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
A11 F212 I1 R1 174 80.0 3892211 96.7% 3763768 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,386,365 T→A F169Y (TTC→TAC)  yfbL → putative M28A family peptidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,386,3650TA95.7% 240.6 / 2.0 70F169Y (TTC→TAC) yfbLputative M28A family peptidase
Reads supporting (aligned to +/- strand):  ref base T (1/2);  new base A (37/30);  total (38/32)
Fisher's exact test for biased strand distribution p-value = 5.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.06e-01

CGGTGTGGCAGGATTACTCGAACTGGCACGTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTTCTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTAATGATAGCACTGGAGATGATTGGCTATTAC  >  NC_000913/2386267‑2386459
                                                                                                  |                                                                                              
cGGTGTGGCAGGATTACTCGAACTGGCACGTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCcttc                                                                                               <  1:571405/100‑1 (MQ=255)
 ggTGTGGCAGGATTACTCGAACTGGCACGTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCctact                                                                                              >  2:682763/1‑100 (MQ=255)
    gtgGCAGGATTACTCGAACTGGCACGTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTTCTTTc                                                                                           <  2:1908039/100‑1 (MQ=255)
    gtgGCAGGATTACTCGAACTGGCACGTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTc                                                                                           <  2:953799/100‑1 (MQ=255)
     tgGCAGGATTACTCGAACTGGCACGTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCg                                                                                          <  2:500435/100‑1 (MQ=255)
        cAGGATTACTCGAACTGGCACGTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTan                                                                                       <  2:954975/100‑2 (MQ=255)
          ggATTACTCGAACTGGCACGTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCg                                                                                     >  2:706338/1‑100 (MQ=255)
            aTTACTCGAACTGGCACGTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTTCTTTCGTAGCGAt                                                                                   <  2:1856054/100‑1 (MQ=255)
               aCTCGAACTGGCACGTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGCTGaa                                                                                >  1:1773500/1‑100 (MQ=255)
               aCTCGAACTGGCACGTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGaa                                                                                >  2:555098/1‑100 (MQ=255)
               aCTCGAACTGGCACGTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGaa                                                                                >  2:1295923/1‑100 (MQ=255)
               aCTCGAACTGGCACGTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGaa                                                                                >  1:1921121/1‑100 (MQ=255)
                cTCGAACTGGCACGTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGaaa                                                                               <  2:1921134/100‑1 (MQ=255)
                cTCGAACTGGCACGTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGaaa                                                                               >  1:765713/1‑100 (MQ=255)
                 tCGAACTGGCACGTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAAt                                                                              <  1:1112213/100‑1 (MQ=255)
                     aCTGGCACGTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATgggg                                                                          <  1:1538019/100‑1 (MQ=255)
                      cTGGCACGTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGa                                                                         >  1:1801547/1‑100 (MQ=255)
                         gCACGTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAgcg                                                                      >  2:1937605/1‑100 (MQ=255)
                          cACGTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAgcgc                                                                     >  2:901033/1‑100 (MQ=255)
                          cACGTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAACAACCGCCCTACTTTCGCAGCCATGAAATGGGGAccgc                                                                     >  1:1692181/1‑100 (MQ=255)
                             gTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGt                                                                  <  1:105950/100‑1 (MQ=255)
                             gTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGt                                                                  >  1:849659/1‑100 (MQ=255)
                               ttGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGtgc                                                                <  1:550902/100‑1 (MQ=255)
                                tGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGtgca                                                               <  2:235464/100‑1 (MQ=255)
                                tGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGtgca                                                               <  1:1895560/100‑1 (MQ=255)
                                   tACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGtgcatgc                                                            <  1:1911783/100‑1 (MQ=255)
                                    aCATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGtgcatgca                                                           <  2:1030321/100‑1 (MQ=255)
                                    aCATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGtgcatgca                                                           >  2:709901/1‑100 (MQ=255)
                                    aCATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGtgcatgca                                                           >  2:795982/1‑100 (MQ=255)
                                    aCATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGtgcatgc                                                            >  1:8889/1‑99 (MQ=255)
                                      aTCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGc                                                         >  1:839832/1‑100 (MQ=255)
                                        cAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCtt                                                       >  2:1328635/1‑100 (MQ=255)
                                        cAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCtt                                                       >  2:1051853/1‑100 (MQ=255)
                                            aaGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCt                                                   <  2:537584/100‑1 (MQ=255)
                                              gTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTg                                                 <  1:352569/100‑1 (MQ=255)
