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
A12 F28 I1 R1	227	52.0	1764248	99.3%	1751898	138.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,601,608	A→G	E136E (GAA→GAG)	hyfA →	hydrogenase 4 component A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,601,608	0	A	G	75.6%	77.5 / 24.5	45	E136E (GAA→GAG)	hyfA	hydrogenase 4 component A
Reads supporting (aligned to +/- strand): ref base A (6/5); new base G (16/18); total (22/23)
Fisher's exact test for biased strand distribution p-value = 7.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.07e-01

TCTGCCCATTTGGCGCAATCAGCGCTTCAGGAAGCCGTCCGGTGAATGCCCATGCGCAATATGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAACCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCGTTCGCGCTTGCCCGAATCAGGCGTTACGGCTGATCACCGGTGATAGCCTGCAACGTCAGATGAAAGAAA  >  NC_000913/2601472‑2601744

tCTGCCCATTTGGCGCAATCAGCGCTTCAGGAAGCCGTCCGGTGAATGCCCATGCGCAATATGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCt                                                                                                                                       <  1:362861/140‑1 (MQ=255)

            gcgcAATCAGCGCTTCAGGAAGCCGTCCGGTGAATGCCCATGCGCAATATGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGAcc                                                                                                                           >  1:553368/1‑140 (MQ=255)

                aaTCAGCGCTTCAGGAAGCCGTCCGGTGAATGCCCATGCGCAATATGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAACCTGGTGTCCAGACCGTcg                                                                                                                       <  1:392071/140‑1 (MQ=255)

                 aTCAGCGCTTCAGGAAGCCGTCCGGTGAATGCCCATGCGCAATATGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTcgc                                                                                                                      >  2:707539/1‑140 (MQ=255)

                           cAGGAAGCCGTCCGGTGAATGCCCATGCGCAATATGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGc                                                                                                            >  2:180362/1‑140 (MQ=255)

                            aGGAAGCCGTCCGGTGAATGCCCATGCGCAATATGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTcgcg                                                                                                                     >  2:484323/1‑130 (MQ=255)

                            aGGAAGCCGTCCGGTGAATGCCCATGCGCAATATGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTcgcg                                                                                                                     <  1:484323/130‑1 (MQ=255)

                            aGGAAGCCGTCCGGTGAATGCCCATGCGCAATATGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAACCTGGTGTCCAGACCGTCGCGGTGAAATGCg                                                                                                           <  1:467900/140‑1 (MQ=255)

                              gAAGCCGTCCGGTGAATGCCCATGCGCAATATGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGAc                                                                                                         <  1:707539/140‑1 (MQ=255)

                                   cGTCCGGTGAATGCCCATGCGCAATATGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCtgtg                                                                                                    >  2:271015/1‑140 (MQ=255)

                                     tCCGGTGAATGCCCATGCGCAATATGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGAc                                                                                                         >  2:343356/1‑133 (MQ=255)

                                     tCCGGTGAATGCCCATGCGCAATATGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGAc                                                                                                         <  1:343356/133‑1 (MQ=255)

                                     tCCGGTGAATGCCCATGCGCAATATGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAACCTGGTGTCCAGACCGTCGCGGTGAAAt                                                                                                              <  2:416655/128‑1 (MQ=255)

                                     tCCGGTGAATGCCCATGCGCAATATGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAACCTGGTGTCCAGACCGTCGCGGTGAAAt                                                                                                              >  1:416655/1‑128 (MQ=255)

                                        ggTGAATGCCCATGCGCAATATGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAACCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGAtt                                                                                               >  2:654913/1‑140 (MQ=255)

                                               gCCCATGCGCAATATGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGcc                                                                                        >  2:779723/1‑140 (MQ=255)

                                                 ccATGCGCAATATGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAg                                                                                      <  1:180362/140‑1 (MQ=255)

                                                      cgcAATATGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGt                                                                                 >  1:828005/1‑140 (MQ=255)

                                                      cgcAATATGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGt                                                                                 >  1:756917/1‑140 (MQ=255)

                                                            atGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGcc                                                                           <  2:553368/140‑1 (MQ=255)

                                                             tGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCt                                                                          <  1:382314/140‑1 (MQ=255)

                                                             tGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGATGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCt                                                                          <  1:592261/140‑1 (MQ=255)

                                                                ttttCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAACCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCg                                                                       >  2:57842/1‑140 (MQ=255)

                                                                     aGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCGTTcgc                                                                  >  2:117642/1‑140 (MQ=255)

                                                                      ggCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCGTTcgcg                                                                 <  2:603014/140‑1 (MQ=255)

                                                                                 cactcaAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCGTTCGCGCTTGCCCGAAt                                                      >  2:410734/1‑140 (MQ=255)

