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	2,660,342	C→T	37.8%	L234L (CTG→TTG)	glpG →	predicted intramembrane serine protease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,660,342	0	C	T	37.8%	32.4 / 33.6	58	L234L (CTG→TTG)	glpG	predicted intramembrane serine protease
Reads supporting (aligned to +/- strand): ref base C (16/20); new base T (4/18); total (20/38)
Fisher's exact test for biased strand distribution p-value = 5.06e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.55e-01

TGGCTACGTGGCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTGGGATGTCGATGGCGAACGGAGCACACATC  >  minE/2660276‑2660407

tGGCTACGTGGCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGCTg                                                                 >  1:1237988/1‑69 (MQ=255)

tGGCTACGTGGCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGCTg                                                                 >  1:51871/1‑69 (MQ=255)

tGGCTACGTGGCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGCTg                                                                 >  1:2532210/1‑69 (MQ=255)

  gCTACGTGGCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGCTGAt                                                               >  1:1585784/1‑69 (MQ=255)

          gCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGTTGATCTGGATTg                                                       <  1:1960428/69‑1 (MQ=255)

          gCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGTTGATCTGGATTg                                                       <  1:114956/69‑1 (MQ=255)

          gCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGTTGATCTGGATTg                                                       <  1:2045809/69‑1 (MQ=255)

          gCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGTTGATCTGGATTg                                                       <  1:2238402/69‑1 (MQ=255)

          gCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGTTGATCTGGATTg                                                       <  1:2427165/69‑1 (MQ=255)

          gCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGTTGATCTGGATTg                                                       <  1:2468626/69‑1 (MQ=255)

          gCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGTTGATCTGGATTg                                                       <  1:2602042/69‑1 (MQ=255)

          gCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGTTGATCTGGATTg                                                       <  1:2610814/69‑1 (MQ=255)

          gCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGTTGATCTGGATTg                                                       <  1:3045641/69‑1 (MQ=255)

          gCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGTTGATCTGGATTg                                                       <  1:3222050/69‑1 (MQ=255)

          gCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGTTGATCTGGATTg                                                       <  1:3247805/69‑1 (MQ=255)

          gCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGTTGATCTGGATTg                                                       <  1:398304/69‑1 (MQ=255)

          gCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGTTGATCTGGATTg                                                       <  1:529248/69‑1 (MQ=255)

          gCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGTTGATCTGGATTg                                                       <  1:927408/69‑1 (MQ=255)

          gCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGTTGATCTGGATTg                                                       <  1:1862535/69‑1 (MQ=255)

          gCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGTTGATCTGGATTg                                                       <  1:1267097/69‑1 (MQ=255)

          gCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGTTGATCTGGATTg                                                       <  1:1355392/69‑1 (MQ=255)

          gCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGTTGATCTGGATTg                                                       <  1:1463433/69‑1 (MQ=255)

            gAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGTTGATCTGGATTGTc                                                     >  1:1959529/1‑69 (MQ=255)

            gAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGTTGATCTGGATTGTc                                                     >  1:1007124/1‑69 (MQ=255)

            gAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGTTGATCTGGATTGTc                                                     >  1:3289070/1‑69 (MQ=255)

            gAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGTTGATCTGGATTGTc                                                     >  1:2746099/1‑69 (MQ=255)

                          aaGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGa                                       <  1:1918285/69‑1 (MQ=255)

                          aaGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGa                                       <  1:899857/69‑1 (MQ=255)

                          aaGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGa                                       <  1:2935985/69‑1 (MQ=255)

                          aaGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGa                                       <  1:1690176/69‑1 (MQ=255)

                          aaGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGa                                       <  1:2514740/69‑1 (MQ=255)

                          aaGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGa                                       <  1:1729115/69‑1 (MQ=255)

                          aaGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCACTGATCTGGATTGTCGCCGGATGGTTTGa                                       <  1:3216501/69‑1 (MQ=255)

                            gTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGAtt                                     >  1:228723/1‑69 (MQ=255)

                                   ttACCTGCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTgg                              <  1:1766003/69‑1 (MQ=255)

                                   ttACCTGCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTgg                              <  1:1482345/69‑1 (MQ=255)

                                   ttACCTGCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTgg                              <  1:3145323/69‑1 (MQ=255)

                                    tACCTGCAACGTGGGTTAATTATCTTTGCGCTGATCt                                                             >  1:1379930/1‑37 (MQ=255)

                                    tACCTGCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTggg                             >  1:1910104/1‑69 (MQ=255)

                                    tACCTGCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTggg                             >  1:1719302/1‑69 (MQ=255)

                                    tACCTGCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTggg                             >  1:227462/1‑69 (MQ=255)

                                         gCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTgg                              <  1:1706445/63‑1 (MQ=255)

                                         gCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTgg                              <  1:3007272/63‑1 (MQ=255)

                                         gCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTgg                              <  1:3003423/63‑1 (MQ=255)

                                         gCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTgg                              <  1:2187242/63‑1 (MQ=255)

                                         gCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTgg                              <  1:65455/63‑1 (MQ=255)

                                         gCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTgg                              <  1:621716/63‑1 (MQ=255)

                                         gCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTgg                              <  1:404900/63‑1 (MQ=255)

                                         gCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTgg                              <  1:459592/63‑1 (MQ=255)

                                         gCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTgg                              <  1:273750/63‑1 (MQ=255)

                                         gCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTGGGATGTc                        >  1:3226917/1‑69 (MQ=255)

                                         gCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTGGGATGTc                        >  1:3410780/1‑69 (MQ=255)

                                         gCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATT‑TCGCCGGATGGTTTGATTTGTTTgg                              <  1:2343554/62‑1 (MQ=255)

                                                         aTCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTGGGATGTCGATGGCGAACGGAGca        >  1:2905643/1‑69 (MQ=255)

                                                         aTCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTGGGATGTCGATGGCGAACGGAGca        >  1:2620770/1‑69 (MQ=255)

                                                         aTCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTGGGATGTCGATGGCGAACGGAGca        >  1:2341228/1‑69 (MQ=255)

                                                         aTCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTGGGATGTCGATGGCGAACGGAGca        >  1:322529/1‑69 (MQ=255)

                                                         aTCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTGGGATGTCGATGGCGAACGGAGca        >  1:3018967/1‑69 (MQ=255)

                                                                cgcTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTGGGATGTCGATGGCGAACGGAGCACACATc  <  1:1484003/68‑1 (MQ=255)

TGGCTACGTGGCGAACGCGATCCGCAAAGTGGCATTTACCTGCAACGTGGGTTAATTATCTTTGCGCTGATCTGGATTGTCGCCGGATGGTTTGATTTGTTTGGGATGTCGATGGCGAACGGAGCACACATC  >  minE/2660276‑2660407

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A