                                              gTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTg                                                 >  2:424705/1‑100 (MQ=255)
                                              gTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTg                                                 <  2:1363134/100‑1 (MQ=255)
                                               tACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGa                                                >  1:1935710/1‑100 (MQ=255)
                                                aCCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAg                                               >  1:1506098/1‑100 (MQ=255)
                                                 ccGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTTCTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAg                                               >  2:143928/1‑99 (MQ=255)
                                                 ccGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGTGCGGTGCATGCAGCTTCGCTTGAGc                                              >  1:538138/1‑100 (MQ=255)
                                                 ccGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGc                                              >  2:784513/1‑100 (MQ=255)
                                                 ccGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGc                                              >  2:1799544/1‑100 (MQ=255)
                                                  cGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCg                                             >  2:1795351/1‑100 (MQ=255)
                                                  cGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCg                                             >  2:1795366/1‑100 (MQ=255)
                                                     aaaCAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTcc                                          <  1:1271166/100‑1 (MQ=255)
                                                      aaCAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCa                                         >  2:1380171/1‑100 (MQ=255)
                                                        cAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCCCCCTACTTTCGTAGCGATTAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTcc                                          <  2:1814841/97‑1 (MQ=255)
                                                          ggCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGa                                     >  2:1812978/1‑100 (MQ=255)
                                                                 aGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTAAt                              <  1:1322587/100‑1 (MQ=255)
                                                                 aGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTAAt                              <  1:901032/100‑1 (MQ=255)
                                                                 aGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTAAt                              <  2:1154118/100‑1 (MQ=255)
                                                                  gCTGGTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTAATg                             <  2:1623855/100‑1 (MQ=255)
                                                                     ggTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGTGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTAATGATa                          <  2:538140/100‑1 (MQ=255)
                                                                     ggTCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTAATGATa                          >  2:879292/1‑100 (MQ=255)
                                                                       tCGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTAATGATAGc                        <  1:795980/100‑1 (MQ=255)
                                                                        cGCCTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTAATGATAGCa                       >  1:45995/1‑100 (MQ=255)
                                                                          ccTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTAATGATAGCACt                     >  1:577845/1‑100 (MQ=255)
                                                                           cTATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTAATGATAGCACTg                    >  1:746580/1‑100 (MQ=255)
                                                                            tATGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTAATGATAGCACTgg                   <  2:849660/100‑1 (MQ=255)
                                                                             aTGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTAATGATAGCACTGga                  <  2:1653469/100‑1 (MQ=255)
                                                                             aTGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTAATGATAGCACTGga                  <  2:1343532/100‑1 (MQ=255)
                                                                             aTGCGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTAATGATAGCACTGga                  <  1:555096/100‑1 (MQ=255)
                                                                                cGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTAATGATAGCACTGGAgat               >  2:825508/1‑100 (MQ=255)
                                                                                cGTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCCTCGCTTGAGCGTCCAGTGAAATTAATGATAGCACTGGAgat               >  2:1120674/1‑100 (MQ=255)
                                                                                 gTCGGAAGAACCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTAATGATAGCACTGGAgatg              >  2:1031459/1‑100 (MQ=255)
                                                                                       agaaCCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTAATGATAGCACTGGAGATGATTGGc        >  2:521943/1‑100 (MQ=255)
                                                                                       agaaCCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTAATGATAGCACTGGAGATGATTGGc        <  2:1353940/100‑1 (MQ=255)
                                                                                         aaCCGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTAATGATAGCACTGGAGATGATTGGCTa      <  1:118349/100‑1 (MQ=255)
                                                                                           ccGCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTTATGATAGCACTGGAGATGATTGGCTAtt    >  1:877199/1‑100 (MQ=255)
                                                                                             gCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTAATGATAGCACTGGAGATGATTGGCTATTAc  >  2:510415/1‑100 (MQ=255)
                                                                                             gCCCTACTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTAATGATAGCACTGGAGATGATTGGCTATTAc  <  1:1937592/100‑1 (MQ=255)
                                                                                                  |                                                                                              
CGGTGTGGCAGGATTACTCGAACTGGCACGTTTGTTACATCAGCAAGTACCGAAAACAGGCGTGCAGCTGGTCGCCTATGCGTCGGAAGAACCGCCCTTCTTTCGTAGCGATGAAATGGGGAGCGCGGTGCATGCAGCTTCGCTTGAGCGTCCAGTGAAATTAATGATAGCACTGGAGATGATTGGCTATTAC  >  NC_000913/2386267‑2386459

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A