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
A2 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,336,421	T→C	56.2%	F269F (TTT→TTC)	fdoH →	formate dehydrogenase‑O, Fe‑S subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,336,421	0	T	C	56.2%	22.2 / 62.4	82	F269F (TTT→TTC)	fdoH	formate dehydrogenase‑O, Fe‑S subunit
Reads supporting (aligned to +/- strand): ref base T (16/20); new base C (20/26); total (36/46)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.68e-01

GAAACCGTGAAATTCTGGAAAGGCATCTGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCAGTATCTTCCACTACGTGGGTGTCGGTCCGAACCGTGCGGATGAGGAAGAGAATAA  >  minE/2336356‑2336483

gAAACCGTGAAATTCTGGAAAGGCATCTGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCg                                                             <  1:1865011/69‑1 (MQ=255)

gAAACCGTGAAATTCTGGAAAGGCATCTGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCg                                                             <  1:1579527/69‑1 (MQ=255)

    ccGTGAAATTCTGGAAAGGCATCTGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCa                                                         <  1:275293/69‑1 (MQ=255)

    ccGTGAAATTCTGGAAAGGCATCTGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCa                                                         <  1:2720948/69‑1 (MQ=255)

      gTGAGATTCTGGAAAGGCATCTGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCAGt                                                       <  1:2263320/69‑1 (MQ=255)

      gTGAAATTCTGGAAAGGCATCTGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCAGt                                                       <  1:375768/69‑1 (MQ=255)

         aaaTTCTGGAAAGGCATCTGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCAGTa                                                      <  1:582154/67‑1 (MQ=255)

         aaaTTCTGGAAAGGCATCTGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCAGTa                                                      <  1:1894145/67‑1 (MQ=255)

         aaaTTCTGGAAAGGCATCTGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCAGTa                                                      <  1:392941/67‑1 (MQ=255)

         aaaTTCTGGAAAGGCATCTGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCAGTa                                                      <  1:3382081/67‑1 (MQ=255)

         aaaTTCTGGAAAGGCATCTGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCAGTa                                                      <  1:159047/67‑1 (MQ=255)

         aaaTTCTGGAAAGGCATCTGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCAGTa                                                      <  1:3022816/67‑1 (MQ=255)

         aaaTTCTGGAAAGGCATCTGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCAGTa                                                      <  1:3005629/67‑1 (MQ=255)

         aaaTTCTGGAAAGGCATCTGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCAGTa                                                      <  1:2691380/67‑1 (MQ=255)

                ggAAAGGCATCTGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCAGTATCTTCCAc                                              <  1:1243648/68‑1 (MQ=255)

                      gCATCTGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCAGTATCTTCCACTACGTgg                                       >  1:3017379/1‑69 (MQ=255)

                      gCATCTGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCAGTATCTTCCACTACGTgg                                       >  1:304547/1‑69 (MQ=255)

                      gCATCTGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCAGTATCTTCCACTACGTgg                                       >  1:308853/1‑69 (MQ=255)

                      gCATCTGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCAGTATCTTCCACTACGTgg                                       >  1:1156832/1‑69 (MQ=255)

                      gCATCTGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCAGTATCTTCCACTACGTgg                                       >  1:404976/1‑69 (MQ=255)

                        aTCTGGATACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:1260425/69‑1 (MQ=255)

                        aTCTGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACgtgtgt                                     <  1:2068845/69‑1 (MQ=255)

                        aTCTGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:2875917/69‑1 (MQ=255)

                        aTCTGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:1909653/69‑1 (MQ=255)

                        aTCTGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:286319/69‑1 (MQ=255)

                        aTCTGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:2980596/69‑1 (MQ=255)

                        aTCTGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:216826/69‑1 (MQ=255)

                        aTCTGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:1878838/69‑1 (MQ=255)

                        aTCTGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:2483140/69‑1 (MQ=255)

                        aTCTGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:1881921/69‑1 (MQ=255)

                        aTCTGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:114890/69‑1 (MQ=255)

                        aTCTGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:767389/69‑1 (MQ=255)

                        aTCTGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:613357/69‑1 (MQ=255)

                        aTCTGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:603679/69‑1 (MQ=255)

                        aTCTGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:567379/69‑1 (MQ=255)

                        aTCTGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:1504288/69‑1 (MQ=255)

                        aTCTGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:1062612/69‑1 (MQ=255)

                        aTCTGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:163248/69‑1 (MQ=255)

                        aTCTGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:1698998/69‑1 (MQ=255)

                        aTCTGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:47951/69‑1 (MQ=255)

                        aTCTGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:1801054/69‑1 (MQ=255)

                        aTCTGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:180159/69‑1 (MQ=255)

                        aTCTGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:1815689/69‑1 (MQ=255)

                        aTCTGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:1874963/69‑1 (MQ=255)

                           tGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCAGTTTCTTCCACTACGTGGGTGTc                                  >  1:2210874/1‑69 (MQ=255)

                           tGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCAGTATCTTc                                                 >  1:3382803/1‑54 (MQ=255)

                           tGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCAGTATCTTc                                                 >  1:94952/1‑54 (MQ=255)

                           tGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCAGTATCTTCCACTACGTGGGTGTc                                  >  1:363255/1‑69 (MQ=255)

