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	609,015	A→G	20.3%	D413D (GAT→GAC)	pflB ←	pyruvate formate lyase I

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	Exported	609,015	0	A	G	20.3%	263.3 / 59.9	133	D413D (GAT→GAC)	pflB	pyruvate formate lyase I
Reads supporting (aligned to +/- strand): ref base A (40/66); new base G (16/11); total (56/77)
Fisher's exact test for biased strand distribution p-value = 5.12e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.34e-01

Only 100 of 140 total aligned reads displayed.

GCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAAGAGGTGTCGATGGACACTT  >  Exported/608948‑609085

gcgcACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCg                                                                     <  1:1110034/71‑1 (MQ=255)

 cgcACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgt                                                                    <  1:1980355/71‑1 (MQ=255)

  gcACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgtt                                                                   >  1:3664825/1‑71 (MQ=255)

  gcACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgtt                                                                   >  1:4528867/1‑71 (MQ=255)

  gcACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgt                                                                    >  1:140475/1‑70 (MQ=255)

   cACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgttg                                                                  <  1:2154030/71‑1 (MQ=255)

   cACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCgctg                                                                  >  1:3185884/1‑71 (MQ=255)

      caaagaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCGctgttg                                                               <  1:5360228/69‑1 (MQ=255)

      caaagaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCGctgttg                                                               <  1:3782391/69‑1 (MQ=255)

      cGAAGATCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGttgttg                                                               <  1:2340665/71‑1 (MQ=255)

      cGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGttgttg                                                               <  1:4459885/71‑1 (MQ=255)

      cGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGttgttg                                                               <  1:3985486/71‑1 (MQ=255)

       gaagaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGa                                                              <  1:217997/71‑1 (MQ=255)

       aaagaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCGctgttg                                                               >  1:633249/2‑70 (MQ=255)

       aaagaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCGctgttg                                                               >  1:1616873/2‑70 (MQ=255)

       aaagaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCGctgttg                                                               >  1:4544652/2‑70 (MQ=255)

        aagaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGttgttg                                                               >  1:4654861/1‑69 (MQ=255)

        aagaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCGctgttg                                                               >  1:2232396/1‑69 (MQ=255)

          gaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCGCTGTTGAAGt                                                           >  1:24494/1‑71 (MQ=255)

           aaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAAtcgtcgc                                                                    <  1:3580464/61‑2 (MQ=255)

           aaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCGCTGTTGAAGTc                                                          <  1:1569837/71‑1 (MQ=255)

             cTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGaa                                                             >  1:5081927/1‑66 (MQ=255)

                 aTTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACg                                                    <  1:1878427/71‑1 (MQ=255)

                   ttGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCg                                                        <  1:5176578/65‑1 (MQ=255)

                   ttGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCg                                                        <  1:659474/65‑1 (MQ=255)

                    tGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCAt                                                 >  1:268613/1‑71 (MQ=255)

                      tttACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgttg                                                                  <  1:172749/52‑1 (MQ=255)

                      tttACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCAt                                                 >  1:4548540/1‑69 (MQ=255)

                        tACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAg                                              <  1:1626106/70‑1 (MQ=255)

                         aCCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAgg                                             <  1:3253912/70‑1 (MQ=255)

                          ccAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGt                                            <  1:1329495/70‑1 (MQ=255)

                            aaCGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCAt                                         <  1:2096741/71‑1 (MQ=255)

                              cGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCg                                       <  1:4051844/71‑1 (MQ=255)

                              cGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCg                                       >  1:822877/1‑71 (MQ=255)

                                accattGGGCTGACGCAGCAGGCAATCGCGTAATCGTCGCTGTTGAAGTCAGTACGCATCAGATCGTCAtt                                     <  1:2958484/69‑1 (MQ=255)

                                 tcatcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTc                                           >  1:1007848/1‑64 (MQ=255)

                                 tcatcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTc                                           >  1:947131/1‑64 (MQ=255)

                                 tcatcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTc                                           >  1:1557215/1‑64 (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)

                                    ttgggCTGACGCAGCAGGCAATCGCGTAATCGTCGCTGTTGAAGTCAGTACGCATCAg                                              <  1:5126323/56‑1 (MQ=255)

                                    ttgggCTGACGCAGCAGGCAATCGCGTAATCGTCGCTGTTGAAGTCAGTACGCATCAGATCGTCATTTTCa                                 >  1:5684195/3‑71 (MQ=255)

                                    tcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCg                                                        <  1:2755966/48‑1 (MQ=255)

                                      gggCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCAt                                <  1:4952891/70‑1 (MQ=255)

                                      gggCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATa                               >  1:230515/1‑71 (MQ=255)

                                           tACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTg                            >  1:683461/1‑69 (MQ=255)

                                            aCGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGt                                                           >  1:3345073/1‑37 (MQ=255)

                                             cGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCaga                        <  1:2738835/71‑1 (MQ=255)

                                              gcagcaGGCAATCGCGTAATCGTCGCTGTTGAAGTCAGTACGCATCAGATCGTCATTTTCATACTGCaagg                       <  1:4350307/71‑4 (MQ=255)

                                              gcagcaGGCAATCGCGTAATCGTCGCTGTTGAAGTCAGTACGCATCAGATCGTCATTTTCATACTGCaagg                       <  1:3895082/71‑4 (MQ=255)

