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	2,642,048	C→T	64.0%	D561D (GAC→GAT)	ggt →	gamma‑glutamyltranspeptidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,642,048	0	C	T	64.0%	34.3 / 35.3	61	D561D (GAC→GAT)	ggt	gamma‑glutamyltranspeptidase
Reads supporting (aligned to +/- strand): ref base C (13/9); new base T (29/10); total (42/19)
Fisher's exact test for biased strand distribution p-value = 2.57e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.29e-01

AAGGTCAGAAAGTGGCGCTGAAAGAGGCGATGGGCAGTACACAAAGCATTATGGTTGGGCCGGACGGTGAGTTGTACGGCGCATCCGACCCGCGCTCGGTGGATGATTTAACGGCGGGG  >  minE/2641984‑2642102

aaGGTCAGAAAGTGGCGCTGAAAGAGGCGATGGGCAGTACACAAAGCATTATGGTTGGGCCGGACGGTg                                                    <  1:1414058/69‑1 (MQ=255)

aaGGTCAGAAAGTGGCGCTGAAAGAGGCGATGGGCAGTACACAAAGCATTATGGTTGGGCCGGACGGTg                                                    <  1:3360148/69‑1 (MQ=255)

 aGGTCAGAAAGTGGCGCTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGTGTCGGATGGTGa                                                   >  1:1942167/1‑69 (MQ=255)

 aGGTCAGAAAGTGGCGCTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGa                                                   >  1:316081/1‑69 (MQ=255)

 aGGTCAGAAAGTGGCGCTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGa                                                   >  1:936181/1‑69 (MQ=255)

 aGGTCAGAAAGTGGCGCTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGa                                                   >  1:1259824/1‑69 (MQ=255)

 aGGTCAGAAAGTGGCGCTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGa                                                   >  1:281193/1‑69 (MQ=255)

 aGGTCAGAAAGTGGCGCTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGa                                                   >  1:1338811/1‑69 (MQ=255)

 aGGTCAGAAAGTGGCGCTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGa                                                   >  1:3235241/1‑69 (MQ=255)

 aGGTCAGAAAGTGGCGCTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGa                                                   >  1:1439919/1‑69 (MQ=255)

 aGGTCAGAAAGTGGCGCTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGa                                                   >  1:2072458/1‑69 (MQ=255)

 aGGTCAGAAAGTGGCGCTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGa                                                   >  1:376881/1‑69 (MQ=255)

 aGGTCAGAAAGTGGCGCTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGa                                                   >  1:1646940/1‑69 (MQ=255)

 aGGTCAGAAAGTGGCGCTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGa                                                   >  1:1808599/1‑69 (MQ=255)

                gcTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGAg                                                  >  1:2920714/1‑55 (MQ=255)

                gcTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGAg                                                  >  1:240136/1‑55 (MQ=255)

                gcTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGAg                                                  >  1:2913809/1‑55 (MQ=255)

                gcTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGAg                                                  >  1:2905366/1‑55 (MQ=255)

                gcTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGAg                                                  >  1:2734872/1‑55 (MQ=255)

                gcTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGAg                                                  >  1:2534023/1‑55 (MQ=255)

                gcTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGAg                                                  >  1:3103206/1‑55 (MQ=255)

                gcTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGAg                                                  >  1:639045/1‑55 (MQ=255)

                gcTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGAg                                                  >  1:680447/1‑55 (MQ=255)

                gcTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGAg                                                  >  1:827306/1‑55 (MQ=255)

                gcTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGAg                                                  >  1:845707/1‑55 (MQ=255)

                gcTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGAg                                                  >  1:938635/1‑55 (MQ=255)

                gcTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGAg                                                  >  1:970480/1‑55 (MQ=255)

                gcTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGAg                                                  >  1:1923160/1‑55 (MQ=255)

                gcTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGAg                                                  >  1:1298445/1‑55 (MQ=255)

                gcTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGAg                                                  >  1:1367870/1‑55 (MQ=255)

                gcTGAATGAGGCGATGGGCAGCACGCAAAGCATTATGGTTGGGTCGGATGGTGAg                                                  >  1:2070673/1‑55 (MQ=255)

                                ggCAGTACACAAAGCATTATGGTTGGGCCGGACGGTGAGTTGTACGGCGCATCCGACCCGCGCTCGGTg                    >  1:2519690/1‑69 (MQ=255)

                                ggCAGTACACAAAGCATTATGGTTGGGCCGGACGGTGAGTTGTACGGCGCATCCGACCCGCGCTCGGTg                    >  1:1191284/1‑69 (MQ=255)

                                ggCAGTACACAAAGCATTATGGTTGGGCCGGACGGTGAGTTGTACGGCGCATCCGACCCGCGCTCGGTg                    >  1:2863551/1‑69 (MQ=255)

                                ggCAGTACACAAAGCATTATGGTTGGGCCGGACGGTGAGTTGTACGGCGCATCCGACCCGCGCTCGGTg                    >  1:1283925/1‑69 (MQ=255)

                                ggCAGTACACAAAGCATTATGGTTGGGCCGGACGGTGAGTTGTACGGCGCATCCGACCCGCGCTCGGTg                    >  1:2023896/1‑69 (MQ=255)

                                     tACACAAAGCATTATGGTTGGGCCGGACGGTGAGTTGTACGGCGCATCCGACCCGCGCTCGGTGgatga               >  1:616323/1‑69 (MQ=255)

