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 F2 I1 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA Exported 608,985 C→T 21.2% P423P (CCG→CCA)  pflB ← pyruvate formate lyase I

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported608,9850CT21.2% 266.5 / 61.3 132P423P (CCG→CCA) pflBpyruvate formate lyase I
Reads supporting (aligned to +/- strand):  ref base C (42/62);  new base T (15/13);  total (57/75)
Fisher's exact test for biased strand distribution p-value = 2.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.77e-01

Only 100 of 145 total aligned reads displayed.

GCGTACAGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCT  >  Exported/608917‑609052
                                                                    |                                                                   
gCGTACAGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCgg                                                                   >  1:5340523/1‑71 (MQ=255)
 cGTACAGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCgg                                                                   <  1:493001/70‑1 (MQ=255)
   tACAGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCt                                                                <  1:4018357/71‑1 (MQ=255)
     cAGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTa                                                              >  1:5663115/1‑71 (MQ=255)
     cAGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTa                                                              >  1:2240311/1‑71 (MQ=255)
     cAGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTa                                                              >  1:5572364/1‑71 (MQ=255)
      aGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTAc                                                             <  1:1128710/71‑1 (MQ=255)
      aGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTAc                                                             <  1:196137/71‑1 (MQ=255)
        cATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACg                                                            >  1:2583007/1‑70 (MQ=255)
         aTGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTa                                                              >  1:3132667/1‑67 (MQ=255)
          tGGTTTTCGGCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACg                                                            <  1:4912499/68‑1 (MQ=255)
          tGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACAATCATCGGGCTTACg                                                            <  1:508464/68‑1 (MQ=255)
            gTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACgcagc                                                        <  1:1461504/70‑1 (MQ=255)
            gTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACgcagc                                                        >  1:1569553/1‑70 (MQ=255)
             ttttCGCCAGGTTTGCACGCGCACCGATGAACTGCATTTGTTTACCAACGATCATCGGGCTTa                                                              <  1:4923260/63‑1 (MQ=255)
             ttttCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCtt                                                               <  1:1943784/62‑1 (MQ=255)
             ttttCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACgcagc                                                        >  1:4480111/1‑69 (MQ=255)
             ttttCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCagcaa                                                      <  1:4812571/71‑1 (MQ=255)
              tttCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCagcaag                                                     >  1:5117703/1‑71 (MQ=255)
              tttCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCagcaag                                                     >  1:5591309/1‑71 (MQ=255)
              tttCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCagcaag                                                     >  1:3055222/1‑71 (MQ=255)
               ttCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCagcaag                                                     >  1:2391923/1‑70 (MQ=255)
               ttCGCCAGGTTAGCGCGTGCACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACgcagcagg                                                     >  1:5184458/1‑68 (MQ=255)
               ttCGCCAGGTTAGCGCGTGCACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACgcagcagg                                                     >  1:5207214/1‑68 (MQ=255)
               ttCGCCAGGTTAGCGCGTGCACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACgcagcagg                                                     >  1:5332640/1‑68 (MQ=255)
               ttCGCCAGGTTAGCGCGTGCACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACgcagcagg                                                     >  1:32789/1‑68 (MQ=255)
                tCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCt                                                                <  1:5587630/58‑1 (MQ=255)
                tCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCagcaagc                                                    <  1:5547664/70‑1 (MQ=255)
                tCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCagcaagc                                                    <  1:3043363/70‑1 (MQ=255)
                tCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCagcaagc                                                    <  1:2032018/70‑1 (MQ=255)
                  gCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAgcaagcaa                                                  <  1:4224293/70‑1 (MQ=255)
                  gCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAgcaagcaa                                                  <  1:4653418/70‑1 (MQ=255)
                     aGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGc                                              >  1:945354/1‑71 (MQ=255)
                     aGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGc                                              >  1:1211034/1‑71 (MQ=255)
                     aGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGc                                              >  1:2480333/1‑71 (MQ=255)
                      ggTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCg                                             <  1:224252/71‑1 (MQ=255)
                       gTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCt                                                                <  1:4766030/51‑1 (MQ=255)
                       gTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCt                                                                <  1:4772410/51‑1 (MQ=255)
                       gTTAGCGCGTGCACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGt                                            <  1:2925223/71‑1 (MQ=255)
                           gCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCgg                                                                   <  1:2511788/44‑1 (MQ=255)
                           gCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCgg                                                                   <  1:4919366/44‑1 (MQ=255)
                            cACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCagcaagc                                                    <  1:2138586/58‑1 (MQ=255)
                               gcgcACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCg                                    <  1:1110034/71‑1 (MQ=255)
                                cgcACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgt                                   <  1:1980355/71‑1 (MQ=255)
                                 gcACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgtt                                  >  1:1677563/1‑71 (MQ=255)
                                 gcACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgtt                                  >  1:3664825/1‑71 (MQ=255)
                                 gcACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgt                                   >  1:140475/1‑70 (MQ=255)
                                 gcACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACGCAgcaggcaa                                                  <  1:4796127/55‑1 (MQ=255)
                                  cACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGc                                              <  1:4355125/58‑1 (MQ=255)
