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	1,168,929	C→T	47.8%	V56I (GTC→ATC)	ynjF ←	predicted phosphatidyl transferase, inner membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,168,929	0	C	T	47.8%	3.8 / 58.5	69	V56I (GTC→ATC)	ynjF	predicted phosphatidyl transferase, inner membrane protein
Reads supporting (aligned to +/- strand): ref base C (11/25); new base T (23/10); total (34/35)
Fisher's exact test for biased strand distribution p-value = 1.68e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGACCATCAAGCAGCCTGTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGCCGATGGCAAATCCCACT  >  minE/1168894‑1168996

cAGACCATCATGCAGCCTGTTCAACAAAATGACGATTAGCGCCGCCAGATAccagccca                                              >  1:706621/1‑59 (MQ=255)

cAGACCATCAAGCAGCCTGTTCAACAAAATGACGATTAg                                                                  >  1:449231/1‑39 (MQ=255)

cAGACCATCAAGCAGCCTGTTCAACAAAATGACGATTAGCGCCGCCAGa                                                        >  1:2418550/1‑49 (MQ=255)

cAGACCATCAAGCAGCCTGTTCAACAAAATGACGATTAGCGCCGCCAGATAccagccca                                              >  1:1948736/1‑59 (MQ=255)

cAGACCATCAAGCAGCCTGTTCAACAAAATGACGATTAGCGCCGCCAGATAccagccca                                              >  1:2783641/1‑59 (MQ=255)

cAGACCATCAAGCAGCCTGTTCAACAAAATGACGATTAGCGCCGCCAGATAccagccca                                              >  1:3087268/1‑59 (MQ=255)

cAGACCATCAAGCAGCCTGTTCAACAAAATGACGATTAGCGCCGCCAGATAccagccca                                              >  1:3310630/1‑59 (MQ=255)

cAGACCATCAAGCAGCCTGTTCAACAAAATGACGATTAGCGCCGCCAGATAccagccca                                              >  1:27138/1‑59 (MQ=255)

cAGACCATCAAGCAGCCTGTTCAACAAAATGACGATTAGCGCCGCCAGATAccagccca                                              >  1:1461833/1‑59 (MQ=255)

cAGACCATCAAGCAGCCTGTTCAACAAAATGACGATTAGCGCCGCCAGATAccagccca                                              >  1:1451053/1‑59 (MQ=255)

cAGACCATCAAGCAGCCTGTTCAACAAAATGACGATTAGCGCCGCCAGATAccagccca                                              >  1:1422407/1‑59 (MQ=255)

cAGACCATCAAGCAGCCTGTTCAACAAAATGACGATTAGCGCCGCCAGATAccagccca                                              >  1:538662/1‑59 (MQ=255)

cAGACCATCAAGCAGCCTGTTCAACAAAATGACGATTAGCGCCGCCAGATAccagccca                                              >  1:1346980/1‑59 (MQ=255)

cAGACCATCAAGCAGCCTGTTCAACAAAATGACGATTAGCGCCGCCAGATAccagccca                                              >  1:202263/1‑59 (MQ=255)

cAGACCATCAAGCAGCCTGTTCAACAAAATGACGATTAGCGCCGCCAGATAccagccca                                              >  1:2193324/1‑59 (MQ=255)

cAGACCATCAAGCAGCCTGTTCAACAAAATGACGATTAGCGCCGCCAGATAccagccca                                              >  1:2405717/1‑59 (MQ=255)

cAGACCATCAAGCAGCCTGTTCAACAAAATGACGATTAGCGCCGCCAGATAccagccca                                              >  1:2401891/1‑59 (MQ=255)

cAGACCATCAAGCAGCCTGTTCAACAAAATGACGATTAGCGCCGCCAGATAccagccca                                              >  1:102682/1‑59 (MQ=255)

cAGACCATCAAGCAGCCTGTTCAACAAAATGACGATTAGCGCCGCCAGATAccagccca                                              >  1:2237372/1‑59 (MQ=255)

cAGACCATCAAGCAGCCTGTTCAACAAAATGACGATTAGCGCCGCCAGATAccag                                                  >  1:170434/1‑55 (MQ=255)

cAGACCATCAAGCAGCCTGTTCAACAAAATGACGATTAGCGC‑‑CCAGATAccagccca                                              >  1:1031071/1‑57 (MQ=255)

cAGACCATCAAGCAGCCTGTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGaaa                                    >  1:2763838/1‑69 (MQ=255)

cAGACCATCAAGCAGCCTGTTAAACAAAATGACGATTAGCGCCGCCAGATAccagcaca                                              >  1:2635123/1‑59 (MQ=255)

cAGACCATCAAGCAGCCTCTTCAACAAAATGACGATTAGCGCCGCCAGATAccagccca                                              >  1:769789/1‑59 (MQ=255)

cAGACCAT‑AAGCAGCCTGTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAAc                                   >  1:1927711/1‑69 (MQ=255)

   aCCATCAAGCAGCCTGTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACgg                                 <  1:790208/69‑1 (MQ=255)

            cagcCTGTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAg                        <  1:978043/69‑1 (MQ=255)

            cagcCTGTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAg                        <  1:641152/69‑1 (MQ=255)

            cagcCTGTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAg                        <  1:64681/69‑1 (MQ=255)

            cagcCTGTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAg                        <  1:684261/69‑1 (MQ=255)

            cagcCTGTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAg                        <  1:749643/69‑1 (MQ=255)

            cagcCTGTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAg                        <  1:1051314/69‑1 (MQ=255)

            cagcCTGTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAg                        <  1:1765931/69‑1 (MQ=255)

            cagcCTGTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAg                        <  1:172579/69‑1 (MQ=255)

            cagcCTGTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAg                        <  1:1266210/69‑1 (MQ=255)

            cagcCTGTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAg                        <  1:1849217/69‑1 (MQ=255)

            cagcCTGTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAg                        <  1:1080751/69‑1 (MQ=255)

            cagcCTGTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAg                        <  1:2236907/69‑1 (MQ=255)

              gcCTGTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAg                        <  1:2497802/67‑1 (MQ=255)

                cTGTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACg                    <  1:765954/69‑1 (MQ=255)

                cTGTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACg                    <  1:1193844/69‑1 (MQ=255)

                cTGTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACg                    <  1:265400/69‑1 (MQ=255)

                cTGTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACg                    <  1:1264753/69‑1 (MQ=255)

                  gTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGcc                  <  1:2220304/69‑1 (MQ=255)

                  gTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGcc                  <  1:2916307/69‑1 (MQ=255)

                     caacaaAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGCCGa                >  1:1112976/1‑68 (MQ=255)

                     caacaaAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGCCGa                >  1:927067/1‑68 (MQ=255)

                     caacaaAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGCCGAt               >  1:865914/1‑69 (MQ=255)

                     caacaaAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGCCGAt               >  1:628393/1‑69 (MQ=255)

                     caacaaAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGCCGAt               >  1:1758517/1‑69 (MQ=255)

                     caacaaAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGCCGAt               >  1:3122806/1‑69 (MQ=255)

                     caacaaAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGCCGAt               >  1:2389350/1‑69 (MQ=255)

                     caacaaAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGCCGAt               >  1:2461197/1‑69 (MQ=255)

                     caacaaAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGCCGAt               >  1:272375/1‑69 (MQ=255)

                         aaaaTGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGCCGATGGCa           <  1:797648/69‑1 (MQ=255)

                         aaaaTGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGCCGATGGCa           <  1:793738/69‑1 (MQ=255)

                         aaaaTGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGCCGATGGCa           <  1:2837149/69‑1 (MQ=255)

                           aaTGACGATTAGCGCCGCCAGATACCAGCCCATCGCCAGaaaa                                   <  1:3314156/43‑2 (MQ=37)

                           aaTGACGATTAGCGCCGCCAGATACCAGCCCAGCGCCAGaaaa                                   <  1:3022615/43‑2 (MQ=255)

                           aaTGACGATTAGCGCCGCCAGATACCAGCCCAGCGCCAGaaaa                                   <  1:917053/43‑2 (MQ=255)

                           aaTGACGATTAGCGCCGCCAGATACCAGCCCAGCGCCAGaaaa                                   <  1:2508698/43‑2 (MQ=255)

                           aaTGACGATTAGCGCCGCCAGATACCAGCCCAGCGCCAGaaaa                                   <  1:2532269/43‑2 (MQ=255)

                           aaTGACGATTAGCGCCGCCAGATACCAGCCCAGCGCCAGaaaa                                   <  1:1248702/43‑2 (MQ=255)

                           aaTGACGATTAGCGCCGCCAGATACCAGCCCAGCGCCAGaaaa                                   <  1:1800816/43‑2 (MQ=255)

                           aaTGACGATTAGCGCCGCCAGATACCAGCCCAGCGCCAGaaaa                                   <  1:3284264/43‑2 (MQ=255)

                           aaTGACGATTAGCGCCGCCAGATACCAGCCCAGCGCCAGaaaa                                   <  1:312157/43‑2 (MQ=255)

                            aTGACGATTAGCGCCGCCAGATACCAGCCCAGCGCCAGaaaa                                   <  1:620905/42‑2 (MQ=255)

                            aTGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGCCGATGGCAAAt        <  1:569057/69‑1 (MQ=255)

                            aTGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGCCGATGGCAAAt        <  1:1391582/69‑1 (MQ=255)

                              gacgacTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGCCGATGGCAAATcc      <  1:1781765/69‑1 (MQ=255)

                              gacgacTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGCCGATGGCAAATcc      <  1:2933589/69‑1 (MQ=255)

                              gacgacTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGCCGATGGCAAATcc      <  1:2191438/69‑1 (MQ=255)

                              gacgacTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGCCGATGGCAAATcc      <  1:926154/69‑1 (MQ=255)

                                 gacTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACg                    <  1:2027375/52‑1 (MQ=255)

                                  acTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGGACGCCGATGGCAAATCCCACt  >  1:138434/1‑69 (MQ=255)

                                  acTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGCCGATGGCAAATCCCACt  >  1:2403629/1‑69 (MQ=255)

                                  acTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGCCGATGGCAAATCCCACt  >  1:2350743/1‑69 (MQ=255)

CAGACCATCAAGCAGCCTGTTCAACAAAATGACGACTAGCGCCGCCAGATACCAGCCCAGCGCCAGAAACGGCAGAGCCAGCACGCCGATGGCAAATCCCACT  >  minE/1168894‑1168996

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A