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	445,418	T→C	100%	E766E (GAA→GAG)	kdpD ←	fused sensory histidine kinase in two‑component regulatory system with KdpE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	445,418	0	T	C	92.4%	22.0 / ‑4.3	13	E766E (GAA→GAG)	kdpD	fused sensory histidine kinase in two‑component regulatory system with KdpE
Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (0/12); total (1/12)
Fisher's exact test for biased strand distribution p-value = 7.69e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GCGTTCTCCAGCAGATTAATCAGCACCCGTTCAAAGAGTGGCCCGTCAACGTGGATTAAGGTCAGCGGTTCTGGCAGAGAAAGATTGATGGGCGACGATAAACCCGGTTCCAGCATTTGCAGCGCGCTGCC  >  minE/445350‑445480

gcgTTCTCCAGCAGATTAATCAGCACCCGTTCAAAGAGTGGCCCGTCAACGTGGATTAAGGTCAGCGGt                                                                <  1:3074079/69‑1 (MQ=255)

             ggttAATCAGCACCCGTTCAAAGAGTGGCCCGTCAACGTGGATTAAGGTCAGCGGCTCTGGCAGAGaaa                                                   <  1:1710525/67‑1 (MQ=255)

             ggttAATCAGCACCCGTTCAAAGAGTGGCCCGTCAACGTGGATTAAGGTCAGCGGCTCTGGCAGAGaaa                                                   <  1:1946028/67‑1 (MQ=255)

             ggttAATCAGCACCCGTTCAAAGAGTGGCCCGTCAACGTGGATTAAGGTCAGCGGCTCTGGCAGAGaaa                                                   <  1:2110061/67‑1 (MQ=255)

             ggttAATCAGCACCCGTTCAAAGAGTGGCCCGTCAACGTGGATTAAGGTCAGCGGCTCTGGCAGAGaaa                                                   <  1:2180661/67‑1 (MQ=255)

             ggttAATCAGCACCCGTTCAAAGAGTGGCCCGTCAACGTGGATTAAGGTCAGCGGCTCTGGCAGAGaaa                                                   <  1:2560114/67‑1 (MQ=255)

             ggttAATCAGCACCCGTTCAAAGAGTGGCCCGTCAACGTGGATTAAGGTCAGCGGCTCTGGCAGAGaaa                                                   <  1:2684012/67‑1 (MQ=255)

             ggttAATCAGCACCCGTTCAAAGAGTGGCCCGTCAACGTGGATTAAGGTCAGCGGCTCTGGCAGAGaaa                                                   <  1:3155955/67‑1 (MQ=255)

             ggttAATCAGCACCCGTTCAAAGAGTGGCCCGTCAACGTGGATTAAGGTCAGCGGCTCTGGCAGAGaaa                                                   <  1:792514/67‑1 (MQ=255)

             ggttAATCAGCACCCGTTCAAAGAGTGGCCCGTCAACGTGGATTAAGGTCAGCGGCTCTGGCAGAGaaa                                                   <  1:930831/67‑1 (MQ=255)

             ggttAATCAGCACCCGTTCAAAGAGTGGCCCGTCAACGTGGATTAAGGGCAGCGGCTCTGGCAGAGaaa                                                   <  1:2543767/67‑1 (MQ=255)

                            gTTCAAAGAGTGGCCCGTCAACGTGGATTAAGGTCAGCGGCTCTGGCAGAGaaa                                                   <  1:2706540/54‑1 (MQ=255)

                                               aaCGTGGATTAAGGTCAGCGGCTCTGGCAGAGaaa                                                   <  1:397271/35‑1 (MQ=255)

                                                               aGCGGTTCTGGCAGAGAAAGATTGATGGGCGACGATAAACCCTGTTCCAGCATTTGCAGCGCGCTGcc  >  1:1057419/1‑68 (MQ=255)

GCGTTCTCCAGCAGATTAATCAGCACCCGTTCAAAGAGTGGCCCGTCAACGTGGATTAAGGTCAGCGGTTCTGGCAGAGAAAGATTGATGGGCGACGATAAACCCGGTTCCAGCATTTGCAGCGCGCTGCC  >  minE/445350‑445480

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