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
A1 F8 I0 R2	422	46.8	3726540	94.7%	3529033	61.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	2,841,727	C→T	77.2%	A126T (GCC→ACC)	hycH ←	protein required for maturation of hydrogenase 3

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,841,727	0	C	T	77.2%	206.6 / 62.0	105	A126T (GCC→ACC)	hycH	protein required for maturation of hydrogenase 3
Reads supporting (aligned to +/- strand): ref base C (16/8); new base T (40/41); total (56/49)
Fisher's exact test for biased strand distribution p-value = 1.66e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 108 total aligned reads displayed.

CATGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCCTGCTGCTGCGAA  >  W3110S.gb/2841664‑2841791

catGCTATTGCCAACTCAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTcc                                                           >  1:3268086/1‑71 (MQ=255)

catGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTcc                                                           >  1:1870702/1‑71 (MQ=255)

 atGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCt                                                          <  1:965519/71‑1 (MQ=255)

 atGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCt                                                          <  1:3153439/71‑1 (MQ=255)

 atGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCt                                                          <  1:570172/71‑1 (MQ=255)

 atGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCt                                                          <  1:2611776/71‑1 (MQ=255)

 atGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCt                                                          <  1:2282952/71‑1 (MQ=255)

 atGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCt                                                          <  1:2157816/71‑1 (MQ=255)

 atGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCt                                                          <  1:778045/71‑1 (MQ=255)

 atGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCt                                                          <  1:1870449/71‑1 (MQ=255)

 atGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCt                                                          <  1:1686830/71‑1 (MQ=255)

       ttGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCtgatg                                                      <  1:633491/69‑1 (MQ=255)

         gCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTcat                                                          >  1:1872680/1‑61 (MQ=255)

         gCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAata                                                  >  1:1882932/1‑71 (MQ=255)

         gCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAata                                                  >  1:2387421/1‑71 (MQ=255)

         gCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAat                                                   >  1:1852053/1‑70 (MQ=255)

           cAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATc                                                <  1:1067824/71‑1 (MQ=255)

           cAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATc                                                <  1:943329/71‑1 (MQ=255)

           cAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATc                                                <  1:580096/71‑1 (MQ=255)

            aaCACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCa                                               <  1:2440487/71‑1 (MQ=255)

               tcaGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCtgat                                                       >  1:2878138/2‑60 (MQ=255)

               acaGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCtgat                                                       >  1:3555387/1‑60 (MQ=255)

               acaGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCtgat                                                       >  1:1044073/1‑60 (MQ=255)

               acaGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCtgat                                                       >  1:2966865/1‑60 (MQ=255)

               acaGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCtgat                                                       >  1:1207469/1‑60 (MQ=255)

               acaGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCtgat                                                       >  1:1859511/1‑60 (MQ=255)

               acaGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCtgat                                                       >  1:1283088/1‑60 (MQ=255)

               acaGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCtgat                                                       >  1:1377191/1‑60 (MQ=255)

               acaGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCtga                                                        >  1:2730809/1‑59 (MQ=255)

               acaGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCtga                                                        >  1:401929/1‑59 (MQ=255)

               acaGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCtga                                                        >  1:2976527/1‑59 (MQ=255)

                     tAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGgtgt                                                                <  1:212224/45‑1 (MQ=255)

                        aaCGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACtt                                   <  1:385292/71‑1 (MQ=255)

                        aaCGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACtt                                   <  1:1474432/71‑1 (MQ=255)

                        aaCGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACtt                                   <  1:3004849/71‑1 (MQ=255)

                        aaCGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACtt                                   <  1:2205157/71‑1 (MQ=255)

                        aaCGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACtt                                   <  1:1007662/71‑1 (MQ=255)

                        aaCGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACtt                                   <  1:2163439/71‑1 (MQ=255)

                              agtcaCGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAg                              >  1:2821686/1‑70 (MQ=255)

                               gtcaCGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACtt                                   <  1:463267/64‑1 (MQ=255)

                               gtcaCGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACtt                                   <  1:205154/64‑1 (MQ=255)

                               gtcaCGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACtt                                   <  1:2638027/64‑1 (MQ=255)

                               gtcaCGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACtt                                   <  1:1109477/64‑1 (MQ=255)

                               gtcaCGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACtt                                   <  1:2132030/64‑1 (MQ=255)

                               gtcaCGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCa                            <  1:2049960/71‑1 (MQ=255)

                                 caCGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTaa                                 >  1:2057050/1‑64 (MQ=255)

                                 caCGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTaa                                 >  1:470079/1‑64 (MQ=255)

                                 caCGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCAtt                          >  1:827321/1‑71 (MQ=255)

                                  aCGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTg                         >  1:1426813/1‑71 (MQ=255)

                                  aCGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTg                         <  1:1461637/71‑1 (MQ=255)

                                  aCGCAGTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTg                         <  1:1882324/71‑1 (MQ=255)

                                  aCGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTg                         <  1:714902/71‑1 (MQ=255)

                                  aCGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTg                         <  1:2928745/71‑1 (MQ=255)

