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	2,771,983	C→T	20.3%	N436N (AAC→AAT)	aceB →	malate synthase A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,771,983	0	C	T	20.3%	115.2 / 18.6	78	N436N (AAC→AAT)	aceB	malate synthase A
Reads supporting (aligned to +/- strand): ref base C (38/24); new base T (2/14); total (40/38)
Fisher's exact test for biased strand distribution p-value = 5.68e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01

AAGAAGGTATGCGCGCCAACATTCGCGTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTACCTCGATC  >  minE/2771919‑2772049

aagaagGTATGCGCGCCAACATTCGCGTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAATGGCt                                                                >  1:2010886/1‑69 (MQ=255)

aagaagGTATGCGCGCCAACATTCGCGTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAATGGCt                                                                >  1:1935634/1‑69 (MQ=255)

         tGCGCGCCAACATTCGCGTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGa                                                       >  1:999553/1‑69 (MQ=255)

         tGCGCGCCAACATTCGCGTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGa                                                       >  1:1688596/1‑69 (MQ=255)

                          gTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCTGATTTATGGCCTGATGGaa                                      <  1:870675/69‑1 (MQ=255)

                          gTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGaa                                      <  1:1934808/69‑1 (MQ=255)

                          gTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGaa                                      <  1:2603535/69‑1 (MQ=255)

                          gTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGaa                                      <  1:2105614/69‑1 (MQ=255)

                          gTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGaa                                      <  1:2093997/69‑1 (MQ=255)

                          gTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGaa                                      <  1:2745689/69‑1 (MQ=255)

                          gTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGaa                                      <  1:2081292/69‑1 (MQ=255)

                          gTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGaa                                      <  1:2755207/69‑1 (MQ=255)

                          gTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGaa                                      <  1:2244406/69‑1 (MQ=255)

                          gTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGaa                                      <  1:224485/69‑1 (MQ=255)

                          gTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGaa                                      <  1:3205933/69‑1 (MQ=255)

                          gTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGaa                                      <  1:1754945/69‑1 (MQ=255)

                          gTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGaa                                      <  1:1234192/69‑1 (MQ=255)

                          gTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGaa                                      <  1:3291804/69‑1 (MQ=255)

                          gTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGaa                                      <  1:1575400/69‑1 (MQ=255)

                          gTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGaa                                      <  1:508564/69‑1 (MQ=255)

                          gTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGaa                                      <  1:232998/69‑1 (MQ=255)

                          gTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATCGCCTGATGGaa                                      <  1:443559/69‑1 (MQ=255)

                            ggCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGaa                                      <  1:3287385/67‑1 (MQ=255)

                               tgtgCAGTACATCGAAGCGTTGATCTCTGGCAATGGCTGTGTGCCGATTTATGGCCTGATGGAAGATgc                                 <  1:611058/69‑1 (MQ=255)

                               tgtgCAGTACATCGAAGCGTGGATCTCTGGCAATGGCTGTGTGCCGATTTATGGCCTGATGGAAGATgc                                 <  1:2895388/69‑1 (MQ=255)

                               tgtgCAGTACATCGAAGCGTGGATCTCTGGCAATGGCTGTGTGCCGATTTATGGCCTGATGGAAGATgc                                 <  1:2343859/69‑1 (MQ=255)

                               tgtgCAGTACATCGAAGCGTGGATCTCTGGCAATGGCTGTGTGCCGATTTATGGCCTGATGGAAGATgc                                 <  1:2428200/69‑1 (MQ=255)

                               tgtgCAGTACATCGAAGCGTGGATCTCTGGCAATGGCTGTGTGCCGATTTATGGCCTGATGGAAGATgc                                 <  1:2602445/69‑1 (MQ=255)

                               tgtgCAGTACATCGAAGCGTGGATCTCTGGCAATGGCTGTGTGCCGATTTATGGCCTGATGGAAGATgc                                 <  1:1177121/69‑1 (MQ=255)

                               tgtgCAGTACATCGAAGCGTGGATCTCTGGCAATGGCTGTGTGCCGATTTATGGCCTGATGGAAGATgc                                 <  1:2808008/69‑1 (MQ=255)

                               tgtgCAGTACATCGAAGCGTGGATCTCTGGCAATGGCTGTGTGCCGATTTATGGCCTGATGGAAGATgc                                 <  1:828779/69‑1 (MQ=255)

                               tgtgCAGTACATCGAAGCGTGGATCTCTGGCAATGGCTGTGTGCCGATTTATGGCCTGATGGAAGATgc                                 <  1:2976023/69‑1 (MQ=255)

                               tgtgCAGTACATCGAAGCGTGGATCTCTGGCAATGGCTGTGTGCCGATTTATGGCCTGATGGAAGATgc                                 <  1:741994/69‑1 (MQ=255)

