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	1,807,079	T→C	35.1%	T433T (ACT→ACC)	emrB →	multidrug efflux system protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,807,079	0	T	C	35.1%	33.2 / 29.7	54	T433T (ACT→ACC)	emrB	multidrug efflux system protein
Reads supporting (aligned to +/- strand): ref base T (29/6); new base C (15/4); total (44/10)
Fisher's exact test for biased strand distribution p-value = 7.28e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGTTCAACCCGAATGCCCAGGCGATGTACAGTCAACTGGAAGGGCTTGGG  >  minE/1807015‑1807142

tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat                                                             >  1:1685279/1‑67 (MQ=255)

tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat                                                             >  1:2034562/1‑67 (MQ=255)

tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat                                                             >  1:3080239/1‑67 (MQ=255)

tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat                                                             >  1:2046910/1‑67 (MQ=255)

tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat                                                             >  1:3280266/1‑67 (MQ=255)

tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat                                                             >  1:3021388/1‑67 (MQ=255)

tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat                                                             >  1:410887/1‑67 (MQ=255)

tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat                                                             >  1:1688002/1‑67 (MQ=255)

tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat                                                             >  1:54483/1‑67 (MQ=255)

tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat                                                             >  1:677363/1‑67 (MQ=255)

tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat                                                             >  1:1454930/1‑67 (MQ=255)

tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat                                                             >  1:1412986/1‑67 (MQ=255)

tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGaat                                                             >  1:1400453/1‑67 (MQ=255)

tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTAGACCGaat                                                             >  1:182287/1‑67 (MQ=255)

tCGGTACGTCCATAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTAAGTTGACCGaat                                                             >  1:1736555/1‑67 (MQ=255)

          gATAACCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAAccc                                                   >  1:2913360/1‑69 (MQ=255)

          gATAACCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAAccc                                                   >  1:2509535/1‑69 (MQ=255)

          gATAACCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAAccc                                                   >  1:2901747/1‑69 (MQ=255)

          gATAACCACGACCATGTCGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAAccc                                                   >  1:1010062/1‑69 (MQ=255)

          caTAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGAATCGGTGAAccc                                                   <  1:341012/68‑1 (MQ=255)

          caTAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGAATCGGTGAAccc                                                   <  1:2080330/68‑1 (MQ=255)

          caTAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGAATCGGTGAAccc                                                   <  1:315477/68‑1 (MQ=255)

          caTAACGACGACGATGTGGACTAACCGCGAGTCGATGCACCATGCTCAGTTGACCGAATCGGTGAAccc                                                   <  1:3338679/68‑1 (MQ=255)

             aaCCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTa                                                        >  1:2609675/1‑61 (MQ=255)

             aaCCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAAccc                                                   >  1:2764320/1‑66 (MQ=255)

             aaCCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCg                                                  >  1:2480902/1‑67 (MQ=255)

             aaCCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGt                                                 >  1:896833/1‑68 (MQ=255)

             aaCCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGt                                                 >  1:2987470/1‑68 (MQ=255)

             aaCCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGt                                                 >  1:519192/1‑68 (MQ=255)

             aaCCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGt                                                 >  1:766624/1‑68 (MQ=255)

             aaCCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGt                                                 >  1:853984/1‑68 (MQ=255)

             aaCCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGt                                                 >  1:2533764/1‑68 (MQ=255)

             aaCCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGt                                                 >  1:1336392/1‑68 (MQ=255)

             aaCCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGt                                                 >  1:2050279/1‑68 (MQ=255)

             aaCCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGt                                                 >  1:1979293/1‑68 (MQ=255)

             aaCCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGt                                                 >  1:1939249/1‑68 (MQ=255)

             aaCCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGt                                                 >  1:1657737/1‑68 (MQ=255)

             aaCCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGt                                                 >  1:1836883/1‑68 (MQ=255)

              acaaCGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGTTc                                               >  1:2720635/4‑69 (MQ=255)

              aCCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGTTc                                               >  1:1234871/1‑69 (MQ=255)

              aCCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGTTc                                               >  1:1476846/1‑69 (MQ=255)

              aCCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGTTc                                               >  1:1895334/1‑69 (MQ=255)

                                     cgAGTGGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGTTCAACCCGAATGCCCAGGCGATGTa                        <  1:396752/69‑1 (MQ=255)

                                     cgAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGTTCAACCCGAATGCCCAGGCGATGTa                        <  1:120036/69‑1 (MQ=255)

                                     cgAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGTTCAACCCGAATGCCCAGGCGATGTa                        <  1:1521472/69‑1 (MQ=255)

                                     cgAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGTTCAACCCGAATGCCCAGGCGATGTa                        <  1:1785210/69‑1 (MQ=255)

                                     cgAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGTTCAACCCGAATGCCCAGGCGATGTa                        <  1:3205706/69‑1 (MQ=255)

                                     cgAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGTTCAACCCGAATGCCCAGGCGATGTa                        <  1:2111912/69‑1 (MQ=255)

                                                      cgcAGTTGACTGAGTCGGTAAACCCGTTCAACCCGAATGCCCAGGCGATGTACAGTCAACTGGAAGGGc       >  1:246213/1‑69 (MQ=255)

                                                      cgcAGTTGACTGAGTCGGTAAACCCGTTCAACCCGAATGCCCAGGCGATGTACAGTCAACTGGAAGGGc       >  1:2739576/1‑69 (MQ=255)

                                                          gTTGACTGAGTCGGTAAACCCGTTCAACCCGAATGCCCAGGCGATGTACAGTCAACTGGAAGGGCTTgg   >  1:3190420/1‑69 (MQ=255)

                                                          gTTGACTGAGTCGGTAAACCCGTTCAACCCGAATGCCCAGGCGATGTACAGTCAACTGGAAGGGCTTgg   >  1:693489/1‑69 (MQ=255)

                                                           ttGACTGAGTCGGTAAACCCGTTCAACCCGAATGCCCAGGCGATGTACAGTCAACTGGAAGGGCTTggg  >  1:1917362/1‑69 (MQ=255)

                                                           ttGACTGAGTCGGTAAACCCGTTCAACCCGAATGCCCAGGCGATGTACAGTCAACTGGAAGGGCTTggg  >  1:3072449/1‑69 (MQ=255)

TCGGCACGTCGATAACCACGACCATGTGGACCAACCGCGAGTCGATGCACCATGCGCAGTTGACTGAGTCGGTAAACCCGTTCAACCCGAATGCCCAGGCGATGTACAGTCAACTGGAAGGGCTTGGG  >  minE/1807015‑1807142

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