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
A6 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 609,012 G→A 6.0% D414D (GAC→GAT)  pflB ← pyruvate formate lyase I

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE609,0120GA 6.0% 371.7 / 8.3 117D414D (GAC→GAT) pflBpyruvate formate lyase I
Reads supporting (aligned to +/- strand):  ref base G (38/72);  new base A (3/4);  total (41/76)
Fisher's exact test for biased strand distribution p-value = 6.95e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.97e-01

Only 100 of 122 total aligned reads displayed.

TTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAAGAGGTGTCGATGGACA  >  minE/608942‑609082
                                                                      |                                                                      
ttGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAg                                                                        >  1:3045171/1‑71 (MQ=255)
 tGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAg                                                                        <  1:1345190/70‑1 (MQ=255)
 tGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGt                                                                       >  1:1450037/1‑71 (MQ=255)
   cACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCa                                                                     >  1:1403558/1‑71 (MQ=255)
   cACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCa                                                                     >  1:1887477/1‑71 (MQ=255)
     cgtgcACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTc                                                                   <  1:3689070/68‑1 (MQ=255)
      gcgcACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCg                                                                  <  1:2264441/71‑1 (MQ=255)
        gcACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgtt                                                                <  1:2275509/71‑1 (MQ=255)
         cACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCgctg                                                               <  1:444757/71‑1 (MQ=255)
            caaagaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCgctgtt                                                             >  1:2861963/3‑70 (MQ=255)
            cGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGttgttg                                                            <  1:404777/71‑1 (MQ=255)
            cGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGAAAGCAATAGCGTAGTCATCGttgttg                                                            <  1:76445/71‑1 (MQ=255)
            cGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGAAAGCAATAGCGTAGTCATCGttgttg                                                            <  1:3363081/71‑1 (MQ=255)
             gaagaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGttgttg                                                            >  1:2659473/1‑70 (MQ=255)
             gaagaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGa                                                           <  1:2835979/71‑1 (MQ=255)
              aagaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGaa                                                          <  1:2336403/71‑1 (MQ=255)
              aagaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCGctgttg                                                            >  1:2354153/1‑69 (MQ=255)
                gaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgttgt                                                              <  1:909458/65‑1 (MQ=255)
                gaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgttgt                                                              <  1:1567467/65‑1 (MQ=255)
                gaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGt                                                        <  1:3471068/71‑1 (MQ=255)
                gaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGt                                                        <  1:3833286/71‑1 (MQ=255)
                gaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGt                                                        >  1:2804005/1‑71 (MQ=255)
                gaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGt                                                        <  1:2700263/71‑1 (MQ=255)
                 aaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTc                                                       <  1:1842783/71‑1 (MQ=255)
                  aCTGCATTTGTTTAGCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgttgt                                                              <  1:1304360/63‑1 (MQ=255)
                  aCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgttgt                                                              <  1:303174/63‑1 (MQ=255)
                  aCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgttgt                                                              <  1:1416918/63‑1 (MQ=255)
                  aCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgttgt                                                              <  1:2532501/63‑1 (MQ=255)
                  aCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgttgt                                                              <  1:7253/63‑1 (MQ=255)
                   cTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCg                                                     >  1:1524361/1‑71 (MQ=255)
                      cATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCgg                                                    <  1:908338/69‑1 (MQ=255)
                      cATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCgg                                                    <  1:785074/69‑1 (MQ=255)
                        tttGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGttgttg                                                            <  1:1793417/59‑1 (MQ=255)
                        tttGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACg                                                 >  1:1357/1‑70 (MQ=255)
                         ttGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGa                                                   >  1:3136309/1‑67 (MQ=255)
                         ttGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGa                                                   >  1:2575094/1‑67 (MQ=255)
                         ttGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCa                                               >  1:1980019/1‑71 (MQ=255)
                          tGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCa                                               <  1:3882253/70‑1 (MQ=255)
                           gTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCAt                                              >  1:1297535/1‑70 (MQ=255)
                            tttACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgttg                                                               <  1:144171/52‑1 (MQ=255)
                            tttACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgttg                                                               <  1:1340539/52‑1 (MQ=255)
                            tttACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATc                                             <  1:2813371/70‑1 (MQ=255)
                            tttACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATc                                             <  1:1992040/70‑1 (MQ=255)
                              tACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGaa                                                          >  1:1184445/1‑55 (MQ=255)
                                ccAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGt                                         <  1:2234179/70‑1 (MQ=255)
                                ccAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTc                                        <  1:2214462/71‑1 (MQ=255)
                                ccAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTc                                        <  1:534087/71‑1 (MQ=255)
                                 cAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCg                                                     >  1:1200391/1‑57 (MQ=255)
                                   aCGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGa                                                   >  1:2496742/1‑57 (MQ=255)
