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 1,786,551 T→G 34.0% T87T (ACT→ACG)  smpA → small membrane lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,786,5510TG34.0% 77.3 / 78.3 100T87T (ACT→ACG) smpAsmall membrane lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (27/39);  new base G (13/21);  total (40/60)
Fisher's exact test for biased strand distribution p-value = 8.32e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCATTTGGTACGAATACCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACAAACCTG  >  minE/1786489‑1786615
                                                              |                                                                
ccATTTGGTACGAATACCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCaa                                                            >  1:1929715/1‑69 (MQ=255)
ccATTTGGTACGAATACCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCaa                                                            >  1:308385/1‑69 (MQ=255)
ccATTTGGTACGAATACCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCaa                                                            >  1:591666/1‑69 (MQ=255)
   tttGGTACGAATACCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAac                                                          <  1:394346/68‑1 (MQ=255)
   tttGGTACGAATACCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAac                                                          <  1:1823852/68‑1 (MQ=255)
   tttGGTACGAATACCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAac                                                          <  1:1995113/68‑1 (MQ=255)
   tttGGTACGAATACCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAac                                                          <  1:547222/68‑1 (MQ=255)
   tttGGTACGAATACCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAac                                                          <  1:1120652/68‑1 (MQ=255)
     tGGTACGAATACCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAacgct                                                       >  1:2354095/1‑69 (MQ=255)
     tGGTACGAATACCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAacgct                                                       >  1:2554585/1‑69 (MQ=255)
     tGGTACGAATACCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAacgct                                                       >  1:855611/1‑69 (MQ=255)
     tGGTACGAATACCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAacgct                                                       >  1:202786/1‑69 (MQ=255)
        tACGAATACCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAacgctga                                                     <  1:1408317/68‑1 (MQ=255)
        tACGAATACCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAacgctga                                                     <  1:2851288/68‑1 (MQ=255)
        tACGAATACCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAacgctga                                                     <  1:2742299/68‑1 (MQ=255)
        tACGAATACCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAacgctga                                                     <  1:1485094/68‑1 (MQ=255)
        tACGAATACCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAacgctga                                                     <  1:1026728/68‑1 (MQ=255)
        tACGAATACCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAacgctga                                                     <  1:1977656/68‑1 (MQ=255)
        tACGAATACCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAacgctga                                                     <  1:2655963/68‑1 (MQ=255)
          caaaTACCTGGTTCTATGTCTTCC‑CCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAacgctgacgct                                                 <  1:2345983/67‑1 (MQ=255)
          cGAATACCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAacgctga                                                     <  1:2968638/66‑1 (MQ=255)
            aaTACCTGGTTCTATGTCTTCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAacgctgacgct                                                 <  1:1941971/68‑1 (MQ=255)
            aaTACCTGGTTCTATGTCTTCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAacgctgacgct                                                 <  1:318492/68‑1 (MQ=255)
            aaTACCTGGTTCTATGTCTTCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAacgctgacgct                                                 <  1:2672425/68‑1 (MQ=255)
            aaTACCTGGTTCTATGTCTTCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAacgctgacgct                                                 <  1:2082605/68‑1 (MQ=255)
            aaTACCTGGTTCTATGTCTTCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAacgctgacgct                                                 <  1:2118481/68‑1 (MQ=255)
            aaTACCTGGTTCTATGTCTTCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAacgctgacgct                                                 <  1:3074326/68‑1 (MQ=255)
            aaTACCTGGTTCTATGTCTTCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAacgctgacgct                                                 <  1:2900309/68‑1 (MQ=255)
            aaTACCTGGTTCTATGTCTTCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAacgctgacgct                                                 <  1:1624062/68‑1 (MQ=255)
            aaTACCTGGTTCTATGTCTTCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAacgctgacgct                                                 <  1:739563/68‑1 (MQ=255)
            aaTACCTGGTTCTATGTCTTCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAacgctgacgct                                                 <  1:1586329/68‑1 (MQ=255)
            aaTACCTGGTTCTATGTCTTCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAacgctgacgct                                                 <  1:1672207/68‑1 (MQ=255)
            aaTACCTGGTTCTATGTCTTCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAacgctgacgct                                                 <  1:1328485/68‑1 (MQ=255)
            aaTACCTGGTTCTATGTCTTCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAacgctgacgct                                                 <  1:467840/68‑1 (MQ=255)
            aaTACCTGGTTCTATGTCTTCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAacgctgacgct                                                 <  1:467418/68‑1 (MQ=255)
            aaTACCTGGTTCTATGTCTTCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAacgctgacgct                                                 <  1:466072/68‑1 (MQ=255)
            aaTACCTGGTTCTATGTCTTCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAacgctgacgct                                                 <  1:935203/68‑1 (MQ=255)
            aaTACCTGGTTCTATGTCTTCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAacgctgacgct                                                 <  1:4242/68‑1 (MQ=255)
            aaTACCTGGTTCTATGTCTTCCGCCAGCAACCTGGTCACGAAGGTGTAACGCAGCAAacgctgacgct                                                 <  1:2940136/68‑1 (MQ=255)
            aaTACCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAacgctgacgct                                                 <  1:1477509/68‑1 (MQ=255)
             aTACCTGGTTCTATGTCTTCCGCCAGCAACCTTGTCATGAAGGTGTAACGCAGCAAacgctgacgct                                                 <  1:729578/67‑1 (MQ=255)
               aCCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAACGCTGACGCTGAcc                                             <  1:2853609/69‑1 (MQ=255)
                      tCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAacgctgacgct                                                 <  1:2314776/58‑1 (MQ=255)
                      tCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAacgctgacgct                                                 <  1:2542756/58‑1 (MQ=255)
                      tCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAacgctgacgct                                                 <  1:1441569/58‑1 (MQ=255)
                      tCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAacgctgacgct                                                 <  1:2284788/58‑1 (MQ=255)
                               tCCGCCGGCAACCTGGTCATGAAGGTGTAACGCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGgtg                             >  1:435396/1‑69 (MQ=255)