                                       cgcaAAGCATTATGGTTGGGTCGGATGGTGAGTTGTACGGCGCATCCGACTCGCGCTTGGT‑GATGAttt            <  1:2763443/67‑1 (MQ=255)

                                        gcaAAGCATTATGGTTGGGTCGGATGGTGAGTTGTACGGCGCATCCGACTCGCGCTTGGTGGATGAttt            <  1:589609/68‑1 (MQ=255)

                                        gcaAAGCATTATGGTTGGGTCGGATGGTGAGTTGTACGGCGCATCCGACTCGCGCTTGGTGGATGAttt            <  1:1478029/68‑1 (MQ=255)

                                        gcaAAGCATTATGGTTGGGTCGGATGGTGAGTTGTACGGCGCATCCGACTCGCGCTTGGTGGATGAttt            <  1:1968420/68‑1 (MQ=255)

                                        gcaAAGCATTATGGTTGGGTCGGATGGTGAGTTGTACGGCGCATCCGACTCGCGCTTGGTGGATGAttt            <  1:725240/68‑1 (MQ=255)

                                        gcaAAGCATTATGGTTGGGTCGGATGGTGAGTTGTACGGCGCATCCGACTCGCGCTTGGTGGATGAttt            <  1:2856636/68‑1 (MQ=255)

                                        gcaAAGCATTATGGTTGGGTCGGATGGTGAGTTGTACGGCGCATCCGACTCGCGCTTGGTGGATGAttt            <  1:1024403/68‑1 (MQ=255)

                                        gcaAAGCATTATGGTTGGGTCGGATGGTGAGTTGTACGGCGCATCCGACTCGCGCTTGGTGGATGAttt            <  1:2390944/68‑1 (MQ=255)

                                        gcaAAGCATTATGGTTGGGTCGGATGGTGAGTTGTAAGGCGCATCCGACTCGCGCTTGGTGGATGAttt            <  1:369707/68‑1 (MQ=255)

                                         caAAGCATTATGGTTGGGTCGGATGGTGAGTTGTACGGCGCATCCGACTCGCGCTTGGTGGATGAttt            <  1:1248063/68‑1 (MQ=255)

                                         caAAGCATTATGGTTGGGCCGGACGGTGAGTTGTACGGCGCATCCGACCCGCGCTCGGTGGATGAttt            <  1:3342268/68‑1 (MQ=255)

                                                  aTGGTTGGGCCGGACGGTGAGTTGTACGGCGGATCCGACCCGCGCTCGGTGGATGATTTAACggggggt  >  1:2174843/1‑68 (MQ=255)

                                                  aTGGTTGGGCCGGACGGTGAGTTGTACGGCGCATCCGACCCGCGCTCGGTGGATGAttt            <  1:1444547/59‑1 (MQ=255)

                                                  aTGGTTGGGCCGGACGGTGAGTTGTACGGCGCATCCGACCCGCGCTCGGTGGATGAttt            <  1:1084877/59‑1 (MQ=255)

                                                  aTGGTTGGGCCGGACGGTGAGTTGTACGGCGCATCCGACCCGCGCTCGGTGGATGAttt            <  1:3145200/59‑1 (MQ=255)

                                                  aTGGTTGGGCCGGACGGTGAGTTGTACGGCGCATCCGACCCGCGCTCGGTGGATGAttt            <  1:3143956/59‑1 (MQ=255)

                                                  aTGGTTGGGCCGGACGGTGAGTTGTACGGCGCATCCGACCCGCGCTCGGTGGATGAttt            <  1:2880348/59‑1 (MQ=255)

                                                  aTGGTTGGGCCGGACGGTGAGTTGTACGGCGCATCCGACCCGCGCTCGGTGGATGAttt            <  1:2430339/59‑1 (MQ=255)

                                                  aTGGTTGGGCCGGACGGTGAGTTGTACGGCGCATCCGACCCGCGCTCGGTGGATGATTTAACGGCgggg  >  1:1708927/1‑69 (MQ=255)

                                                  aTGGTTGGGCCGGACGGTGAGTTGTACGGCGCATCCGACCCGCGCTCGGTGGATGATTTAACGGCgggg  >  1:663346/1‑69 (MQ=255)

                                                  aTGGTTGGGCCGGACGGTGAGTTGTACGGCGCATCCGACCCGCGCTCGGTGGATGATTTAACGGCgggg  >  1:3041266/1‑69 (MQ=255)

                                                  aTGGTTGGGCCGGACGGTGAGTTGTACGGCGCATCCGACCCGCGCTCGGTGGATGATTTAACGGCgggg  >  1:2194005/1‑69 (MQ=255)

                                                  aTGGTTGGGCCGGACGGTGAGTTGTACGGCGCATCCGACCCGCGCTCGGTGGATGATTTAACGGCgggg  >  1:2301417/1‑69 (MQ=255)

                                                  aTGGTTGGGCCGGACGGTGAGTTGTACGGCGCATCCGACCCGCGCTCGGTGGATGATTTAACGGCgggg  >  1:2366551/1‑69 (MQ=255)

AAGGTCAGAAAGTGGCGCTGAAAGAGGCGATGGGCAGTACACAAAGCATTATGGTTGGGCCGGACGGTGAGTTGTACGGCGCATCCGACCCGCGCTCGGTGGATGATTTAACGGCGGGG  >  minE/2641984‑2642102

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A