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	2,020,144	C→T	47.1%	L254L (CTC→CTT)	dkgA →	2,5‑diketo‑D‑gluconate reductase A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,020,144	0	C	T	47.1%	3.2 / 42.7	53	L254L (CTC→CTT)	dkgA	2,5‑diketo‑D‑gluconate reductase A
Reads supporting (aligned to +/- strand): ref base C (15/13); new base T (10/15); total (25/28)
Fisher's exact test for biased strand distribution p-value = 4.12e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACACCTTCACGTATTGCCGAAAACTTTGATGTCTGGGATTTCCGTCTCGACAAAGACGAACTCGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGACCAGTTC  >  minE/2020082‑2020201

acacCTTCACGCATTGTCGAAAACTTTGATGTCTGGGATTTCCGTCTCGACAAAGACGAACTTTGCGaa                                                     >  1:3404561/1‑69 (MQ=255)

acacCTTCACGCATTGTCGAAAACTTTGATGTCTGGGATTTCCGTCTCGACAAAGACGAACTTTGCGaa                                                     >  1:1108806/1‑69 (MQ=255)

acacCTTCACGCATTGTCGAAAACTTTGATGTCTGGGATTTCCGTCTCGACAAAGACGAACTTTGCGaa                                                     >  1:2805498/1‑69 (MQ=255)

acacCTTCACGCATTGTCGAAAACTTTGATGTCTGGGATTTCCGTCTCGACAAAGACGAACTTTGCGaa                                                     >  1:3428640/1‑69 (MQ=255)

acacCTTCACGCATTGTCGAAAACTTTGATGTCTGGGATTTCCGTCTCGACAAAGACGAACTTTGCGaa                                                     >  1:2609626/1‑69 (MQ=255)

acacCTTCACGCATTGTCGAAAACTTTGATGTCTGGGATTTCCGTCTCGACAAAGACGAACTTTGCGaa                                                     >  1:1176381/1‑69 (MQ=255)

acacCTTCACGCATTGTCGAAAACTTTGATGTCTGGGATTTCCGTCTCGACAAAGACGAACTTTGCGaa                                                     >  1:3000181/1‑69 (MQ=255)

acacCTTCACGCATTGTCGAAAACTTTGATGTCTGGGATTTCCGTCTCGACAAAGACGAACTTTGCGa                                                      >  1:131059/1‑68 (MQ=255)

acacCTTCACGCATTGTCGAAAACTTTGATGTCTGGGATTTCCGTCTCGACAAAGACGAACTTTGCGa                                                      >  1:2661086/1‑68 (MQ=255)

acacCTTCACGCATTGTCGAAAACTTTGATGTCTGGGATTTCCGTCTCGACAAAGACGAACTTTGCGa                                                      >  1:119731/1‑68 (MQ=255)

     ttCACGTATTGCCGAAAACTTTGATGTCTGGGATTTCCGTCTCGACAAAGACGAACTCGGCGAAATTGc                                                <  1:2822593/69‑1 (MQ=255)

       cACGTATTGCCGAAAACTTTGATGTCTGGGATTTCCGTCTCGACAAAGACGAACTCGGCGAAATTGCaa                                              >  1:3142058/1‑69 (MQ=255)

         cGTATTGCCGAAAACTTTGATGTCTGGGATTTCCGTCTCGACAAAGACGAACTCGGCGAAATTGCaa                                              <  1:2647293/67‑1 (MQ=255)

         cGTATTGCCGAAAACTTTGATGTCTGGGATTTCCGTCTCGACAAAGACGAACTCGGCGAAATTGCaa                                              <  1:2745734/67‑1 (MQ=255)

         cGTATTGCCGAAAACTTTGATGTCTGGGATTTCCGTCTCGACAAAGACGAACTCGGCGAAATTGCaa                                              <  1:457144/67‑1 (MQ=255)

         cGTATTGCCGAAAACTTTGATGTCTGGGATTTCCGTCTCGACAAAGACGAACTCGGCGAAATTGCaa                                              <  1:3341284/67‑1 (MQ=255)

         cGTATTGCCGAAAACTTTGATGTCTGGGATTTCCGTCTCGACAAAGACGAACTCGGCGAAATTGCaa                                              <  1:1148062/67‑1 (MQ=255)

               gCCGAAAACTTTGATGTCTGGGATTTCCGTCTCGACAAAGACGAACTCGGCGAAATTGCAAAACTCg                                        >  1:2637787/1‑67 (MQ=255)

               gCCGAAAACTTTGATGTCTGGGATTTCCGTCTCGACAAAGACGAACTCGGCGAAATTGCAAAACTCg                                        >  1:666373/1‑67 (MQ=255)

               gCCGAAAACTTTGATGTCTGGGATTTCCGTCTCGACAAAGACGAACTCGGCGAAATTGCAAAACTCg                                        >  1:1655110/1‑67 (MQ=255)

