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
A6 F21 I0 R1	2169	63.0	3952800	76.2%	3012033	62.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,015,027	C→G	12.1%	E348Q (GAA→CAA)	fumA ←	aerobic Class I fumarate hydratase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,015,027	0	C	G	12.1%	151.7 / 11.3	58	E348Q (GAA→CAA)	fumA	aerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand): ref base C (25/26); new base G (2/5); total (27/31)
Fisher's exact test for biased strand distribution p-value = 4.32e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.27e-01

GGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTT  >  minE/1014958‑1015096

ggATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTcc                                                                      <  1:3810923/71‑1 (MQ=255)

ggATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCACGCTTTGCGCAGCTCTTcc                                                                      >  1:839054/1‑71 (MQ=255)

    ctctTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGa                                                                  >  1:2393713/1‑71 (MQ=255)

    ctctTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGa                                                                  >  1:42080/1‑71 (MQ=255)

       tttCATCGGACGGTTAAGGTCAACGCCCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGa                                                                  <  1:3657820/68‑1 (MQ=255)

          cATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGatatat                                                             <  1:2364981/70‑1 (MQ=255)

          cATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGa                                                                  <  1:2362131/65‑1 (MQ=255)

             cGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGc                                                         >  1:1917220/1‑71 (MQ=255)

              ggACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGcc                                                        >  1:1986686/1‑71 (MQ=255)

              ggACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGc                                                         <  1:150915/70‑1 (MQ=255)

                aCGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTg                                                      <  1:1512345/71‑1 (MQ=255)

                   gTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTgggt                                                   <  1:1731115/71‑3 (MQ=255)

                     tAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGatatat                                                             >  1:3020890/1‑59 (MQ=255)

                     tAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTg                                                      >  1:1941656/1‑66 (MQ=255)

                      aaGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATAttt                                                           <  1:3523031/60‑1 (MQ=255)

                      aaGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTAt                                                >  1:1254363/1‑71 (MQ=255)

                       aGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATg                                               >  1:16646/1‑71 (MQ=255)

                           cAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGtt                                             >  1:2462200/1‑69 (MQ=255)

                            aaCGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTc                                            >  1:2295325/1‑69 (MQ=255)

                               tttcACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTGGGTTGTGTTCCAGtt                                       >  1:3721710/4‑71 (MQ=255)

                                ttcACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTGGGTTGTGTTCCAGttt                                      >  1:787777/3‑71 (MQ=255)

                                cgcACCGCTTCGGCTTCTGCCGCTTTTCGCAGCTCTTCCGGGATATATTTGCCTGGATTTTGTTCCAGt                                        <  1:2163730/69‑1 (MQ=255)

                                 tcACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTGGGTTGTGTTCCAGttt                                      <  1:47357/69‑1 (MQ=255)

                                  cACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGttttt                                    >  1:2314172/1‑71 (MQ=255)

                                   aCCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTc                                   >  1:3517774/1‑71 (MQ=255)

                                    ccGCTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTGGGTTGTGTTCCAGTTTTTCg                                  <  1:2290998/71‑1 (MQ=255)

                                     cGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGa                                 <  1:692116/71‑1 (MQ=255)

                                      gCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATAtt                                                            <  1:1404141/43‑1 (MQ=255)

                                       cTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATc                               <  1:437175/71‑1 (MQ=255)

                                       cTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTGGGTTGTGTTCCAGttt                                      <  1:1406777/64‑1 (MQ=255)

                                          cGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCa                             <  1:1165647/70‑1 (MQ=255)

                                          cGCCTTCTCCCGCTTTGCCCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCa                             <  1:2988440/70‑1 (MQ=255)

                                            ccTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGt                                        <  1:108948/57‑1 (MQ=255)

                                             cTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATc                         >  1:1594628/1‑71 (MQ=255)

                                             cTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATc                         >  1:1125790/1‑71 (MQ=255)

                                              ttCTCCCGCTTTGCGCAGCTCTTCCGGGATATAttt                                                           <  1:1315451/36‑1 (MQ=255)

                                              ttCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTTGATTAt                                                <  1:2380/47‑1 (MQ=255)

                                               tctcCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGt                                              >  1:1497999/1‑48 (MQ=255)

                                                ctcCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATc                         >  1:3728427/1‑68 (MQ=255)

                                                 tcCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGAt                          >  1:1121387/1‑66 (MQ=255)

                                                 tcCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGAt                          >  1:1125932/1‑66 (MQ=255)

                                                   ccGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGtt                                       <  1:2576907/51‑1 (MQ=255)

                                                   ccGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTg                    <  1:630993/70‑1 (MQ=255)

                                                   ccGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGa                   <  1:1215642/71‑1 (MQ=255)

                                                     gCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACg                 >  1:2947824/1‑71 (MQ=255)

                                                     gCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACg                 >  1:2299975/1‑71 (MQ=255)

                                                     gCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACg                 >  1:1491615/1‑71 (MQ=255)

                                                      cTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGa                                 <  1:3915817/54‑1 (MQ=255)

                                                        ttGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGtt              >  1:1209672/1‑71 (MQ=255)

                                                        ttGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGtt              >  1:3504198/1‑71 (MQ=255)

                                                         tGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGttttt                                    <  1:381257/48‑1 (MQ=255)

                                                           cgcAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCt                     <  1:3868742/61‑1 (MQ=255)

                                                            gcAGTTCTTGTGGAATGTACTGGCCTGGGTTGTGTTCCAGTTTTTCGATCCAGATACCTTCGCGGGTGAtt          <  1:3451835/71‑2 (MQ=255)

                                                            gcAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGa                                 <  1:1638161/48‑1 (MQ=255)

                                                            gcAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGa            <  1:292661/69‑1 (MQ=255)

                                                              aGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCtt        >  1:1936973/1‑71 (MQ=255)

                                                               gCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTc       >  1:2642122/1‑71 (MQ=255)

                                                                   ttCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCg                                  <  1:2554865/40‑1 (MQ=255)

                                                                   ttCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCg                                  <  1:2120987/40‑1 (MQ=255)

                                                                   ttCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGc     <  1:1835960/69‑1 (MQ=255)

                                                                     ccGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCttt  >  1:1426032/1‑70 (MQ=255)

                                                                     ccGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCttt  >  1:2298172/1‑70 (MQ=255)

                                                                     ccGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCt    <  1:2611960/68‑1 (MQ=255)

GGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGGTTGATCTTCGCTTT  >  minE/1014958‑1015096

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