                               tgtgCAGTACATCGAAGCGTGGATCTCTGGCAATGGCTGTGTGCCGATTTATGGCCTGATGGAAGATgc                                 <  1:2190613/69‑1 (MQ=255)

                               tgtgCAGTACATCGAAGCGTGGATCTCTGGCAATGGCTGTGTGCCGATTTATGGCCTGATGGAAGATgc                                 <  1:133435/69‑1 (MQ=255)

                               tgtgCAGTACATCGAAGCGTGGATCTCTGGCAATGGCTGTGTGCCGATTTATGGCCTGATGGAAGATgc                                 <  1:1606030/69‑1 (MQ=255)

                                gtgCAGTACATCGAAGCGTGGATCTCTGGCAATGGCTGTGTGCCGATTTATGGCCTGATGGAAGATgc                                 <  1:3233434/68‑1 (MQ=255)

                                   cAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATgcggcg                             >  1:218109/1‑69 (MQ=255)

                                   cAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATgcggcg                             >  1:3169963/1‑69 (MQ=255)

                                   cAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATgcggcg                             >  1:3149229/1‑69 (MQ=255)

                                            gAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGaa                    >  1:340176/1‑69 (MQ=255)

                                            gAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGaa                    >  1:1187823/1‑69 (MQ=255)

                                            gAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGaa                    >  1:1959438/1‑69 (MQ=255)

                                            gAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGaa                    >  1:583344/1‑69 (MQ=255)

                                            gAAGCGTGGATCTATGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGaa                    >  1:1917033/1‑69 (MQ=255)

                                                    gATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCg            >  1:1644125/1‑69 (MQ=255)

                                                    gATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCg            >  1:134718/1‑69 (MQ=255)

                                                    gATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCg            >  1:2990107/1‑69 (MQ=255)

                                                    gATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCg            >  1:2916755/1‑69 (MQ=255)

                                                    gATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCg            >  1:741184/1‑69 (MQ=255)

                                                    gATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCg            >  1:1277530/1‑69 (MQ=255)

                                                       ctctGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTc               >  1:3314968/1‑63 (MQ=255)

                                                       ctctGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTAc         >  1:531971/1‑69 (MQ=255)

                                                       ctctGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTAc         >  1:589206/1‑69 (MQ=255)

                                                       ctctGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTAc         >  1:1249520/1‑69 (MQ=255)

                                                       ctctGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTAc         >  1:2186763/1‑69 (MQ=255)

                                                       ctctGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTAc         >  1:984733/1‑69 (MQ=255)

                                                       ctctGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTAc         >  1:2620394/1‑69 (MQ=255)

                                                       ctctGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTAc         >  1:1877688/1‑69 (MQ=255)

                                                       ctctGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTAc         >  1:2083498/1‑69 (MQ=255)

                                                       ctctGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTAc         >  1:2802488/1‑69 (MQ=255)

                                                       ctctGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTAc         >  1:1975239/1‑69 (MQ=255)

                                                       ctctGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTAc         >  1:2910133/1‑69 (MQ=255)

                                                       ctctGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTAc         >  1:22230/1‑69 (MQ=255)

                                                       ctctGGCAACGGCTGTGTGACGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTAc         >  1:2464542/1‑69 (MQ=255)

                                                          tGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTACCTc      >  1:3211103/1‑69 (MQ=255)

                                                          tGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTACCTc      >  1:831453/1‑69 (MQ=255)

                                                          tGGCAACGGCTGTGTGCCGATTTATGGCATGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTACCTc      >  1:2656576/1‑69 (MQ=255)

                                                          tGGCAACGGCTGTGTGCCGA‑TTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTACCTCg     >  1:668921/1‑69 (MQ=255)

                                                            gCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCg            >  1:3100376/1‑61 (MQ=255)

                                                            gCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTACCTCGa    >  1:1950979/1‑69 (MQ=255)

                                                            gCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTACCTCGa    >  1:737273/1‑69 (MQ=255)

                                                            gCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCG‑‑GACGGCTGAAATTTCCCGTACCTCGATc  >  1:550006/1‑69 (MQ=255)

                                                              aaCGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTACCTCg     <  1:272724/66‑1 (MQ=255)

                                                              aaCGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTACCTCg     <  1:1056731/66‑1 (MQ=255)

                                                              aaCGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTACCTCg     <  1:2019735/66‑1 (MQ=255)

                                                              aaCGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTACCTCg     <  1:3372478/66‑1 (MQ=255)

                                                              aaCGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTACCTCg     <  1:3286016/66‑1 (MQ=255)

AAGAAGGTATGCGCGCCAACATTCGCGTGGCTGTGCAGTACATCGAAGCGTGGATCTCTGGCAACGGCTGTGTGCCGATTTATGGCCTGATGGAAGATGCGGCGACGGCTGAAATTTCCCGTACCTCGATC  >  minE/2771919‑2772049

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