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	2,497,255	C→T	44.2%	intergenic (‑932/‑2)	emrD ← / → ivbL	multidrug efflux system protein/ilvB operon leader peptide

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,497,255	0	C	T	44.2%	12.9 / 46.5	61	intergenic (‑932/‑2)	emrD/ivbL	multidrug efflux system protein/ilvB operon leader peptide
Reads supporting (aligned to +/- strand): ref base C (13/21); new base T (16/11); total (29/32)
Fisher's exact test for biased strand distribution p-value = 1.26e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01

CATTGTCTCCCCTGTAAAGCTGTGCTTGTATAAATATTGTTAAACACAAAACCAACAAGGTCCCCAATGACTACTTCCATGCTCAACGCAAAACTACTACCAACTGCGCCATCCGCCGCAGTG  >  minE/2497191‑2497313

cATTGTCTCCCCTGTAAAGCTGTGCTTGTATAAATATTGTTAAACACAAAACCAACAAGGTCCCCAAt                                                         <  1:2162605/68‑1 (MQ=255)

cATTGTCTCCCCTGTAAAGCTGTGCTTGTATAAATATTGTTAAACACAAAACCAACAAGGTCCCCAAt                                                         <  1:817028/68‑1 (MQ=255)

cATTGTCTCCCCTGTAAAGCTGTGCTTGTATAAATATTGTTAAACACAAAACCAACAAGGTCCCCAAt                                                         <  1:1401050/68‑1 (MQ=255)

cATTGTCTCCCCTGTAAAGCTGTGCTTGTATAAATATTGTTAAACACAAAACCAACAAGGTCCCCAAt                                                         <  1:3387413/68‑1 (MQ=255)

cATTGTCTCCCCTGTAAAGCTGTGCTTGTATAAATATTGTTAAACACAAAACCAACAAGGTCCCCAAt                                                         <  1:1587437/68‑1 (MQ=255)

           cTGTAAAGCTGTGCTTGTATAAATATTGTTAAACACAAAACCAACAAGGTCCCCAATGACTACTTc                                                <  1:2216881/66‑1 (MQ=255)

           cTGTAAAGCTGTGCTTGTATAAATATTGTTAAACACAAAACCAACAAGGTCCCCAATGACTACTTc                                                <  1:2600276/66‑1 (MQ=255)

                aaGCTGTGCTTGTATAAATATTGTTAAACACAAAACCAACAAGGTCCCCAATGACTACTTc                                                <  1:1196062/61‑1 (MQ=255)

                aaGCTGTGCTTGTATAAATATTGTTAAACACAAAACCAACAAGGTCCCCAATGACTACTTc                                                <  1:3392369/61‑1 (MQ=255)

                aaGCTGTGCTTGTATAAATATTGTTAAACACAAAACCAACAAGGTCCCCAATGACTACTTc                                                <  1:2247810/61‑1 (MQ=255)

                aaGCTGTGCTTGTATAAATATTGTTAAACACAAAACCAACAAGGTCCCCAATGACTACTTc                                                <  1:2311249/61‑1 (MQ=255)

                aaGCTGTGCTTGTATAAATATTGTTAAACACAAAACCAACAAGGTCCCCAATGACTACTTc                                                <  1:18310/61‑1 (MQ=255)

                aaGCTGTGCTTGTATAAATATTGTTAAACACAAAACCAACAAGGTCCCCAATGACTACTTc                                                <  1:179123/61‑1 (MQ=255)

                                aaTATTGTTAAACACAAATCCAACAAGGTCCCCAATGACTACTTCCATGCTCAACGCaa                                  >  1:406637/1‑59 (MQ=255)

                                aaTATTGTTAAACACAAAACCAACAAGGTCCCCAATGACTAGTTCCATGCTCAACGCaa                                  >  1:92070/1‑59 (MQ=255)