                            aTGTCTGGGATTTCCGTCTCGACAAAGACGAACTCGGCGAAATTGCAAAACTCGATCAGGGCAAGCGt                          <  1:481701/68‑1 (MQ=255)

                               tCTGGGATTTCCGTCTCGACAAAGACGAACTCGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCg                      >  1:1684719/1‑69 (MQ=255)

                               tCTGGGATTTCCGTCTCGACAAAGACGAACTCGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCg                      >  1:235957/1‑69 (MQ=255)

                               tCTGGGATTTCCGTCTCGACAAAGACGAACTCGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCg                      >  1:671372/1‑69 (MQ=255)

                               tCTGGGATTTCCGTCTCGACAAAGACGAACTCGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCg                      >  1:8323/1‑69 (MQ=255)

                               tCTGGGATTTCCGTCTCGACAAAGACGAACTCGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCg                      >  1:917950/1‑69 (MQ=255)

                               tCTGGGATTTCCGTCTCGACAAAGACGAACTCGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCg                      >  1:1118935/1‑69 (MQ=255)

                                     aTTTCCGTCTCGACAAAGACGAACTCGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCg                >  1:19615/1‑69 (MQ=255)

                                     aTTTCCGTCTCGACAAAGACGAACTCGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCg                >  1:1367732/1‑69 (MQ=255)

                                        tCCGTCTCGACAAAGACGAACTCGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGCTc             >  1:707504/1‑69 (MQ=255)

                                        tCCGTCTCGACAAAGACGAACTCGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATc             >  1:951930/1‑69 (MQ=255)

                                             ctcGACAAAGACGAACTCGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGAc        <  1:2297814/69‑1 (MQ=255)

                                             ctcGACAAAGACGAACTCGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGAc        <  1:2181281/69‑1 (MQ=255)

                                             ctcGACAAAGACGAACTCGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGAc        <  1:1207736/69‑1 (MQ=255)

                                                  taaaGACGAACTTGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGACCAg     <  1:2546096/66‑1 (MQ=255)

                                                  cAAAGACGAACTTGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGACCAg     <  1:1002559/67‑1 (MQ=255)

                                                  cAAAGACGAACTTGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGACCAg     <  1:1153304/67‑1 (MQ=255)

                                                  cAAAGACGAACTTGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGACCAg     <  1:1258330/67‑1 (MQ=255)

                                                  cAAAGACGAACTTGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGACCAg     <  1:71360/67‑1 (MQ=255)

                                                  cAAAGACGAACTTGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGACCAg     <  1:1266983/67‑1 (MQ=255)

                                                  cAAAGACGAACTTGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGACCAg     <  1:131771/67‑1 (MQ=255)

                                                  cAAAGACGAACTTGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGACCAg     <  1:624584/67‑1 (MQ=255)

                                                  cAAAGACGAACTTGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGACCAg     <  1:1896574/67‑1 (MQ=255)

                                                  cAAAGACGAACTTGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGACCAg     <  1:2013334/67‑1 (MQ=255)

                                                  cAAAGACGAACTTGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGACCAg     <  1:2386908/67‑1 (MQ=255)

                                                  cAAAGACGAACTTGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGACCAg     <  1:3333252/67‑1 (MQ=255)

                                                  cAAAGACGAACTTGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGACCAg     <  1:2713613/67‑1 (MQ=255)

                                                  cAAAGACGAACTCGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGACCAg     <  1:1566312/67‑1 (MQ=255)

                                                  cAAAGACGAACTCGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGACCAg     <  1:2311018/67‑1 (MQ=255)

                                                  cAAAGACGAACTCGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGACCAg     <  1:1046462/67‑1 (MQ=255)

                                                   aaaGACGAACTTGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGACCAg     <  1:540451/66‑1 (MQ=255)

                                                    aaGACGAACTCGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGACCAGTTc  >  1:1407209/1‑68 (MQ=255)

                                                           aCTTGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGACCAg     <  1:933567/58‑1 (MQ=255)

ACACCTTCACGTATTGCCGAAAACTTTGATGTCTGGGATTTCCGTCTCGACAAAGACGAACTCGGCGAAATTGCAAAACTCGATCAGGGCAAGCGTCTCGGTCCCGATCCTGACCAGTTC  >  minE/2020082‑2020201

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