                                                                                   ctcaAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAACCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCGTTCGCGCTTGCCCGAATCa                                                    <  1:654913/140‑1 (MQ=255)

                                                                                            ggCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAACCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCGTTCGCGCTTGCCCGAATCAGGCGTTACg                                           >  1:587529/1‑140 (MQ=255)

                                                                                                 agaaAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCGTTCGCGCTTGCCCGAATCAGGCGTTACGGCTGa                                      <  2:141654/140‑1 (MQ=255)

                                                                                                    aaaCGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCGTTCGCGCTTGCCCGAATCAGGCGTTACGGCTGATCa                                   <  1:432496/140‑1 (MQ=255)

                                                                                                     aaCGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCGTTCGCGCTTGCCCGAATCAGGCGTTACGGCTGATCAc                                  <  1:410734/140‑1 (MQ=255)

                                                                                                     aaCGCGCCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCGTTCGCGCTTGCCCGAATCAGGCGTTACGGCTGATCAc                                  <  2:756917/140‑1 (MQ=255)

                                                                                                          gcCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCGTTCGCGCTTGCCCGAATCAGGCGTTACGGCTGATCACCGGTg                             <  2:561749/140‑1 (MQ=255)

                                                                                                          gcCAACACAACATGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCATTCGCGCTTGCCCGAATCAGGCGTTACGGCTGATCACCGGTg                             <  1:779723/140‑1 (MQ=255)

                                                                                                              acacaacaTGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCGTTCGCGCTTGCCCGAATCAGGCGTTACGGCTGATCACCGGTGATAg                         <  1:146602/140‑1 (MQ=255)

                                                                                                               cacaacaTGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCGTTCGCGCTTGCCCGAATCAGGCGTTACGGCTGATCACCGGTGa                            >  1:81070/1‑136 (MQ=255)

                                                                                                               cacaacaTGCTTTGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCGTTCGCGCTTGCCCGAATCAGGCGTTACGGCTGATCACCGGTGa                            <  2:81070/136‑1 (MQ=255)

                                                                                                                         tttGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCGTTCGCGCTTGCCCGAATCAGGCGTTACGGCTGATCACCGGTGATAGCCTGCAACGTc              >  2:424352/1‑140 (MQ=255)

                                                                                                                         tttGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCGTTCGCGCTTGCCCGAATCAGGCGTTACGGCTGATCACCGGTGATAGCCTGCAACGTc              >  1:608408/1‑140 (MQ=255)

                                                                                                                         tttGCTGCGCTGGGAACCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCGTTCGCGCTTGCCCGAATCAGGCGTTACGGCTGATCACCGGTGATAGCCTGCAACGTc              >  1:637244/1‑140 (MQ=255)

                                                                                                                          ttGCTGCGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCGTTCGCGCTTGCCCGAATCAGGCGTTACGGCTGATCACCGGTGATAGCCTGCAACGTCa             <  1:424352/140‑1 (MQ=255)

                                                                                                                          ttGCTGCGCTGGGAACCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCGTTCGCGCTTGCCCGAATCAGGCGTTACGGCTGATCACCGGTGATAGCCTGCAACGTCa             <  2:587529/140‑1 (MQ=255)

                                                                                                                            gctgcGCTGGGAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCGTTCGCGCTTGCCCGAATCAGGCGTTACGGCTGATCACCGGTGATAGCCTGCAACGTCAGa           >  1:311627/1‑140 (MQ=255)

                                                                                                                              tgcGCTGGGAACCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTCCCAGAAGGTCCGGCCTGCGTTCGCGCTTGCCCGAATCAGGCGTTACGGCTGATCACCGGTGATAGCCTGCAACGTCAGATg         >  2:179631/1‑140 (MQ=255)

                                                                                                                                     ggAGCCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCGTTCGCGCTTGCCCGAATCAGGCGTTACGGCTGATCACCGGTGATAGCCTGCAACGTCAGATgaaagaaa  >  1:188780/1‑140 (MQ=255)

TCTGCCCATTTGGCGCAATCAGCGCTTCAGGAAGCCGTCCGGTGAATGCCCATGCGCAATATGTTTTTCAGGCTGAAGGCTCACTCAAAGACGGCGAAGAAAACGCGCCAACACAACATGCTTTGCTGCGCTGGGAACCTGGTGTCCAGACCGTCGCGGTGAAATGCGACCTGTGTGATTTCTTGCCAGAAGGTCCGGCCTGCGTTCGCGCTTGCCCGAATCAGGCGTTACGGCTGATCACCGGTGATAGCCTGCAACGTCAGATGAAAGAAA  >  NC_000913/2601472‑2601744

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A