                                  cACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGc                                              <  1:3759162/58‑1 (MQ=255)
                                  cACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCgctg                                 >  1:3185884/1‑71 (MQ=255)
                                   aCCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACgcagc                                                        <  1:2560571/47‑1 (MQ=16)
                                    ccGAAGAACTGCATTTGTTTACCAACGATCATCGGCCTTACgcag                                                         <  1:771054/45‑1 (MQ=255)
                                     caaagaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCgctgtt                               >  1:514048/3‑70 (MQ=255)
                                     caaagaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCGctgttg                              <  1:3782391/69‑1 (MQ=255)
                                     cGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACgca                                                          <  1:2036588/43‑1 (MQ=255)
                                     cGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCg                                             <  1:192719/56‑1 (MQ=255)
                                     cGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGttgttg                              <  1:3985486/71‑1 (MQ=255)
                                     cGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGttgttg                              <  1:2209975/71‑1 (MQ=255)
                                      gaagaaCTGCATTTGTTTACCAACGATCATCGGGCTTACgcagca                                                       >  1:2612485/1‑45 (MQ=255)
                                      gaagaaCTGCATTTGTTTACCAACGATCATCGGGCTTACgcagca                                                       >  1:4493100/1‑45 (MQ=255)
                                      gaagaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGa                             <  1:217997/71‑1 (MQ=255)
                                      aaagaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCGctgttg                              >  1:1616873/2‑70 (MQ=255)
                                      aaagaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCGctgttg                              >  1:4544652/2‑70 (MQ=255)
                                      aaagaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCGctgttg                              >  1:633249/2‑70 (MQ=255)
                                       aagaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATa                                                >  1:4163056/1‑51 (MQ=255)
                                       aagaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGc                                              <  1:3781532/53‑1 (MQ=255)
                                       aagaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGttgttg                              >  1:4654861/1‑69 (MQ=255)
                                       aagaaCTGCATTTGCTTACCAATCACCATTGGGCTGACgcagc                                                        >  1:1492323/1‑43 (MQ=16)
                                       aagaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAAtc                                                >  1:4440321/1‑50 (MQ=255)
                                        agaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCagcaggc                                                    <  1:3828394/46‑1 (MQ=16)
                                        agaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCagcaggc                                                    <  1:3829407/46‑1 (MQ=16)
                                          aaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAAtcgtcgc                                   <  1:3580464/61‑2 (MQ=255)
                                          aaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCGCTGTTGAAGTc                         <  1:1569837/71‑1 (MQ=255)
                                            cTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGaa                            >  1:5081927/1‑66 (MQ=255)
                                             tGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTc                                        <  1:762743/53‑1 (MQ=255)
                                             tGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTc                                        <  1:2918683/53‑1 (MQ=255)
                                              gCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAAt                                                 >  1:1195933/1‑43 (MQ=255)
                                              gCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAAt                                                 >  1:515316/1‑43 (MQ=255)
                                                 tttGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATa                                                <  1:2369170/41‑1 (MQ=255)
                                                  ttGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTc                                        <  1:3881398/48‑1 (MQ=255)
                                                  ttGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCg                       <  1:5176578/65‑1 (MQ=255)
                                                   tGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCAt                >  1:268613/1‑71 (MQ=255)
                                                    gTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGa                     >  1:5244188/1‑65 (MQ=255)
                                                     tttACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgttg                                 <  1:172749/52‑1 (MQ=255)
                                                     tttACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCAt                >  1:4548540/1‑69 (MQ=255)
                                                        aCCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAgg            <  1:3253912/70‑1 (MQ=255)
                                                           aaCGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCAt        <  1:2096741/71‑1 (MQ=255)
                                                             cGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCg      <  1:4051844/71‑1 (MQ=255)
                                                             cGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCg      >  1:822877/1‑71 (MQ=255)
                                                              gATCATCGGTCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGt     >  1:3346541/1‑71 (MQ=255)
                                                               accattGGGCTGACGCAGCAGGCAATCGCGTAATCGTCGCTGTTGAAGTCAGTACGCATCAGATCGTCAtt    <  1:2958484/69‑1 (MQ=255)
                                                                tcatcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTc          >  1:1007848/1‑64 (MQ=255)
                                                                tcatcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTtc   <  1:2113837/71‑1 (MQ=255)
                                                                tcatcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTtc   <  1:3016969/71‑1 (MQ=255)
                                                                 catcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTtct  >  1:5542797/1‑71 (MQ=255)
                                                                 catcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTtct  >  1:4750025/1‑71 (MQ=255)
                                                                 catcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTtct  >  1:1482523/1‑71 (MQ=255)
                                                                  atcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTtct  <  1:439156/70‑1 (MQ=255)
                                                                   tcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCg                       <  1:2755966/48‑1 (MQ=255)
                                                                    |                                                                   
GCGTACAGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCT  >  Exported/608917‑609052

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