                               tCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAacgctgacgct                                                 >  1:2277104/1‑49 (MQ=255)
                               tCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGgtg                             >  1:2555855/1‑69 (MQ=255)
                               tCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGgtg                             >  1:762289/1‑69 (MQ=255)
                               tCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGgtg                             >  1:804350/1‑69 (MQ=255)
                               tCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGgtg                             >  1:490502/1‑69 (MQ=255)
                               tCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGgtg                             >  1:937989/1‑69 (MQ=255)
                               tCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGgtg                             >  1:2732891/1‑69 (MQ=255)
                               tCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGgtg                             >  1:2693833/1‑69 (MQ=255)
                               tCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGgtg                             >  1:1242715/1‑69 (MQ=255)
                               tCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGgtg                             >  1:1394818/1‑69 (MQ=255)
                               tCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGgtg                             >  1:1749177/1‑69 (MQ=255)
                               tCCGCCAGCAACCTGGTCATGAAGGTGTAACGCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGgtg                             >  1:1973051/1‑69 (MQ=255)
                                  gCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGgtgtg                           <  1:2766505/68‑1 (MQ=255)
                                  gCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGgtgtg                           <  1:121878/68‑1 (MQ=255)
                                  gCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGgtgtg                           <  1:713364/68‑1 (MQ=255)
                                   ccAGCAACCAGGTCATGAAGGTGTAACTCAGCAAacgctga                                                     <  1:2876811/41‑1 (MQ=255)
                                   ccAGCAACCAGGTCATGAAGGTGTAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGgtgtg                           <  1:231396/67‑1 (MQ=255)
                                     aGCAACCTGGTCATGAAGGTGTAACGCAGCAAacgctgacgct                                                 <  1:278456/43‑1 (MQ=38)
                                       cAACCAGGTCATGAAGGTGTAACTCAGCAAacgctga                                                     <  1:2276853/37‑1 (MQ=255)
                                         aCCAGGTCATGAAGGTGTAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCaa                   <  1:2689461/69‑1 (MQ=255)
                                         aCCAGGTCATGAAGGTGTAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCaa                   <  1:1774082/69‑1 (MQ=255)
                                          ccAGGTCATGAAGGTGTAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGTCCaa                   <  1:977086/68‑1 (MQ=255)
                                                cATGAAGGTGTAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAatat                >  1:1962513/1‑65 (MQ=255)
                                                cATGAAGGTGTAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGa             >  1:713902/1‑68 (MQ=255)
                                                cATGAAGGTGTAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGa             >  1:2867829/1‑68 (MQ=255)
                                                cATGAAGGTGTAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGa             >  1:2986486/1‑68 (MQ=255)
                                                cATGAAGGTGTAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGAt            >  1:2260312/1‑69 (MQ=255)
                                                cATGAAGGTGTAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGAt            >  1:202945/1‑69 (MQ=255)
                                                cATGAAGGTGTAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGAt            >  1:710534/1‑69 (MQ=255)
                                                cATGAAGGTGTAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGAt            >  1:2947306/1‑69 (MQ=255)
                                                    taGGTGTAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACa        <  1:3367319/68‑1 (MQ=255)
                                                    aaGGTGTAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACa        <  1:2387552/69‑1 (MQ=255)
                                                    aaGGTGTAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACa        <  1:2995856/69‑1 (MQ=255)
                                                    aaGGTGTAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACa        <  1:232929/69‑1 (MQ=255)
                                                    aaGGTGTAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACa        <  1:3390324/69‑1 (MQ=255)
                                                    aaGGTGTAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACa        <  1:1223883/69‑1 (MQ=255)
                                                          tAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACaaa      >  1:1881748/1‑65 (MQ=255)
                                                          tAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACAAACCt   >  1:1445683/1‑68 (MQ=255)
                                                          tAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACAAACCt   >  1:247507/1‑68 (MQ=255)
                                                          tAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACAAACCt   >  1:935084/1‑68 (MQ=255)
                                                          tAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACAAACCTg  >  1:1388450/1‑69 (MQ=255)
                                                          tAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACAAACCTg  >  1:1736065/1‑69 (MQ=255)
                                                          tAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACAAACCTg  >  1:2831629/1‑69 (MQ=255)
                                                          tAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACAAACCTg  >  1:2483425/1‑69 (MQ=255)
                                                          tAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACAAACCTg  >  1:1495768/1‑69 (MQ=255)
                                                          tAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACAAACCTg  >  1:1699486/1‑69 (MQ=255)
                                                          tAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACAAACCTg  >  1:3267174/1‑69 (MQ=255)
                                                          tAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACAAACCTg  >  1:3000938/1‑69 (MQ=255)
                                                            aCTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACaa       <  1:1455680/62‑1 (MQ=255)
                                                            aCTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACaa       <  1:16992/62‑1 (MQ=255)
                                                            aCTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACaa       <  1:1883309/62‑1 (MQ=255)
                                                            aCTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACaa       <  1:3427811/62‑1 (MQ=255)
                                                            aCTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACaa       <  1:306466/62‑1 (MQ=255)
                                                              |                                                                
CCATTTGGTACGAATACCTGGTTCTATGTCTTCCGCCAGCAACCAGGTCATGAAGGTGTAACTCAGCAAACGCTGACGCTGACCTTTAACAGTAGCGGTGTGTTGACCAATATTGATAACAAACCTG  >  minE/1786489‑1786615

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