                                aaTATTGTTAAACACAAAACCAACAAGGTCCCCAATGACTACTTCCATGCTCAACGCaa                                  >  1:2414143/1‑59 (MQ=255)

                                aaTATTGTTAAACACAAAACCAACAAGGTCCCCAATGACTACTTCCATGCTCAACGCaa                                  >  1:2597420/1‑59 (MQ=255)

                                aaTATTGTTAAACACAAAACCAACAAGGTCCCCAATGACTACTTCCATGCTCAACGCaa                                  >  1:2345231/1‑59 (MQ=255)

                                aaTATTGTTAAACACAAAACCAACAAGGTCCCCAATGACTACTTCCATGCTCAACGCaa                                  >  1:2709219/1‑59 (MQ=255)

                                aaTATTGTTAAACACAAAACCAACAAGGTCCCCAATGACTACTTCCATGCTCAACGCaa                                  >  1:3004272/1‑59 (MQ=255)

                                aaTATTGTTAAACACAAAACCAACAAGGTCCCCAATGACTACTTCCATGCTCAACGCaa                                  >  1:581644/1‑59 (MQ=255)

                                aaTATTGTTAAACACAAAACCAACAAGGTCCCCAATGACTACTTCCATGCTCAACGCaa                                  >  1:2473548/1‑59 (MQ=255)

                                aaTATTGTTAAACACAAAACCAACAAGGTCCCCAATGACTACTTCCATGCTCAACGCAAAACTACTAcc                        <  1:1288167/69‑1 (MQ=255)

                                aaTATTGTTAAACACAAAACCAACAAGGTCCCCAATGACTACTTCCATGCTCAACGCAAAACTACTAcc                        <  1:3422416/69‑1 (MQ=255)

                                aaTATTGTTAAACACAAAACCAACAAGGTCCCCAATGACTACTTCCATGCTCAACGCAAAACTACTAcc                        <  1:3368489/69‑1 (MQ=255)

                                aaTATTGTTAAACACAAAACCAACAAGGTCCCCAATGACTACTTCCATGCTCAACGCAAAACTACTAcc                        <  1:1659843/69‑1 (MQ=255)

                                  tatTGTTAAACACAAAACCAACAAGGTCCCTAATGacta                                                    >  1:1726226/1‑39 (MQ=255)

                                  tatTGTTAAACACAAAACCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCTAAACTACTACCaa                      >  1:2846942/1‑69 (MQ=255)

                                  tatTGTTAAACACAAAACCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCTAAACTACTACCaa                      >  1:2843075/1‑69 (MQ=255)

                                  tatTGTTAAACACAAAACCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCAAAACTACTACCaa                      >  1:2855186/1‑69 (MQ=255)

                                  tatTGTTAAACACAAAACCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCAAAACTACTACCaa                      >  1:105282/1‑69 (MQ=255)

                                  tatTGTTAAACACAAAACCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCAAAACTACTACCaa                      >  1:631080/1‑69 (MQ=255)

                                  tatTGTTAAACACAAAACCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCAAAACTACTACCaa                      >  1:3405449/1‑69 (MQ=255)

                                  tatTGTTAAACACAAAACCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCAAAACTACTACCaa                      >  1:3401564/1‑69 (MQ=255)

                                  tatTGTTAAACACAAAACCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCAAAACTACTACCaa                      >  1:3280945/1‑69 (MQ=255)

                                  tatTGTTAAACACAAAACCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCAAAACTACTACCaa                      >  1:3277213/1‑69 (MQ=255)

                                  tatTGTTAAACACAAAACCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCAAAACTACTACCaa                      >  1:2852890/1‑69 (MQ=255)

                                  tatTGTTAAACACAAAACCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCAAAACTACTACCaa                      >  1:1715057/1‑69 (MQ=255)

                                  tatTGTTAAACACAAAACCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCAAAACTACTACCaa                      >  1:2035389/1‑69 (MQ=255)

                                  tatTGTTAAACACAAAACCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCAAAACTACTACCaa                      >  1:2358444/1‑69 (MQ=255)

                                  tatTGTTAAACACAAAACCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCAAAACTACTACCaa                      >  1:1038776/1‑69 (MQ=255)

                                  tatTGTTAAACACAAAACCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCAAAACTACTACCa                       >  1:1731514/1‑68 (MQ=255)

                                   atTGTTAAACACAAAACCAACAAGGTCCCCAATGACTACTTCCATGCTCAACGCAAAACTACTACCAAc                     >  1:2871312/1‑69 (MQ=255)

                                            cacaAAACCAACAAGGTCCCCAATGACTACTTCCATg                                            >  1:380169/1‑37 (MQ=255)

                                            cacaAAACCAACAAGGTCCCCAATGACTACTTCCATGCTCAACGCAAAACTACTACCAACTGCGCCATc            >  1:1952912/1‑69 (MQ=255)

                                            cacaAAACCAACAAGGTCCCCAATGACTACTTCCATGCTCAACGCAAAACTACTACCAACTGCGCCATc            >  1:2048721/1‑69 (MQ=255)

                                                 aaCCAACGAGGTCCCTAATGACTACTTCCATGTTCAACGCAAAACTACTACCAACTGCGCCATccg          <  1:1074924/66‑1 (MQ=255)

                                                 aaCCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCAAAACTACTACCAACTGCGCCATccg          <  1:1301813/66‑1 (MQ=255)

                                                 aaCCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCAAAACTACTACCAACTGCGCCATccg          <  1:1956753/66‑1 (MQ=255)

                                                 aaCCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCAAAACTACTACCAACTGCGCCATccg          <  1:3434159/66‑1 (MQ=255)

                                                 aaCCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCAAAACTACTACCAACTGCGCCATccg          <  1:2607964/66‑1 (MQ=255)

                                                 aaCCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCAAAACTACTACCAACTGCGCCATccg          <  1:3402514/66‑1 (MQ=255)

                                                 aaCCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCAAAACTACTACCAACTGCGCCATccg          <  1:1773170/66‑1 (MQ=255)

                                                 aaCCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCAAAACTACTACCAACTGCGCCATccg          <  1:1522953/66‑1 (MQ=255)

                                                 aaCCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCAAAACTACTACCAACTGCGCCATccg          <  1:2522819/66‑1 (MQ=255)

                                                 aaCCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGCAAAACTACTACCAACTGCGCCATccg          <  1:2550130/66‑1 (MQ=255)

                                                 aaCCAACAAGGTCCCTAATGACTACTTCCATGTTCAACGAAAAACTACTACCAACTGCGCCATccg          <  1:3093947/66‑1 (MQ=255)

                                                  aCCAACAAGGTCCCCAATGACTACTTCCATGCTCAACGCAAAACTACTACCAACTGCGCCATCcgccgc      <  1:2686689/69‑1 (MQ=255)

                                                   ccAACAAGGTCCCCAATGACTACTTCCATGCTCAACGCAAAACTACTACCAACTGCGCCATCCGCCGCa     <  1:2443875/69‑1 (MQ=255)

                                                      acaaGGTCCCCAATGACTACTTCCATGCTCAACGCAAAACTACTACCAACTGCGCCATCCGCCGCAGTg  <  1:1119226/69‑1 (MQ=255)

                                                      acaaGGTCCCCAATGACTACTTCCATGCTCAACGCAAAACTACTACCAACTGCGCCATCCGCCGCAGTg  <  1:2226227/69‑1 (MQ=255)

CATTGTCTCCCCTGTAAAGCTGTGCTTGTATAAATATTGTTAAACACAAAACCAACAAGGTCCCCAATGACTACTTCCATGCTCAACGCAAAACTACTACCAACTGCGCCATCCGCCGCAGTG  >  minE/2497191‑2497313

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