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	2,631,652	T→C	38.8%	I289I (ATT→ATC)	livH →	leucine/isoleucine/valine transporter subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,631,652	0	T	C	38.8%	32.9 / 46.6	72	I289I (ATT→ATC)	livH	leucine/isoleucine/valine transporter subunit
Reads supporting (aligned to +/- strand): ref base T (35/9); new base C (8/20); total (43/29)
Fisher's exact test for biased strand distribution p-value = 2.36e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCTCTCTTCTGCCTATCTGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAGTATGAAACCGATG  >  minE/2631591‑2631720

cgcTCTCTTCTGCCTATCTGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGtgc                                                               >  1:2022976/1‑69 (MQ=255)

cgcTCTCTTCTGCCTATCTGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGtgc                                                               >  1:2026764/1‑69 (MQ=255)

cgcTCTCTTCTGCCTATCTGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGtgc                                                               >  1:2579456/1‑69 (MQ=255)

cgcTCTCTTCTGCCTATCTGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGtgc                                                               >  1:3359193/1‑69 (MQ=255)

cgcTCTCTTCTGCCTATCTGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGtgc                                                               >  1:1720776/1‑69 (MQ=255)

cgcTCTCTTCTGCCTATCTGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGtgc                                                               >  1:1211003/1‑69 (MQ=255)

cgcTCTCTTCTGCCTATCTGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGtgc                                                               >  1:1005115/1‑69 (MQ=255)

cgcTCTCTTCTGCCTATCTGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGtgc                                                               >  1:1309452/1‑69 (MQ=255)

         ctGCCTATCTGAGTACGTAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGTGCTGCTGGt                                                        <  1:1347809/67‑1 (MQ=255)

         ctGCCTATCTGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGTGCTGCTGGt                                                        <  1:413454/67‑1 (MQ=255)

                  tGAGTACGGAATATAAAGATTTGGTCTCATTCGCCCTGCTGATTCTGGTGCTGCTGGt                                                        <  1:43339/58‑1 (MQ=255)

                  tGAGTACGGAATATAAAGATGTGGTCTCTTTCGCCCTGCTGATTCTGGTGCTGCTGGt                                                        >  1:1883012/1‑58 (MQ=255)

                  tGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGTGCTGCTGGt                                                        >  1:1754836/1‑58 (MQ=255)

                  tGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGTGCTGCTGGt                                                        <  1:278261/58‑1 (MQ=255)

                  tGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGTGCTGCTGGt                                                        >  1:1945666/1‑58 (MQ=255)

                  tGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGTGCTGCTGGt                                                        >  1:1942922/1‑58 (MQ=255)

                  tGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGTGCTGCTGGt                                                        >  1:1163727/1‑58 (MQ=255)

                  tGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGTGCTGCTGGt                                                        >  1:1863349/1‑58 (MQ=255)

                  tGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGTGCTGCTGGt                                                        >  1:2279457/1‑58 (MQ=255)

                  tGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGTGCTGCTGGt                                                        >  1:1728902/1‑58 (MQ=255)

                  tGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGTGCTGCTGGt                                                        <  1:244233/58‑1 (MQ=255)

                  tGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGTGCTGCTGGt                                                        >  1:554652/1‑58 (MQ=255)

                  tGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGTGCTGCTGGt                                                        >  1:2471415/1‑58 (MQ=255)

                  tGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGTGCTGCTGGt                                                        >  1:3279273/1‑58 (MQ=255)

                  tGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGTGCTGCTGGt                                                        >  1:1500948/1‑58 (MQ=255)

                  tGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGATGATTCTGGTGCTGCTGGt                                                        >  1:510786/1‑58 (MQ=255)

                           aaTATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGTGCTGCTGGt                                                        <  1:177139/49‑1 (MQ=255)

                                   gATGTGGTCTCATTCGCCCTGCTGATTCTGTTGCTGCTGGt                                                        <  1:3174640/41‑1 (MQ=255)

                                        ggTCTCATTCGCCCTGCTGATTCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGa                          >  1:946611/1‑66 (MQ=255)

                                        ggTCTCATTCGCCCTGCTGATTCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGa                          >  1:438953/1‑66 (MQ=255)

                                        ggTCTCATTCGCCCTGCTGATTCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGa                          >  1:1700823/1‑66 (MQ=255)

                                        ggTCTCATTCGCCCTGCTGATTCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTAGCCCGGa                          >  1:3017296/1‑66 (MQ=255)

                                             cATTCGCCCTGCTGATTCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTaga                    >  1:2552823/1‑67 (MQ=255)

                                             cATTCGCCCTGCTGATTCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTaga                    >  1:1216067/1‑67 (MQ=255)

                                             cATTCGCCCTGCTGATTCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTaga                    >  1:2369891/1‑67 (MQ=255)

                                                tCGCCCTGCTGATTCTGGTGCGGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAg               <  1:911035/69‑1 (MQ=255)

                                                 cGCCCTGCTGTTCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGATAg               <  1:2000737/68‑1 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCTGTATTCTTGGTCGCCCGGAGGTAGAGAAAg               <  1:3193973/65‑1 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGa                          >  1:681072/1‑54 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAg               <  1:388191/65‑1 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAg               <  1:3405794/65‑1 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAg               <  1:3197942/65‑1 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAg               <  1:3142578/65‑1 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAg               <  1:3045821/65‑1 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAg               <  1:2551115/65‑1 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAg               <  1:3302450/65‑1 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAg               <  1:2597428/65‑1 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAg               <  1:16497/65‑1 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAg               <  1:1657486/65‑1 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAg               <  1:1576090/65‑1 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAg               <  1:1215752/65‑1 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAg               <  1:2058588/65‑1 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAg               <  1:1142810/65‑1 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAg               <  1:2743776/65‑1 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAg               <  1:2758471/65‑1 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAg               <  1:276445/65‑1 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAg               <  1:2854312/65‑1 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAGTAt            >  1:3231612/1‑68 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAGTAt            >  1:561326/1‑68 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAGTAt            >  1:3109777/1‑68 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAGTAt            >  1:1169150/1‑68 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAGTAt            >  1:1828515/1‑68 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAGTAt            >  1:2841685/1‑68 (MQ=255)

                                                    ccTGCTGATCCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAGTAt            >  1:2906975/1‑68 (MQ=255)

                                                        ctgATTCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAGTATGaaa        >  1:1064392/1‑68 (MQ=255)

                                                        ctgATTCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAGTATGaaa        >  1:3344492/1‑68 (MQ=255)

                                                        ctgATTCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAGTATGaaa        >  1:2472874/1‑68 (MQ=255)

                                                        ctgATTCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAGTATGaaa        >  1:3044086/1‑68 (MQ=255)

                                                        ctgATTCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAGTATGaa         >  1:1723444/1‑67 (MQ=255)

                                                          gATTCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAGTATGAAAcc      <  1:1102710/68‑1 (MQ=255)

                                                          gATTCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAGTATGAAACCg     >  1:2612591/1‑69 (MQ=255)

                                                          gATTCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAGTATGAAACCg     >  1:836794/1‑69 (MQ=255)

                                                             tCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAGTATGAAACCGATg  >  1:190044/1‑69 (MQ=255)

CGCTCTCTTCTGCCTATCTGAGTACGGAATATAAAGATGTGGTCTCATTCGCCCTGCTGATTCTGGTGCTGCTGGTGATGCCGACCGGTATTCTGGGTCGCCCGGAGGTAGAGAAAGTATGAAACCGATG  >  minE/2631591‑2631720

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