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 1,490,568 C→A 48.0% G155G (GGG→GGT)  nuoL ← NADH:ubiquinone oxidoreductase, membrane subunit L

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,490,5680CA48.0% 30.1 / 104.1 104G155G (GGG→GGT) nuoLNADH:ubiquinone oxidoreductase, membrane subunit L
Reads supporting (aligned to +/- strand):  ref base C (23/31);  new base A (44/6);  total (67/37)
Fisher's exact test for biased strand distribution p-value = 1.38e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 104 total aligned reads displayed.

GTCACGACGAACGCTTTCATTGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAGGTACATCAGCAGCAGGTT  >  minE/1490512‑1490630
                                                        |                                                              
gTCACGACGAACGCTTTCATTGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGa                                                    <  1:1050210/69‑1 (MQ=255)
gTCACGACGAACGCTTTCATTGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGa                                                    <  1:83924/69‑1 (MQ=255)
gTCACGACGAACGCTTTCATTGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGa                                                    <  1:1088983/69‑1 (MQ=255)
gTCACGACGAACGCTTTCATTGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGa                                                    <  1:327466/69‑1 (MQ=255)
gTCACGACGAACGCTTTCATTGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGa                                                    <  1:2349189/69‑1 (MQ=255)
 tCACGACGAACGCTTTCATTGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGa                                                    <  1:1141974/68‑1 (MQ=255)
  cACGACGAACGCTTTCATTGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGAt                                                   >  1:3334594/1‑68 (MQ=255)
   acgacgAACGCTTTCATTGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGATAg                                                 <  1:1183609/69‑1 (MQ=255)
   acgacgAACGCTTTCATTGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGATAg                                                 <  1:277061/69‑1 (MQ=255)
      acgaACGCTTTCATTGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAg                                              <  1:2655473/69‑1 (MQ=255)
      acgaACGCTTTCATTGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAg                                              <  1:660913/69‑1 (MQ=255)
      acgaACGCTTTCATTGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAg                                              <  1:404060/69‑1 (MQ=255)
      acgaACGCTTTCATTGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAg                                              <  1:1856846/69‑1 (MQ=255)
       ggaACGCTTTCATTGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAg                                              <  1:838396/67‑1 (MQ=255)
           cGCTTTCATTGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAg                                         <  1:2055468/69‑1 (MQ=255)
           cGCTTTCATTGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAg                                         <  1:2070125/69‑1 (MQ=255)
           cGCTTTCATTGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAg                                         <  1:1903306/69‑1 (MQ=255)
           cGCTTTCATTGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAg                                         <  1:166038/69‑1 (MQ=255)
           cGCTTTCATTGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAg                                         <  1:1697740/69‑1 (MQ=255)
                  aTTGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCa                                    <  1:1762814/67‑1 (MQ=255)
                    tGCCGCTGCGGCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGcc                                >  1:1069404/1‑69 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTTTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGcc                                >  1:1912830/1‑69 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGcc                                <  1:2740385/69‑1 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGcc                                <  1:805883/69‑1 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGcc                                <  1:346277/69‑1 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGcc                                <  1:1745234/69‑1 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCg                                                             >  1:1397794/1‑40 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGAt                                                           >  1:704900/1‑42 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCGCAGGCCCACGcc                                >  1:1315214/1‑69 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGcc                                >  1:3367348/1‑69 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGcc                                >  1:486777/1‑69 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGcc                                >  1:3309176/1‑69 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGcc                                >  1:3263544/1‑69 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGcc                                >  1:3059437/1‑69 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGcc                                >  1:550180/1‑69 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGcc                                >  1:705673/1‑69 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGcc                                >  1:864850/1‑69 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGcc                                >  1:2243057/1‑69 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGcc                                >  1:982314/1‑69 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGcc                                >  1:1319120/1‑69 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGcc                                >  1:1832259/1‑69 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGcc                                >  1:1339377/1‑69 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGcc                                >  1:139468/1‑69 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGcc                                >  1:1419451/1‑69 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGcc                                >  1:1465678/1‑69 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGcc                                >  1:1658238/1‑69 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGcc                                >  1:1721424/1‑69 (MQ=255)
                    tGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCAACGcc                                >  1:729266/1‑69 (MQ=255)
                    tGCCGCTGCGCCATACTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGcc                                >  1:2329386/1‑69 (MQ=255)
                     gCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCTACGCCt                               >  1:275118/1‑69 (MQ=255)
                     gCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCt                               >  1:3231143/1‑69 (MQ=255)