                                              gcagcaAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTc                                           <  1:373776/51‑1 (MQ=255)

                                                agcaagcaATAGCGTAGTCATCGTTGTTGAAGTCCGGa                                                      >  1:3094628/1‑38 (MQ=255)

                                                agcaagcaATAGCGTAGTCATCGTTGTTGAAGTCCGGa                                                      >  1:1982035/1‑38 (MQ=255)

                                                agcaagcaATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGATCTCATACTGCAGagaa                     <  1:1570117/71‑1 (MQ=255)

                                                 gcaggcaaTCGCGTAATCGTCGCTGTTGAAGTCAGTACGCATCAGATCGTCATTTTCATACTGCAAggaag                    <  1:2366258/71‑1 (MQ=255)

                                                 gcaagcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCa                                 <  1:1710426/58‑1 (MQ=255)

                                                 gcaagcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGagaag                    <  1:2007039/71‑1 (MQ=255)

                                                  caagcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCaga                        <  1:154232/66‑1 (MQ=255)

                                                   aagcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGa                                                      >  1:3979835/1‑35 (MQ=255)

                                                   aagcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGa                                                      >  1:1423125/1‑35 (MQ=255)

                                                   aagcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGa                                                      >  1:3000644/1‑35 (MQ=255)

                                                   aagcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGagaa                     >  1:515667/1‑68 (MQ=255)

                                                   aagcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGagaa                     >  1:1216229/1‑68 (MQ=255)

                                                   aagcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAagag                  >  1:3078264/1‑71 (MQ=255)

                                                   aagcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAagag                  <  1:316184/71‑1 (MQ=255)

                                                    ggcaaTCGCGTAATCGTCGCTGTTGAAGTCAGTACGCATCAGATCGTCATTTTCa                                 >  1:905889/2‑55 (MQ=255)

                                                    agcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAagag                  <  1:3330683/70‑1 (MQ=255)

                                                     gcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAAGAGgt                >  1:4337394/1‑71 (MQ=255)

                                                     gcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAAGAGgt                <  1:419717/71‑1 (MQ=255)

                                                     gcaaTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAAGAGgt                <  1:1435471/71‑1 (MQ=255)

                                                       aaTCGCGTAATCGTCGCTGTTGAAGTCAGTACGCATCAGATCGTCATTTTCATACTGCAAGGAAGAGgtga              <  1:4618897/71‑2 (MQ=255)

                                                        aTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCa                                               <  1:2824134/37‑1 (MQ=255)

                                                        aTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCa                                          <  1:4323708/42‑1 (MQ=255)

                                                        aTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAAGAGGTGTc             <  1:5588921/71‑1 (MQ=255)

                                                        aTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAAGAGGTGTc             <  1:1082422/71‑1 (MQ=255)

                                                        aTAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAAGAGGTGTc             >  1:2302400/1‑71 (MQ=255)

                                                         tAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCaga                        <  1:1803017/59‑1 (MQ=255)

                                                         tAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAAGAGGTGTCg            <  1:5383566/71‑1 (MQ=255)

                                                           gCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAg                                              >  1:3662086/1‑35 (MQ=255)

                                                           gCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCAt                                         >  1:4247255/1‑40 (MQ=255)

                                                           gCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTtc                                    >  1:2581567/1‑45 (MQ=255)

                                                           gCGTAATCGTCGCTGTTGAAGTCAGTACGCATCAGATCGTCATTTTCATACTGCAAGGAAGAGGTGACGa           <  1:940828/70‑1 (MQ=255)

                                                           gCGTAATCGTCGCTGTTGAAGTCAGTACGCATCAGATCGTCATTTTCATACTGCAAGGAAGAGGTGACGAt          >  1:2137280/1‑71 (MQ=255)

                                                              tAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGt                                      <  1:1850512/40‑1 (MQ=255)

                                                              tAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAAGAGGTGTCGATGGa       <  1:3301044/71‑1 (MQ=255)

                                                               aGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATAc                              <  1:5126632/47‑1 (MQ=255)

                                                               aGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATAc                              <  1:2223316/47‑1 (MQ=255)

                                                                 tCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCg                                       <  1:3235701/36‑1 (MQ=255)

                                                                 tCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCg                                       <  1:4903047/36‑1 (MQ=255)

                                                                 tCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCg                                       <  1:5290414/36‑1 (MQ=255)

                                                                 tCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTtct                                   <  1:3550239/40‑1 (MQ=255)

                                                                 tCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCagag                       <  1:5667610/52‑1 (MQ=255)

                                                                   aTCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATa                               >  1:770698/1‑42 (MQ=255)

                                                                   aTCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCa                          <  1:4137198/47‑1 (MQ=255)

                                                                   aTCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAAGAGGTGTCGATGGACACtt  >  1:3179307/1‑71 (MQ=255)

                                                                   aTCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAAGAGGTGTCGATGGACACtt  >  1:3379225/1‑71 (MQ=255)

                                                                   aTCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAAGAGGTGTCGATGGACACtt  >  1:445539/1‑71 (MQ=255)

GCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTCTCATACTGCAGAGAAGAGGTGTCGATGGACACTT  >  Exported/608948‑609085

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