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 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,015,481 A→G 24.2% Y196Y (TAT→TAC)  fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,015,4810AG24.2% 215.8 / 70.1 124Y196Y (TAT→TAC) fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base A (38/56);  new base G (12/18);  total (50/74)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01

Only 100 of 134 total aligned reads displayed.

CAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAA  >  minE/1015412‑1015551
                                                                     |                                                                      
cAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGa                                                                        >  1:2520491/1‑70 (MQ=255)
cAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGAt                                                                       <  1:2068252/71‑1 (MQ=255)
cAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGAt                                                                       <  1:2061669/71‑1 (MQ=255)
 aGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGa                                                                        >  1:1410421/1‑69 (MQ=255)
    gTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATagag                                                                   <  1:3478245/71‑1 (MQ=255)
    gTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATa                                                                      >  1:1316827/1‑68 (MQ=255)
     tGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAgaga                                                                  <  1:1084939/71‑1 (MQ=255)
     tGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAgaga                                                                  <  1:3181154/71‑1 (MQ=255)
          aTCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGt                                                             >  1:377443/1‑71 (MQ=255)
          aTCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGt                                                             >  1:5617337/1‑71 (MQ=255)
             ttctCGACGAGGAAGTTTTTCAGTTTGCCGGGAGTCAGCAGGGCTTTGGTTTCCTGGTAGAGATACGtttt                                                          >  1:399374/1‑71 (MQ=255)
             ttctCGACGAGGAAGTTTTTCAGTTTGCCGGGAGTCAGCAGGGCTTTGGTTTCCTAGTAGAGATACGttt                                                           >  1:3581867/1‑68 (MQ=255)
             ttctCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGa                                                                        >  1:5182584/1‑57 (MQ=255)
             ttctCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGa                                                                        >  1:5276588/1‑57 (MQ=255)
             ttctCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCt                                                           >  1:3010719/1‑70 (MQ=255)
              tctcGACGAGGAAGTTTTTCAGTTTGCCGGGCGTCAGCATGGCTTTGGTTTCCTGGTAGAGAt                                                                 <  1:4334658/63‑1 (MQ=255)
              tctcGACGAGGAAGTTTTTCAGTTTGCCGGGCGTCAGCAGGGCTTTGGTTTCCTGGTAGAGAt                                                                 <  1:460578/63‑1 (MQ=255)
              tctcGACGAGGAAGTTTTTCAGTTTGCCGGGCGTCAGCAGGGCTTTGGTTTCCTGGTAGAGAt                                                                 <  1:2717369/63‑1 (MQ=255)
              tctcGACGAGGAAGTTTTTCAGTTTGCCGGGCGTCAGCAGGGCTTTGGTTTCCTGGTAGAGAt                                                                 <  1:2530501/63‑1 (MQ=255)
              tctcAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATAc                                                               <  1:5426159/65‑1 (MQ=255)
              tctcAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATAc                                                               <  1:4694561/65‑1 (MQ=255)
               ctcAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCt                                                           <  1:4258569/68‑1 (MQ=255)
                tcAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATagag                                                                   >  1:4370668/1‑59 (MQ=255)
                  aaCCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGt                                                        <  1:3086951/68‑1 (MQ=255)
                        gTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAac                                               <  1:1417246/71‑1 (MQ=255)
                        gTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAac                                               <  1:4787093/71‑1 (MQ=255)
                          aaTTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGcc                                                   >  1:625148/1‑65 (MQ=255)
                          aaTTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAacca                                             >  1:3940664/1‑71 (MQ=255)
                           aTTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTg                                                         <  1:4766448/58‑1 (MQ=255)
                           aTTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAaccac                                            <  1:4047212/71‑1 (MQ=255)
                            tttttCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATa                                                                >  1:5466074/1‑50 (MQ=255)
                            tttttCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATa                                                                >  1:1575859/1‑50 (MQ=255)
                             ttttCAGTTTGCCGGGAGTCAGCAGGGCTTTGGTTTCCTGGTAGAGATAAGTTTTGttgg                                                     >  1:2718277/1‑58 (MQ=255)
                              tttCAGTTTGCCGGGAGTCAGCAGGGCTTTGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAgccgccgc                                         >  1:5472185/1‑69 (MQ=255)
                              tttCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTc                                                            <  1:4008520/52‑1 (MQ=255)
                                tCAGTTTGCCGGGAGTCAGCAGGGCTTTGGTTTCCTGGTAGAGATACGTTTTGTTGGca                                                   >  1:2195172/1‑58 (MQ=255)
                                tCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGc                                                    <  1:4831137/58‑1 (MQ=255)
                                  aGTTTGCCGGGAGTCAGCAGGGCTTTGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCtt                                      <  1:1191864/70‑1 (MQ=255)
                                  aGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCg                                                  >  1:4799489/1‑58 (MQ=255)
                                  aGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCg                                                  >  1:3458132/1‑58 (MQ=255)
                                   gTTTCCCCAGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTg                                    >  1:1338241/1‑71 (MQ=255)
                                      tCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGa                                                 <  1:5494009/55‑1 (MQ=255)
                                      tCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGc                                  >  1:1573830/1‑70 (MQ=255)
                                      tCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGc                                  <  1:3608082/70‑1 (MQ=255)
                                      tCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGc                                  <  1:3885495/70‑1 (MQ=255)
                                        cccGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGa                                <  1:862705/70‑1 (MQ=255)
                                        cccGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGa                                <  1:1886545/70‑1 (MQ=255)
                                            gCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCg                                                  >  1:3268327/1‑48 (MQ=255)
                                              gTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCtt                                                          >  1:2286384/1‑38 (MQ=255)
