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 1,015,522 T→C 23.2% I183V (ATC→GTC) ‡ fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,015,5220TC23.2% 197.4 / 60.0 112I183V (ATC→GTC) ‡fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base T (40/46);  new base C (12/14);  total (52/60)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.79e-01

Only 100 of 117 total aligned reads displayed.

GGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAGATCGATCTGCGCTGGCAGATTGGTGCCGGTA  >  minE/1015455‑1015592
                                                                   |                                                                      
ggCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACa                                                                     <  1:668128/71‑1 (MQ=255)
      aGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGaa                                                               >  1:3129290/1‑71 (MQ=255)
      aGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGaa                                                               >  1:5405961/1‑71 (MQ=255)
       gTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAAt                                                              <  1:3288018/71‑1 (MQ=255)
          gggCTTTGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTg                                                           >  1:4443382/3‑71 (MQ=255)
          gggCTTTGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTg                                                           >  1:3761804/3‑71 (MQ=255)
          gggCTTTGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTg                                                           <  1:289407/69‑1 (MQ=255)
          aCGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTg                                                           >  1:5656091/1‑71 (MQ=255)
          aCGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTg                                                           >  1:2861294/1‑71 (MQ=255)
           cGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGt                                                          <  1:523433/71‑1 (MQ=255)
            gCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTa                                                         <  1:2198266/71‑1 (MQ=255)
            gCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTa                                                         <  1:1073069/71‑1 (MQ=255)
             cTTTGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGTac                                                        >  1:279029/1‑70 (MQ=255)
             cTTTGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGTac                                                        >  1:4437263/1‑70 (MQ=255)
             cTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTAt                                                        <  1:2561958/71‑1 (MQ=255)
              tttGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTg                                                           <  1:2037477/67‑1 (MQ=255)
              tttGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTg                                                           <  1:4939290/67‑1 (MQ=255)
                tGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGTACtc                                                      <  1:4594302/70‑1 (MQ=255)
                tGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGTACtc                                                      <  1:1782442/70‑1 (MQ=255)
                tGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGTACtc                                                      <  1:1224949/70‑1 (MQ=255)
                tGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATtc                                                      <  1:1586922/70‑1 (MQ=255)
                tGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGAGATACAGAGGAATTTGTATtc                                                      <  1:1905209/70‑1 (MQ=255)
                 ggTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATtcgt                                                    >  1:422688/1‑71 (MQ=255)
                 ggTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATtcgt                                                    >  1:5297930/1‑71 (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)
                     tCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGTACTCATCGc                                                 <  1:3758264/70‑1 (MQ=255)
                     tCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGTACTCATCGc                                                 >  1:2245741/1‑70 (MQ=255)
                     tCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATtcgtc                                                   <  1:3839973/68‑1 (MQ=255)
                     tCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGc                                                 >  1:2995995/1‑70 (MQ=255)
                      ccTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCa                                               >  1:3948516/1‑71 (MQ=255)
                       cTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGt                                                          <  1:4192742/59‑1 (MQ=255)
                       cTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGt                                                          <  1:262458/59‑1 (MQ=255)
                        tggtAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGTACTCATCGCCAt                                              >  1:1893027/4‑70 (MQ=255)
                        tggtAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGTACTCATCGCCAt                                              >  1:3978994/4‑70 (MQ=255)
                         gATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTg                                                           <  1:1344612/56‑1 (MQ=255)
                         gATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTg                                                           <  1:1502902/56‑1 (MQ=255)
                          gtAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGTACTCATCGCTATc                                             <  1:2453718/68‑1 (MQ=255)
                          gtAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGTACTCATCGCCATc                                             <  1:1750586/68‑1 (MQ=255)
                          gtAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGTACTCATCGCCATc                                             <  1:184854/68‑1 (MQ=255)
                          aTAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATc                                             <  1:4116209/69‑1 (MQ=255)
                          aTAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATc                                             <  1:1020268/69‑1 (MQ=255)
                          aTAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCaa                                           <  1:3230301/71‑1 (MQ=255)
                          aTAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTAGTCGCCATc                                             <  1:4432689/69‑1 (MQ=255)
                           tAGAGATACGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGTACTCATCGCCAt                                              >  1:1283257/1‑67 (MQ=255)
                           tAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAAc                                          >  1:1370218/1‑71 (MQ=255)
                                aTACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCa                                      >  1:2886802/1‑70 (MQ=255)
                                aTACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCa                                      >  1:2072584/1‑70 (MQ=255)
                                 tACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCAATCAACGGCAt                                     >  1:2007269/1‑70 (MQ=255)
                                  aCGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGTACtcatcg                                                  >  1:791211/1‑56 (MQ=255)
