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
A3 F17 I0 R1 56 60.7 4808188 97.1% 4668750 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,809,581 G→A 49.3% G52G (GGG→GGA)  mprA → DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,809,5810GA49.3% 11.1 / 222.9 144G52G (GGG→GGA) mprADNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (35/38);  new base A (37/34);  total (72/72)
Fisher's exact test for biased strand distribution p-value = 7.39e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01

Only 100 of 149 total aligned reads displayed.

CTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCTG  >  W3110S.gb/2809514‑2809651
                                                                   |                                                                      
   gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                  >  1:3988984/1‑71 (MQ=255)
   gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                  <  1:1537103/71‑1 (MQ=255)
   gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                  <  1:3200826/71‑1 (MQ=255)
   gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTaa                                                                   <  1:3426854/70‑1 (MQ=255)
    tCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                  <  1:3514844/70‑1 (MQ=255)
      tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                  >  1:1607052/1‑68 (MQ=255)
        tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                                    >  1:556286/1‑64 (MQ=255)
        tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                                              <  1:862066/70‑1 (MQ=255)
        tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGAc                                                             >  1:1891236/1‑71 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAATGCTCAGGGAATTAACGAGACgttgtt                                                       <  1:4552688/71‑1 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                       <  1:4097929/71‑1 (MQ=255)
              cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                       >  1:966284/1‑71 (MQ=255)
                catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTa                                                     >  1:2261253/1‑71 (MQ=255)
                catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                     <  1:346496/71‑1 (MQ=255)
                 atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                    <  1:70731/71‑1 (MQ=255)
                 atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                    >  1:1931995/1‑71 (MQ=255)
                 atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                    >  1:1910318/1‑71 (MQ=255)
                  tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                                  <  1:1267337/56‑1 (MQ=255)
                  tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgtt                                                          >  1:3351225/1‑64 (MQ=255)
                  tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgtt                                                          >  1:1293273/1‑64 (MQ=255)
                  tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgtt                                                          >  1:4076305/1‑64 (MQ=255)
                  tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                                   >  1:2744960/1‑71 (MQ=255)
                    caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTa                                                                    >  1:4503291/1‑52 (MQ=255)
                    caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                                 >  1:1867974/1‑71 (MQ=255)
                    caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                                 >  1:3769974/1‑71 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                                    <  1:2109365/65‑1 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                              >  1:751866/1‑71 (MQ=255)
                       agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                              <  1:2899108/71‑1 (MQ=255)
                        gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                              <  1:3132562/70‑1 (MQ=255)
                        gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTg                                             <  1:3656111/71‑1 (MQ=255)
                        gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                              >  1:416768/1‑70 (MQ=255)
                        gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGt                                               >  1:2176124/1‑69 (MQ=255)
                          aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:1790565/71‑1 (MQ=255)
                          aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:3416860/71‑1 (MQ=255)
                          aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:1298280/71‑1 (MQ=255)
                          aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTaa                                                                   >  1:329413/1‑47 (MQ=255)
                          aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTaa                                                                   >  1:1049683/1‑47 (MQ=255)
                           agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgt                                                        <  1:3252910/57‑1 (MQ=255)
                           agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                                    >  1:1119812/1‑45 (MQ=255)
                            gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTg                                             <  1:857593/67‑1 (MQ=255)
                             ctgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTAc                                        <  1:1996262/71‑1 (MQ=255)
                              tgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                         >  1:769270/1‑69 (MQ=255)
                                ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                       >  1:1610033/1‑53 (MQ=255)
                                ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACg                                       <  1:2073254/69‑1 (MQ=255)
                                 tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTa                                         >  1:2971573/1‑66 (MQ=255)
                                 tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                     <  1:1090315/38‑1 (MQ=255)
                                 tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                     <  1:1929841/38‑1 (MQ=255)
                                 tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                     <  1:2503832/38‑1 (MQ=255)
                                 tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                                <  1:481124/43‑1 (MQ=255)
                                  ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                     >  1:1202894/1‑53 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                    >  1:388534/1‑69 (MQ=255)
                                   gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                  <  1:1953496/71‑1 (MQ=255)
                                    agaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTg                                             >  1:2851509/1‑59 (MQ=255)
                                       aCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                       >  1:2867250/1‑46 (MQ=255)
                                       aCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                           <  1:4291982/58‑1 (MQ=255)
                                         cGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgt                                                           <  1:1411143/40‑1 (MQ=255)
                                          gCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGAc                                                             >  1:2314053/1‑37 (MQ=255)
                                          gCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgtt                                                          >  1:3385897/1‑40 (MQ=255)
                                          gCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                           >  1:631678/1‑71 (MQ=255)
                                           cAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                              <  1:2638786/51‑1 (MQ=255)
                                           cAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                              <  1:3929107/51‑1 (MQ=255)
                                           cAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                                              >  1:4150878/1‑35 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                     >  1:411976/1‑42 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGc                                                 <  1:3487692/46‑1 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                  >  1:4573848/1‑61 (MQ=255)
                                             aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                        <  1:3687532/71‑1 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                            >  1:1303813/1‑50 (MQ=255)
                                              tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAg                                 <  1:4067862/61‑1 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                       >  1:2013130/1‑37 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                       >  1:583254/1‑37 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGGATTAACGAGACgttgt                                                        <  1:2734190/36‑1 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                            >  1:3400169/1‑48 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc                     >  1:4318268/1‑71 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                     >  1:3072635/1‑39 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGTAGTCTCAGGAAAAc                     <  1:514482/71‑1 (MQ=255)
                                                aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc                     >  1:4384266/1‑71 (MQ=255)
                                                 aaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTgg                                   >  1:1683888/1‑56 (MQ=255)
                                                  aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTa                                         >  1:2892593/1‑49 (MQ=255)
                                                  aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                   <  1:3523750/71‑1 (MQ=255)
                                                  aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                   <  1:1000849/71‑1 (MQ=255)
                                                     cTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                              >  1:2928460/1‑41 (MQ=255)
                                                     cTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTg                                             >  1:1503991/1‑42 (MQ=255)
                                                     cTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                              <  1:601052/57‑1 (MQ=255)
                                                     cTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                              <  1:3369409/57‑1 (MQ=255)
                                                     cTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg                <  1:3733130/71‑1 (MQ=255)
                                                        aaGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                            >  1:2703599/1‑40 (MQ=255)
                                                        aaGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa              <  1:398821/70‑1 (MQ=255)
                                                        aaGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt             >  1:4672727/1‑71 (MQ=255)
                                                        aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGt                                >  1:4725791/1‑52 (MQ=255)
                                                          ggCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc                     <  1:4649864/61‑1 (MQ=255)
                                                          ggCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc                     <  1:1645102/61‑1 (MQ=255)
                                                          ggCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc                     <  1:2080899/61‑1 (MQ=255)
                                                           gCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCa          <  1:4612693/71‑1 (MQ=255)
                                                            cTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                      >  1:1394359/1‑58 (MQ=255)
                                                            cTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTAAGGAAAACca                   >  1:1825541/1‑61 (MQ=255)
                                                             tCATGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAg         <  1:1483466/70‑1 (MQ=255)
                                                             tCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                              <  1:2266131/49‑1 (MQ=255)
                                                               aGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGcc       <  1:926265/70‑1 (MQ=255)
                                                                gggaATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCtt     >  1:443134/1‑71 (MQ=255)
                                                                   gATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCTg  <  1:1569725/71‑1 (MQ=255)
                                                                   |                                                                      
CTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCTG  >  W3110S.gb/2809514‑2809651

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