                                  aCGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTg                         <  1:2148739/71‑1 (MQ=255)

                                       gTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGACTATCATGCAGCATACTTAACAGCATTGTACTc                    <  1:3161663/71‑1 (MQ=255)

                                       gTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTc                    <  1:1915441/71‑1 (MQ=255)

                                       gTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTc                    <  1:3649195/71‑1 (MQ=255)

                                       gTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTc                    <  1:3307020/71‑1 (MQ=255)

                                       gTCTCCTCACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTc                    <  1:2075665/71‑1 (MQ=255)

                                       gTCTCCTCACCATCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTc                    <  1:2433779/71‑1 (MQ=255)

                                       gTCTCCTCACCATCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTc                    <  1:3484287/71‑1 (MQ=255)

                                         ctcctcACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCa                  >  1:3075439/1‑71 (MQ=255)

                                          tcctcACCATCAAATAGATGGTGTTTTCCTTATGAATATCATGCAGCATACTTAACAGCATTGTa                       >  1:2697660/1‑65 (MQ=255)

                                          tcctcACCATCAAATAGATGGTGTTTTCCTGATGAat                                                   <  1:3322568/37‑1 (MQ=255)

                                          tcctcACCATCAAATAGATGGTGTTTTCCTGATGAat                                                   <  1:1133993/37‑1 (MQ=255)

                                          tcctcACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTa                       >  1:2750956/1‑65 (MQ=255)

                                          tcctcACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTa                       >  1:2697880/1‑65 (MQ=255)

                                          tcctcACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTa                       >  1:3256169/1‑65 (MQ=255)

                                          tcctcACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTa                       >  1:459025/1‑65 (MQ=255)

                                          tcctcACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTa                       >  1:1886864/1‑65 (MQ=255)

                                          tcctcACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTa                       >  1:620185/1‑65 (MQ=255)

                                          tcctcACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCAt                 >  1:416088/1‑71 (MQ=255)

                                          tcctcACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCAt                 >  1:2816484/1‑71 (MQ=255)

                                          tcctcACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCAt                 >  1:1037186/1‑71 (MQ=255)

                                          tcctcACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCAt                 >  1:2822004/1‑71 (MQ=255)

                                          tcctcACCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCAt                 >  1:2817838/1‑71 (MQ=255)

                                          tcctcACCATCAAATAGATGGTGTTTTCATGATGAATATCATGCAGCATACTTAACAGCATTGTa                       >  1:887110/1‑65 (MQ=255)

                                            ctcACCATCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTc               >  1:3700329/1‑71 (MQ=255)

                                            ctcACCATCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTc               >  1:2947241/1‑71 (MQ=255)

                                               aCCATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCctg            >  1:215467/1‑71 (MQ=255)

                                                ccATCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTg                         <  1:946849/57‑1 (MQ=255)

                                                   tCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACtt                                   <  1:958810/44‑1 (MQ=255)

                                                   tCAAATAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCctgctgc        >  1:3322813/1‑71 (MQ=255)

                                                    cAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCctgctgct       >  1:2976567/1‑71 (MQ=255)

                                                     aaaTAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTcc                   >  1:744924/1‑58 (MQ=255)

                                                     aaaTAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCa                  >  1:2559992/1‑59 (MQ=255)

                                                     aaaTAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCa                  >  1:583671/1‑59 (MQ=255)

                                                     aaaTAGATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCa                  >  1:3586626/1‑59 (MQ=255)

                                                      aaTAGATGGCGTTTTCCTGATGAATATCATGTAGCATACTTAACAGCATTGTACTCCATTCctgctgctg      >  1:3693462/1‑70 (MQ=255)

                                                      aaTAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCCtgctgctgc     >  1:2464701/1‑71 (MQ=255)

                                                      aaTAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCCtgctgctgc     >  1:1917040/1‑71 (MQ=255)

                                                      aaTAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCCtgctgctgc     >  1:1878975/1‑71 (MQ=255)

                                                      aaTAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCCtgctgctgc     >  1:845371/1‑71 (MQ=255)

                                                      aaTAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCCtgctgctgc     >  1:132218/1‑71 (MQ=255)

                                                      aaTAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCCtgctgctgc     >  1:420031/1‑71 (MQ=255)

                                                      aaTAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCCtgctgctgc     >  1:3471067/1‑71 (MQ=255)

                                                          gATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCCTGCTGCTGCGaa  <  1:2313171/70‑1 (MQ=255)

                                                          gATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCCTGCTGCTGCGaa  <  1:2771104/70‑1 (MQ=255)

                                                          gATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCCTGCTGCTGCGaa  <  1:2929534/70‑1 (MQ=255)

                                                          gATGGTGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCCTGCTGCTGCGaa  <  1:442125/70‑1 (MQ=255)

CATGCTATTGCCAACACAGAGTAAAACGTCAGTCACGCAGTCTCCTCACCATCAAATAGATGGCGTTTTCCTGATGAATATCATGCAGCATACTTAACAGCATTGTACTCCATTCCTGCTGCTGCGAA  >  W3110S.gb/2841664‑2841791

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A