                                   aCGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCAt                                      >  1:1839732/1‑70 (MQ=255)
                                    cGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAgg                                          <  1:596952/65‑1 (MQ=255)
                                    cGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCg                                    <  1:1121057/71‑1 (MQ=255)
                                    cGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCg                                    <  1:3198513/71‑1 (MQ=255)
                                    cGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCg                                    <  1:3905242/71‑1 (MQ=255)
                                     gATCATCGGGCTTACGCAGCAAGCAATAGCGTAGt                                                                       <  1:3776659/35‑1 (MQ=255)
                                     gATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGt                                   <  1:3827410/71‑1 (MQ=255)
                                     gATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGt                                   <  1:1449555/71‑1 (MQ=255)
                                       tcatcGGGCTTACGCAGCAAGCAATAGCGTAGTCa                                                                     >  1:469559/1‑35 (MQ=255)
                                         atcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgttgtt                                                             <  1:3935854/41‑1 (MQ=255)
                                         atcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTtct                                >  1:2943661/1‑70 (MQ=255)
                                          tcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgtt                                                                <  1:2213414/37‑1 (MQ=255)
                                          tcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCg                                                     <  1:1884846/48‑1 (MQ=255)
                                           cGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCa                              >  1:3156580/1‑70 (MQ=255)
                                           cGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCa                              >  1:850367/1‑70 (MQ=255)
                                            gggCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCg                                                     <  1:2121318/46‑1 (MQ=255)
                                              gCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACt                          <  1:3340462/71‑1 (MQ=255)
                                               cTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATa                            <  1:884056/68‑1 (MQ=255)
                                               cTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTg                         >  1:1478820/1‑71 (MQ=255)
                                               cTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTg                         <  1:3749711/71‑1 (MQ=255)
                                               cTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTAATACTg                         <  1:2620261/71‑1 (MQ=255)
                                                  aCGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGa                                                   >  1:1964762/1‑42 (MQ=255)
                                                   cGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCa                       >  1:1262507/1‑69 (MQ=255)
                                                      agcaagcaATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCagag                    >  1:2136143/1‑69 (MQ=255)
                                                      agcaagcaATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGagaa                  <  1:3280242/71‑1 (MQ=255)
                                                       gcaagcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATAGTTCTCATACTGCAGagaag                 <  1:1125767/71‑1 (MQ=255)
                                                        caagcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAgaga                   <  1:3022563/68‑1 (MQ=255)
                                                        caagcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGagaaga                <  1:3780678/71‑1 (MQ=255)
                                                        caagcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGagaa                  >  1:650405/1‑69 (MQ=255)
                                                        caagcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGagaa                  >  1:2598318/1‑69 (MQ=255)
                                                         aagcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAg                                           >  1:59411/1‑43 (MQ=255)
                                                         aagcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTtct                                <  1:1411631/54‑1 (MQ=255)
                                                         aagcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTtct                                <  1:3266642/54‑1 (MQ=255)
                                                         aagcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTtct                                <  1:2453730/54‑1 (MQ=255)
                                                         aagcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAagag               <  1:2791412/71‑1 (MQ=255)
                                                         aagcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCAACGTTCTCATACTGCAGAGAagag               <  1:1999685/71‑1 (MQ=255)
                                                          agcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCa                                               <  1:591344/38‑1 (MQ=255)
                                                          agcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGt                                   <  1:3252434/50‑1 (MQ=255)
                                                          agcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAagag               <  1:438393/70‑1 (MQ=255)
                                                          agcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAAGAgg              >  1:2176052/1‑71 (MQ=255)
                                                              aTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAagag               >  1:3213885/1‑66 (MQ=255)
                                                                 gCGTAGTCATGGTTGTTGAAGTCCGGACGCATCAGGTCATCATTCTCATACTGCAGAGAAGATGTGTCGAt       <  1:1644853/71‑1 (MQ=255)
                                                                 gCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAAGAGGTGTCGa        <  1:1201388/70‑1 (MQ=255)
                                                                 gCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAAGAGGTGTCGa        <  1:2296389/70‑1 (MQ=255)
                                                                 gCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAAGAGGTGTCGAt       <  1:1485151/71‑1 (MQ=255)
                                                                 gCGTAGTCATAGTTGTTGAAGTCCGGACGCATCAGGTCATCGTtctc                               >  1:2093133/1‑47 (MQ=255)
                                                                  cGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAAGAGGTGTCGAt       <  1:769049/70‑1 (MQ=255)
                                                                  cGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAAGAGGTGTCGATg      <  1:1365343/71‑1 (MQ=255)
                                                                      gTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCg                                    >  1:2404380/1‑37 (MQ=255)
                                                                      gTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAAGAGGTGTCGATGGaca  <  1:2081968/71‑1 (MQ=255)
                                                                      gTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAAGAGGTGTCGATGGac   <  1:2083711/70‑1 (MQ=255)
                                                                      |                                                                      
TTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAAGAGGTGTCGATGGACA  >  minE/608942‑609082

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