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	1,800,617	G→A	44.4%	G107G (GGG→GGA)	proX →	glycine betaine transporter subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,800,617	0	G	A	44.4%	11.7 / 39.5	54	G107G (GGG→GGA)	proX	glycine betaine transporter subunit
Reads supporting (aligned to +/- strand): ref base G (21/9); new base A (6/18); total (27/27)
Fisher's exact test for biased strand distribution p-value = 2.26e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.96e-01

CGCCACTGCATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTATTTGTTAACGGCGCGGCACAGGGTTACCTGATCGATAAGAAAAC  >  minE/1800556‑1800664

cGCCACTGCATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGAGTATTTg                                          <  1:449007/69‑1 (MQ=255)

cGCCACTGCATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGAGTATTTg                                          <  1:2699879/69‑1 (MQ=255)

cGCCACTGCATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGAGTATTTg                                          <  1:2184261/69‑1 (MQ=255)

cGCCACTGCATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGAGTATTTg                                          <  1:3159213/69‑1 (MQ=255)

cGCCACTGCATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGAGTATTTg                                          <  1:2057369/69‑1 (MQ=255)

cGCCACTGCATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGAGTATTTg                                          <  1:1918121/69‑1 (MQ=255)

cGCCACTGCATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGAGTATTTg                                          <  1:3376781/69‑1 (MQ=255)

cGCCACTGCATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGAGTATTTg                                          <  1:1848543/69‑1 (MQ=255)

cGCCACTGCATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGAGTATTTg                                          <  1:430900/69‑1 (MQ=255)

cGCCACTGCATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGAGTATTTg                                          <  1:1702652/69‑1 (MQ=255)

cGCCACTGCATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGAGTATTTg                                          <  1:157810/69‑1 (MQ=255)

cGCCACTGCATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGAGTATTTg                                          <  1:710335/69‑1 (MQ=255)

cGCCACTGCATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGAGTATTTg                                          <  1:1435783/69‑1 (MQ=255)

cGCCACTGCATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGAGTATTTg                                          <  1:1426715/69‑1 (MQ=255)

cGCCACTGCATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGAGTATTTg                                          <  1:1392423/69‑1 (MQ=255)

cGCCACTGCATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGAGTATTTg                                          <  1:1388989/69‑1 (MQ=255)

cGCCACTGCATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGAGTATTTg                                          <  1:1198135/69‑1 (MQ=255)

cGCCACTGCATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGAGTATTTg                                          <  1:1252581/69‑1 (MQ=255)

        cATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTATTTGTTAACGgc                                  >  1:1120574/1‑69 (MQ=255)

        cATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTATTTGTTAACGgc                                  >  1:1443017/1‑69 (MQ=255)

        cATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTATTTGTTAACGgc                                  >  1:1060707/1‑69 (MQ=255)

        cATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTATTTGTTAACGgc                                  >  1:2177993/1‑69 (MQ=255)

        cATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTATTTGTTAACGgc                                  >  1:2171085/1‑69 (MQ=255)

        cATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTATTTGTTAACGgc                                  >  1:829952/1‑69 (MQ=255)

        cATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTATTTGTTAACGgc                                  >  1:1779817/1‑69 (MQ=255)

        cATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTATTTGTTAACGgc                                  >  1:795579/1‑69 (MQ=255)

        cATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTATTTGTTAACGgc                                  >  1:639617/1‑69 (MQ=255)

            acaacaTGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTATTTGtt                                        <  1:3330142/59‑1 (MQ=255)

               acaTGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTATTTGTTAACGgcgc                                >  1:3219398/1‑64 (MQ=255)

               acaTGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTATTTGTTAACGgcgc                                >  1:825303/1‑64 (MQ=255)

               acaTGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTATTTGTTAACGgcgc                                >  1:2778344/1‑64 (MQ=255)

               acaTGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTATTTGTTAACGgcgc                                >  1:933959/1‑64 (MQ=255)

               acaTGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTATTTGTTAACGgcgc                                >  1:1510933/1‑64 (MQ=255)

               acaTGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTATTTGTTAACGgcgc                                >  1:1633733/1‑64 (MQ=255)

               acaTGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTATTTGTTAACGgcgc                                >  1:1958276/1‑64 (MQ=255)

                caTGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTa                                              <  1:1140405/49‑1 (MQ=255)

                caTGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTa                                              <  1:1399744/49‑1 (MQ=255)

                caTGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTa                                              <  1:72497/49‑1 (MQ=255)

                caTGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTa                                              <  1:2825332/49‑1 (MQ=255)

                caTGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTa                                              <  1:3013631/49‑1 (MQ=255)

                caTGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTa                                              <  1:2116546/49‑1 (MQ=255)

                caTGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTa                                              <  1:1785900/49‑1 (MQ=255)

                caTGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTa                                              <  1:3384776/49‑1 (MQ=255)

                                   ggCGATAAGAAATTTTATCGTGAAGGGGTATTTGTTAACGGCGCgg                              >  1:1849323/1‑46 (MQ=255)

                                   ggCGATAAGAAATTTTATCGTGAAGGGGTATTTGTTAACGGCGCgg                              >  1:2159578/1‑46 (MQ=255)

                                   ggCGATAAGAAATTTTATCGTGAAGGGGTATTTGTTAACGGCGCgg                              >  1:2375329/1‑46 (MQ=255)

                                   ggCGATAAGAAATTTTATCGTGAAGGGGTATTTGTTAACGGCGCgg                              >  1:2686363/1‑46 (MQ=255)

                                   ggCGATAAGAAATTTTATCGTGAAGGGGTATTTGTTAACGGCGCgg                              >  1:2552583/1‑46 (MQ=255)

                                        tAAGAAATTTTATCGTGAAGGAGTATTTGTTAACGGCGCGGCACAGGGTTACCTGATCGATAAGAAAAc  >  1:2407320/1‑69 (MQ=255)

                                        tAAGAAATTTTATCGTGAAGGAGTATTTGTTAACGGCGCGGCACAGGGTTACCTGATCGATAAGAAAAc  >  1:1981721/1‑69 (MQ=255)

                                        tAAGAAATTTTATCGTGAAGGAGTATTTGTTAACGGCGCGGCACAGGGTTACCTGATCGATAAGAAAAc  >  1:1603316/1‑69 (MQ=255)

                                        tAAGAAATTTTATCGTGAAGGAGTATTTGTTAACGGCGCGGCACAGGGTTACCTGATCGATAAGAAAAc  >  1:2745288/1‑69 (MQ=255)

                                        tAAGAAATTTTATCGTGAAGGAGTATTTGTTAACGGCGCGGCACAGGGTTACCTGATCGATAAGAAAAc  >  1:138219/1‑69 (MQ=255)

                                        tAAGAAATTTTATCGTGAAGGAGTATTTGTTAACGGCGCGGCACAGGGTTACCTGATCGATAAGAAAAc  >  1:1331914/1‑69 (MQ=255)

CGCCACTGCATGACAACATGTACGAAGCTGCCGGTGGCGATAAGAAATTTTATCGTGAAGGGGTATTTGTTAACGGCGCGGCACAGGGTTACCTGATCGATAAGAAAAC  >  minE/1800556‑1800664

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