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
A4 F195 I0 R2 483 52.1 1908604 98.1% 1872340 138.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,043,503 A→C 7.7% G236G (GGT→GGG)  etk ← tyrosine‑protein kinase, role in O‑antigen capsule formation

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,043,5030AC 7.7% 177.4 / 6.8 52G236G (GGT→GGG) etktyrosine‑protein kinase, role in O‑antigen capsule formation
Reads supporting (aligned to +/- strand):  ref base A (23/25);  new base C (2/2);  total (25/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.23e-01

CTTGGTCCAGCTCGCTGCGCACTTCAGGTAACTGGCGCTGTAAGAATTCAAGGCTTTGTGAATCCTGCGCCGCCTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTCCAGTTCGGTACGCTGGCTCAGGACAAACTGTGTTCCTGGTTTGGCCTTAATGTCCGC  >  NC_000913/1043355‑1043643
                                                                                                                                                    |                                                                                                                                            
cTTGGTCCAGCTCGCTGCGCACTTCAGGTAACTGGCGCTGTAAGAATTCAAGGCTTTGTGAATCCTGCGCCGCCTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGAtcatca                                                                                                                                              >  4:91997/1‑149 (MQ=255)
        aGCTCGCTGCGCACTTCAGGTAACTGGCGCTGTAAGAATTCAAGGCTTTGTGAATCCTGCGCCGCCTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCAt                                                                                                                                      <  2:265544/149‑1 (MQ=255)
        aGCTCGCTGCGCACTTCAGGTAACTGGCGCTGTAAGAATTCAAGGCTTTGTGAATCCTGCGCCGCCTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCAt                                                                                                                                      >  1:454680/1‑149 (MQ=255)
         gCTCGCTGCGCACTTCAGGTAACTGGCGCTGTAAGAATTCAAGGCTTTGTGAATCCTGCGCCGCCTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATg                                                                                                                                     <  2:133595/149‑1 (MQ=255)
           tCGCTGCGCACTTCAGGTAACTGGCGCTGTAAGAATTCAAGGCTTTGTGAATCCTGCGCCGCCTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGt                                                                                                                                   >  4:172723/1‑149 (MQ=255)
           tCGCTGCGCACTTCAGGTAACTGGCGCTGTAAGAATTCAAGGCTTTGTGAATCCTGCGCCGCCTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGt                                                                                                                                   >  2:19915/1‑149 (MQ=255)
                               cTGGCGCTGTAAGAATTCAAGGCTTTGTGAATCCTGCGCCGCCTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGcttt                                                                                                               <  3:91997/149‑1 (MQ=255)
                                    gcTGTAAGAATTCAAGGCTTTGTGAATCCTGCGCCGCCTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTa                                                                                                          <  3:45238/149‑1 (MQ=255)
                                    gcTGTAAGAATTCAAGGCTTTGTGAATCCTGCGCCGCCTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTa                                                                                                          >  3:37451/1‑149 (MQ=255)
                                        tAAGAATTCAAGGCTTTGTGAATCCTGCGCCGCCTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGc                                                                                                      >  1:115371/1‑149 (MQ=255)
                                          aGAATTCAAGGCTTTGTGAATCCTGCGCCGCCTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGt                                                                                                    >  2:373346/1‑149 (MQ=255)
                                            aaTTCAAGGCTTTGTGAATCCTGCGCCGCCTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTc                                                                                                  <  4:161434/149‑1 (MQ=255)
                                                        tgtgAATCCTGCGCCGCCTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCGACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTaaa                                                                                      <  2:187365/149‑1 (MQ=255)
                                                        tgtgAATCCTGCGCCGCCTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTaaa                                                                                      <  3:388840/149‑1 (MQ=255)
                                                         gtgAATCCTGCGCCGCCTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTc                                                                                                  >  3:220673/1‑136 (MQ=255)
                                                         gtgAATCCTGCGCCGCCTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTc                                                                                                  <  4:220673/136‑1 (MQ=255)
                                                           gAATCCTGCGCCGCCTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGt                                                                                                                               <  2:401975/105‑1 (MQ=255)
                                                           gAATCCTGCGCCGCCTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGt                                                                                                                               >  1:401975/1‑105 (MQ=255)
                                                             aTCCTGCGCCGCCTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGttt                                                                                 >  1:363279/1‑149 (MQ=255)
                                                              tCCTGCGCCGCCTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTc                                                                                >  2:308100/1‑149 (MQ=255)
                                                                   cgccgcCTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCa                                                                           >  2:432165/1‑149 (MQ=255)
                                                                    gccgccTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCaa                                                                          <  2:115371/149‑1 (MQ=255)
                                                                       gccTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGTGATGATCCCCAGtt                                                                                                                                        >  2:34856/1‑83 (MQ=255)
                                                                       gccTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGTGATGATCCCCAGtt                                                                                                                                        <  1:34856/84‑2 (MQ=255)
                                                                          tGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGtt                                                                    >  3:438364/1‑149 (MQ=255)
                                                                             cgagcgaTATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAAt                                                                 <  4:443797/149‑1 (MQ=255)
