc      >  1:1140579/1‑67 (MQ=255)
                                                           tACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTCCg    >  1:2559713/1‑69 (MQ=255)
                                                           tACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTCCg    >  1:2699419/1‑69 (MQ=255)
                                                           tACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTCCg    >  1:2496714/1‑69 (MQ=255)
                                                           tACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTCCg    >  1:2397175/1‑69 (MQ=255)
                                                           tACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTCCg    >  1:2383289/1‑69 (MQ=255)
                                                           tACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTCCg    >  1:1756197/1‑69 (MQ=255)
                                                           tACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTCCg    >  1:2281439/1‑69 (MQ=255)
                                                           tACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTCCg    >  1:2134737/1‑69 (MQ=255)
                                                             cTCACCAGCCACTGGTAGTGTGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTCCGtt  >  1:1616368/1‑69 (MQ=255)
                                                             cTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTCCGtt  >  1:1462103/1‑69 (MQ=255)
                                                             cTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTCCGtt  >  1:422311/1‑69 (MQ=255)
                                                             cTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTCCGtt  >  1:1329191/1‑69 (MQ=255)
                                                             cTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTCCGtt  >  1:128974/1‑69 (MQ=255)
                                                             cTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTCCGtt  >  1:2828225/1‑69 (MQ=255)
                                                             cTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTCCGtt  >  1:3357641/1‑69 (MQ=255)
                                                             cTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTCCGt   >  1:153229/1‑68 (MQ=255)
                                                             cTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTCCGt   >  1:2048948/1‑68 (MQ=255)
                                                             cTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTCCGt   >  1:743852/1‑68 (MQ=255)
                                                             cTCACCAGCCAATGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTCCGt   >  1:2539976/1‑68 (MQ=255)
                                                               |                                                                  
AGAATGGTTATCCGTTATTTCTGGCTTACTGGCATCTCTCGCGACCACGCTGTGAAACATACTCACCAGCCACTGGTAGTGGGCATCGATAGCCTTATTGAGATTTAACAAGATGGCATCAATTTCCGTT  >  minE/975471‑975600

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