                                  aCGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGTACtcatcg                                                  >  1:2748907/1‑56 (MQ=255)
                                  aCGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGTACTCATCGCCATcta                                           >  1:2418078/1‑61 (MQ=255)
                                  aCGTCTTGTTTGCCGAACCACCACCTTTGGCGATACaga                                                                   >  1:1900631/1‑39 (MQ=255)
                                  aCGTCTTGTTTGCCGAACCACCACCTTTGGCGATACaga                                                                   >  1:2055945/1‑39 (MQ=255)
                                   cGTTTTGTTGGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGTACTCATCGCCATCTACCGCGTaca                                  <  1:4390952/71‑3 (MQ=255)
                                    gTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTg                                                           <  1:5538074/45‑1 (MQ=255)
                                    gTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTg                                                           <  1:5427927/45‑1 (MQ=255)
                                    gTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTg                                                           <  1:1648357/45‑1 (MQ=255)
                                     ttttgttgGCAGAGCCGCCGCCTTTCGCAACGCAAAGGAATTTGTACTCATCGCCATCTACCGCGTACAgg                                >  1:2328173/3‑70 (MQ=255)
                                      cTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAAt                                                              <  1:1160647/40‑1 (MQ=255)
                                       ttGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTAt                                                        <  1:1750528/45‑1 (MQ=255)
                                       ttGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAga                                <  1:1196073/69‑1 (MQ=255)
                                         gTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCaa                                           >  1:4162793/1‑56 (MQ=255)
                                          tttGCCGAACCACCACCTTTGGCGATACAGAGGAAttt                                                            <  1:4485693/38‑1 (MQ=255)
                                          tttGCCGAACCACCACCTTTGGCGATACAGAGGAAttt                                                            <  1:1429455/38‑1 (MQ=255)
                                          tttGCCGAACCACCACCTTTGGCGATACAGAGGAAttt                                                            <  1:1592012/38‑1 (MQ=255)
                                          tttGCCGAACCACCACCTTTGGCGATACAGAGGAAttt                                                            <  1:3977140/38‑1 (MQ=255)
                                          tttGCCGAACCACCACCTTTGGCGATACAGAGGAAttt                                                            <  1:3911620/38‑1 (MQ=255)
                                          tttGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAgatcgat                           >  1:4978529/1‑71 (MQ=255)
                                          tttGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAgatcgat                           >  1:360859/1‑71 (MQ=255)
                                          tttGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAgatcga                            >  1:453718/1‑70 (MQ=255)
                                            tGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGt                                                          >  1:3242740/1‑38 (MQ=255)
                                               cGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAGATCGATCTgcg                      <  1:4692434/71‑1 (MQ=255)
                                                 aaCCACCACCTTTGGCGATACAGAGGAATTTGTATtcg                                                     >  1:3157211/1‑38 (MQ=255)
                                                 aaCCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAgatcgatc                          <  1:743428/65‑1 (MQ=255)
                                                  accaccaccTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAGATCGATCTGCGCTg                   <  1:725818/71‑1 (MQ=255)
                                                        accTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAGATCGATCt                         <  1:2720264/59‑1 (MQ=255)
                                                         ccTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATa                                    <  1:4584255/47‑1 (MQ=255)
                                                         ccTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATa                                    <  1:4458752/47‑1 (MQ=255)
                                                         ccTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAGATCGATCTGCGCTGGCAGAtt            <  1:4524809/71‑1 (MQ=255)
                                                         ccTTTCGCGATACAGAGGAATTTGTATTCGTCGCCa                                               >  1:1318878/1‑36 (MQ=255)
                                                          cTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAgat                               >  1:2622213/1‑51 (MQ=255)
                                                          cTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAGATCGATCTGCGCTGGCAGATTg           <  1:3775936/71‑1 (MQ=255)
                                                           tttGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAGATCGATCTGCGCTGGCAGATTgg          >  1:2072133/1‑71 (MQ=255)
                                                           tttGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAGATCGATCTGCGCTGGCAGATTgg          >  1:3325390/1‑71 (MQ=255)
                                                            ttGGCGATACAGAGGAATTTGTATTCGTCGCCATCaa                                           >  1:2488213/1‑37 (MQ=255)
                                                            ttGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAga                                >  1:4013716/1‑48 (MQ=255)
                                                            ttGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAg                                 <  1:4629740/47‑1 (MQ=255)
                                                            ttGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAGATCGATCTGCGCTGGCAGATTGGt         >  1:1891320/1‑71 (MQ=255)
                                                            ttGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAGATCGATCTGCGCTGGCAGATTGGt         >  1:4099552/1‑71 (MQ=255)
                                                            ttGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAGATCGATCTGCGCTGGCAGATTGGt         >  1:226183/1‑71 (MQ=255)
                                                                 gATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATa                                    <  1:5315601/39‑1 (MQ=255)
                                                                 gATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATa                                    <  1:4971077/39‑1 (MQ=255)
                                                                 gATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATa                                    <  1:2108055/39‑1 (MQ=255)
                                                                 gATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATa                                    <  1:4176970/39‑1 (MQ=255)
                                                                   tACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAGATCGATCTGCGCTGGCAGATTGGTGCCGGTa  >  1:3207396/1‑71 (MQ=255)
                                                                   tACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAGATCGATCTGCGCTGGCAGATTGGTGCCGGTa  >  1:4344834/1‑71 (MQ=255)
                                                                   |                                                                      
GGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGCGATACAGAGGAATTTGTATTCGTCGCCATCAACGGCATAAAGATCGATCTGCGCTGGCAGATTGGTGCCGGTA  >  minE/1015455‑1015592

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