                           tGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCAGTATCTTCCACTACGTGGGTGTc                                  >  1:1183819/1‑69 (MQ=255)

                           tGGAAACCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGgt                                     <  1:2607448/66‑1 (MQ=255)

                               aaCCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGGTGTCgg                                >  1:1582813/1‑67 (MQ=255)

                               aaCCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGGTGTCGGt                               >  1:98409/1‑68 (MQ=255)

                               aaCCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGGTGTCGGt                               >  1:882988/1‑68 (MQ=255)

                               aaCCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGGTGTCGGt                               >  1:70449/1‑68 (MQ=255)

                               aaCCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGGTGTCGGt                               >  1:3228630/1‑68 (MQ=255)

                               aaCCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGGTGTCGGt                               >  1:1049945/1‑68 (MQ=255)

                               aaCCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGGTGTCGGt                               >  1:1923212/1‑68 (MQ=255)

                               aaCCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGGTGTCGGt                               >  1:1019586/1‑68 (MQ=255)

                               aaCCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGGTGTCGGt                               >  1:107059/1‑68 (MQ=255)

                               aaCCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGGTGTCGGt                               >  1:1270016/1‑68 (MQ=255)

                               aaCCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGGTGTCGGt                               >  1:1403755/1‑68 (MQ=255)

                               aaCCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGGTGTCGGt                               >  1:1403917/1‑68 (MQ=255)

                               aaCCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGGTGTCGGt                               >  1:1484520/1‑68 (MQ=255)

                               aaCCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGGTGTCGGt                               >  1:2801665/1‑68 (MQ=255)

                               aaCCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGGTGTCGGt                               >  1:1996880/1‑68 (MQ=255)

                               aaCCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGGTGTCGGt                               >  1:2101183/1‑68 (MQ=255)

                               aaCCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGGTGTCGGt                               >  1:2119399/1‑68 (MQ=255)

                               aaCCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGGTGTCGGt                               >  1:2469354/1‑68 (MQ=255)

                               aaCCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGGTGTCGGt                               >  1:2473295/1‑68 (MQ=255)

                               aaCCGCTCGCAGCTGTTGGCTTTGCGGCTACCTTCGCAGCCAGTATCTTCCACTACGTGGGTGTCGGt                               >  1:265994/1‑68 (MQ=255)

                                                ggCTTTGCGGCTACCTTTGCGGCCAGTATCTTCCACTACGTGGGTGTCGGTCCGAACCGTGCGGATGa              >  1:2231345/1‑68 (MQ=255)

                                                ggCTTTGCGGCTACCTTTGCGGCCAGTATCTTCCACTACGTGGGTGTCGGTCCGAACCGTGCGGATGa              >  1:1727093/1‑68 (MQ=255)

                                                ggCTTTGCGGCTACCTTTGCGGCCAGTATCTTCCACTACGTGGGTGTCGGTCCGAACCGTGCGGATGa              >  1:3125227/1‑68 (MQ=255)

                                                ggCTTTGCGGCTACCTTTGCGGCCAGTATCTTCCACTACGTGGGTGTCGGTCCGAACCGTGCGGATGa              >  1:1484396/1‑68 (MQ=255)

                                                ggCTTTGCGGCTACCTTTGCGGCCAGTATCTTCCACTACGTGGGTGTCGGTCCGAACCGTGCGGATGa              >  1:2600678/1‑68 (MQ=255)

                                                     tgctgcTACCTTCGCAGCCAGTATCTTCCACTACTTgtgt                                     <  1:1205130/40‑1 (MQ=16)

                                                     tGCGGCTACCTTTGCGGCCAGTATCTTCCACTACGTGGGTGTCGGTCCGAACCGTGCGGATGAGGAag         >  1:2683000/1‑68 (MQ=255)

                                                           tACCTTTGCGGCCAGTATCTTCCACTACGTGGGTGTCGGTCCGAACCGTGCGGATGAGTAAGAtaataa  <  1:2187032/69‑1 (MQ=255)

                                                           tACCTTTGCGGCCAGTATCTTCCACTACGTGGGTGTCGGTCCGAACCGTGCGGATGAGGAAGAGaataa  <  1:2222599/69‑1 (MQ=255)

                                                           tACCTTTGCGGCCAGTATCTTCCACTACGTGGGTGTCGGTCCGAACCGTGCGGATGAGGAAGAGaataa  <  1:608242/69‑1 (MQ=255)

                                                           tACCTTTGCGGCCAGTATCTTCCACTACGTGGGTGTCGGTCCGAACCGTGCGGATGAGGAAGAGaataa  <  1:1312644/69‑1 (MQ=255)

                                                            aCCTTTGCGGCCAGTATCTTCCACTACGTGGGTGTCGGTCCGAACCGTGCGGATGAGGAAGAGaataa  <  1:835780/68‑1 (MQ=255)

GAAACCGTGAAATTCTGGAAAGGCATCTGGAAACCGCTCGCGGCTGTTGGCTTTGCGGCTACCTTTGCGGCCAGTATCTTCCACTACGTGGGTGTCGGTCCGAACCGTGCGGATGAGGAAGAGAATAA  >  minE/2336356‑2336483

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