                                                                                          gTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTCCAGTTCg                                                    <  1:19915/149‑1 (MQ=255)
                                                                                           ttGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTCCAGTTCgg                                                   <  2:454680/149‑1 (MQ=255)
                                                                                                 aTAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTCCAGTTCGGTACGCt                                             >  2:413326/1‑149 (MQ=255)
                                                                                                        ttAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTCCAGTTCGGTACGCTGGCTCAg                                      >  1:114832/1‑149 (MQ=255)
                                                                                                          aGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTCCAGTTCGGTACGCTGGCTCAGGa                                    <  1:308100/149‑1 (MQ=255)
                                                                                                             gATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTCCAGTTCGGTACGCTGGCTCAGGACaa                                 >  1:342394/1‑149 (MQ=255)
                                                                                                               tGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTCCAGTTCGGTACGCTGGCTCAGGACAAAc                               <  2:443736/149‑1 (MQ=255)
                                                                                                                gCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTCCAGTTCGGTACGCTGGCTCAGGACAAACt                              >  3:437222/1‑149 (MQ=255)
                                                                                                                     tCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGct                                                                                                                 >  1:365720/1‑61 (MQ=255)
                                                                                                                     tCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGct                                                                                                                 <  2:365720/61‑1 (MQ=255)
                                                                                                                        gAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTCCAGTTCGGTACGCTGGCTCAGGACAAACTGTGTTCCt                      <  4:92410/149‑1 (MQ=255)
                                                                                                                         aaTACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTCCAGTTCGGTACGCTGGCTCAGGACAAACTGTGTTCCTg                     >  2:16843/1‑149 (MQ=255)
                                                                                                                          aTACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTCCAGTTCGGTACGCTGGCTCAGGACAAACTGTGTTCCTgg                    <  2:342394/149‑1 (MQ=255)
                                                                                                                             cGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTCCAGTTCGGTACGCTGGCTCAGGACAAACTGTGTTCCTGGttt                 <  1:432165/149‑1 (MQ=255)
                                                                                                                              gAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTc                                                           >  3:123926/1‑106 (MQ=255)
                                                                                                                              gAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTc                                                           <  4:123926/106‑1 (MQ=255)
                                                                                                                                gTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTCCAGTTCGGTACGCTGGCTCAGGACAAACTGTGTTCCTGGTTTGGc              <  3:243621/149‑1 (MQ=255)
                                                                                                                                  ccatgaCTGGTGATGATCCCCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTCCAGTTCGGTACGCTGGCTCAGGACAAACTGTGTTCCTGGTTTGGCCt            >  4:411779/6‑149 (MQ=255)
                                                                                                                                   catgaCTGGTGATGATCCCCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTCCAGTTCGGTACGCTGGCTCAGGACAAACTGTGTTCCTGGTTTGGCCtt           <  3:411779/145‑1 (MQ=255)
                                                                                                                                    tCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTCCAGTTCGGTACGCTGGCTCAGGACAAACTGTGTTCCTGGTTTGGCCTTa          >  4:474527/1‑149 (MQ=255)
                                                                                                                                     cAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTCCAGTTCGGTACGCTGGCTCAGGACAAACTGTGTTCCTGGTTTGGCCTTaa         <  2:114832/149‑1 (MQ=255)
                                                                                                                                      aaCTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTCCAGTTCGGTACGCTGGCTCAGGACAAACTGTGTTCCTGGTTTGGCCTTAAt        >  4:334490/1‑149 (MQ=255)
                                                                                                                                      aaCTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTCCAGTTCGGTACGCTGGCTCAGGACAAACTGTGTTCCTGGTTTGGCCTTAAt        <  4:438364/149‑1 (MQ=255)
                                                                                                                                          ggggATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTCCAGTTCGGTACGCTGGCTCAGGACAAACTGTGTTCCTGGTTTGGCCTTAATGTcc    >  1:390795/1‑149 (MQ=255)
                                                                                                                                           gggATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCt                                                                                               <  1:275689/57‑1 (MQ=255)
                                                                                                                                           gggATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCt                                                                                               >  2:275689/1‑57 (MQ=255)
                                                                                                                                            ggATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTCCAGTTCGGTACGCTGGCTCAGGACAAACTGTGTTCCTGGTTTGGCCTTAATGTCcgc  <  4:37451/149‑1 (MQ=255)
                                                                                                                                                    |                                                                                                                                            
CTTGGTCCAGCTCGCTGCGCACTTCAGGTAACTGGCGCTGTAAGAATTCAAGGCTTTGTGAATCCTGCGCCGCCTGGCGAGCGATATTCTGTTGCAAATAGTTGTTAGCGATGCTGTTCAGAATACGAGTAATCAACTGGGGATCATCACCAGTCATGGTAAGTTCCAGCATCCCGCTTTCTTTACTGCGTTCGCTAACGGTAAAGGTTTCCTGCAATGCGTTAATCGCTTCCAGTTCGGTACGCTGGCTCAGGACAAACTGTGTTCCTGGTTTGGCCTTAATGTCCGC  >  NC_000913/1043355‑1043643

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A