                     gCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCt                               >  1:3329263/1‑69 (MQ=255)
                     gCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCt                               <  1:2189320/69‑1 (MQ=255)
                     gCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCt                               >  1:228642/1‑69 (MQ=255)
                     gCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCt                               >  1:3126019/1‑69 (MQ=255)
                     gCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCt                               >  1:1554519/1‑69 (MQ=255)
                            cgcCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGa                                                    <  1:136081/41‑1 (MQ=255)
                               cATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCg                      >  1:1946332/1‑68 (MQ=255)
                               cATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGa                     >  1:1305302/1‑69 (MQ=255)
                               cATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGa                     >  1:1202591/1‑69 (MQ=255)
                               cATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGa                     >  1:1967166/1‑69 (MQ=255)
                               cATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGa                     >  1:1558116/1‑69 (MQ=255)
                               cATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGa                     >  1:549574/1‑69 (MQ=255)
                               cATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGa                     >  1:47711/1‑69 (MQ=255)
                               cATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGa                     >  1:463617/1‑69 (MQ=255)
                               cATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGa                     >  1:341752/1‑69 (MQ=255)
                               cATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGa                     >  1:3237553/1‑69 (MQ=255)
                               cATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGa                     >  1:3112285/1‑69 (MQ=255)
                               cATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGa                     >  1:2219177/1‑69 (MQ=255)
                               cATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGa                     >  1:282758/1‑69 (MQ=255)
                               cATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGa                     >  1:1050552/1‑69 (MQ=255)
                               cATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGa                     >  1:1258816/1‑69 (MQ=255)
                               cATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGa                     >  1:873324/1‑69 (MQ=255)
                               cATTCTTCGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGa                     >  1:1292570/1‑69 (MQ=255)
                                  tcttcGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGc                                       >  1:3261709/1‑48 (MQ=255)
                                  tcttcGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAgg                   >  1:780142/1‑68 (MQ=255)
                                  tcttcGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAgg                   >  1:2101957/1‑68 (MQ=255)
                                  tcttcGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAgg                   >  1:1739937/1‑68 (MQ=255)
                                  tcttcGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAgg                   >  1:3343847/1‑68 (MQ=255)
                                  tcttcGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAgg                   >  1:1203623/1‑68 (MQ=255)
                                  tcttcGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAgg                   >  1:1900824/1‑68 (MQ=255)
                                   cttcGGATCGGTGTAATAGAACCCGATCAGCAGATTGGAGCACAGGCCCACGCCTTCCCAGCCGAGGTa                 >  1:702939/1‑69 (MQ=255)
                                   cttcGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAGGTa                 >  1:2422681/1‑69 (MQ=255)
                                   cttcGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAGGTa                 >  1:1016088/1‑69 (MQ=255)
                                   cttcGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAGGTa                 <  1:2766525/69‑1 (MQ=255)
                                   cttcGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAGGTa                 >  1:738239/1‑69 (MQ=255)
                                   cttcGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAGGTa                 >  1:1233963/1‑69 (MQ=255)
                                   cttcGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAGGTa                 >  1:3292456/1‑69 (MQ=255)
                                   cttcGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAGGTa                 >  1:3308500/1‑69 (MQ=255)
                                   cttcGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCACAGCCGAGGTa                 >  1:292083/1‑69 (MQ=255)
                                    ttcGGATCGGTGTAATAGAAACCGATCAGCAGATAGGAGCACAg                                         <  1:391415/44‑1 (MQ=255)
                                                  aTAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAGGTACATCAGCAGCAGGtt  <  1:2908115/69‑1 (MQ=255)
                                                  aTAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAGGTACATCAGCAGCAGGtt  <  1:88182/69‑1 (MQ=255)
                                                     gAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAGGTACATCAGCAGCAGGtt  <  1:3128132/66‑1 (MQ=255)
                                                     gAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAGGTACATCAGCAGCAGGtt  <  1:592687/66‑1 (MQ=255)
                                                     gAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAGGTACATCAGCAGCAGGtt  <  1:1979686/66‑1 (MQ=255)
                                                     gAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAGGTACATCAGCAGCAGGtt  <  1:2791980/66‑1 (MQ=255)
                                                     gAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAGGTACATCAGCAGCAGGtt  <  1:2304903/66‑1 (MQ=255)
                                                     gAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAGGTACATCAGCAGCAGGtt  <  1:1741056/66‑1 (MQ=255)
                                                     gAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAGGTACATCAGCAGCAGGtt  <  1:929451/66‑1 (MQ=255)
                                                        |                                                              
GTCACGACGAACGCTTTCATTGCCGCTGCGCCATTCTTCGGATCGGTGTAATAGAACCCGATCAGCAGATAGGAGCACAGGCCCACGCCTTCCCAGCCGAGGTACATCAGCAGCAGGTT  >  minE/1490512‑1490630

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