                                               tCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCg                                                  <  1:5152596/45‑1 (MQ=255)
                                                 aGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTgg                                   >  1:247607/1‑58 (MQ=255)
                                                 aGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGaa                      >  1:3129290/1‑71 (MQ=255)
                                                 aGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGaa                      >  1:5405961/1‑71 (MQ=255)
                                                  gTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGttt                                                      <  1:2255237/38‑1 (MQ=255)
                                                  gTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAAt                     <  1:3288018/71‑1 (MQ=255)
                                                   tAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCg                                                  <  1:1165737/41‑1 (MQ=255)
                                                   tAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAaccaccac                                         <  1:629610/50‑1 (MQ=255)
                                                   tAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAaccaccac                                         <  1:1364505/50‑1 (MQ=255)
                                                   tAACGCTTTGGGTTCCTGATAGAGATACGTCTTGTTTGCCGAaccaccac                                         <  1:1187300/50‑1 (MQ=255)
                                                    aaCGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGaa                                                >  1:5173167/1‑42 (MQ=255)
                                                    aaCGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAaccaccac                                         <  1:1484955/49‑1 (MQ=255)
                                                     gggCTTTGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTg                  <  1:289407/69‑1 (MQ=255)
                                                     gggCTTTGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTg                  >  1:4443382/3‑71 (MQ=255)
                                                     aCGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTgg                                   >  1:2317734/1‑54 (MQ=255)
                                                     aCGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTg                  <  1:2210864/71‑1 (MQ=255)
                                                     aCGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTg                  >  1:5656091/1‑71 (MQ=255)
                                                     aCGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTg                  >  1:2861294/1‑71 (MQ=255)
                                                      cGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGt                 <  1:523433/71‑1 (MQ=255)
                                                       gCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTa                <  1:1073069/71‑1 (MQ=255)
                                                       gCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTa                <  1:2198266/71‑1 (MQ=255)
                                                        cTTTGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCttt                                     >  1:1305058/1‑49 (MQ=255)
                                                        cTTTGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGTac               >  1:4437263/1‑70 (MQ=255)
                                                         tttGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTg                  <  1:2037477/67‑1 (MQ=255)
                                                         tttGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTg                  <  1:4939290/67‑1 (MQ=255)
                                                           tGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGTACtc             <  1:1782442/70‑1 (MQ=255)
                                                           tGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCtt                                      <  1:5695635/45‑1 (MQ=255)
                                                           tGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATtc             <  1:1586922/70‑1 (MQ=255)
                                                            ggTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGc                                  <  1:288495/48‑1 (MQ=255)
                                                            ggTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGc                                  <  1:4533583/48‑1 (MQ=255)
                                                            ggTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATtcgt           >  1:422688/1‑71 (MQ=255)
                                                            ggTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATtcgt           >  1:3400818/1‑71 (MQ=255)
                                                            ggTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATtcg            >  1:1547230/1‑70 (MQ=255)
                                                             gTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATtcgt           <  1:4363897/70‑1 (MQ=255)
                                                              tttCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGAt                               <  1:4619618/49‑1 (MQ=255)
                                                              tttCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGAt                               <  1:5346723/49‑1 (MQ=255)
                                                              tttCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGaa                      >  1:5251844/1‑58 (MQ=255)
                                                                tCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGc                                  <  1:3300920/44‑1 (MQ=9)
                                                                tCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGTACTCATCGc        <  1:3758264/70‑1 (MQ=255)
                                                                tCCTGGTAGAGATACGTTTTGTTGGCAGAGCC‑CCGCCTTTCGCAACGCAAAGGaa                      <  1:1819799/55‑1 (MQ=255)
                                                                tCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGa                                >  1:921680/1‑46 (MQ=255)
                                                                tCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATAc                             >  1:3922263/1‑49 (MQ=255)
                                                                tCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATtcgtc          <  1:3839973/68‑1 (MQ=255)
                                                                tCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGc        <  1:4641737/70‑1 (MQ=255)
                                                                tCCTGATAGAGATACGTCTTGTTAGCCGAACCACCACCTTTGGCGa                                >  1:638196/1‑46 (MQ=255)
                                                                 ccTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCa      >  1:3948516/1‑71 (MQ=255)
                                                                  cTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGt                 <  1:262458/59‑1 (MQ=255)
                                                                  cTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGt                 <  1:4192742/59‑1 (MQ=255)
                                                                    gATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTg                  <  1:1502902/56‑1 (MQ=255)
                                                                     aTAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATc    <  1:1020268/69‑1 (MQ=255)
                                                                     aTAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCaa  <  1:3230301/71‑1 (MQ=255)
                                                                     |                                                                      
CAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAA  >  minE/1015412‑1015551

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A