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	1,050,833	A→G	55.8%	H341R (CAT→CGT)	ydhK →	conserved inner membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,050,833	0	A	G	55.8%	13.1 / 46.5	61	H341R (CAT→CGT)	ydhK	conserved inner membrane protein
Reads supporting (aligned to +/- strand): ref base A (8/19); new base G (13/21); total (21/40)
Fisher's exact test for biased strand distribution p-value = 5.91e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01

TGCAAAGTAGTCAGGAATTACATCGTCTGCAAAGCGGTGTAGATGATCATACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTA  >  minE/1050785‑1050889

tGCAAAGTAGTCAGGAATTACATCGTCTGCAAAGCGGTGTAGATGATCATACCAGACTCCCACg                                           <  1:738842/64‑1 (MQ=255)

tGCAAAGTAGTCAGGAATTACATCGTCTGCAAAGCGGTGTAGATGATCATACCAGACTCCCACg                                           <  1:2899592/64‑1 (MQ=255)

tGCAAAGTAGTCAGGAATTACATCGTCTGCAAAGCGGTGTAGATGATCATACCAGACTCCAACg                                           <  1:1674938/64‑1 (MQ=255)

tGCAAAGTAGTCAGGAATTACATCGTCTGCAAAGAGGTGTAGATGATCATACCAGACTCCCACg                                           <  1:847759/64‑1 (MQ=255)

            aGGAATTACATCGTCTGCAAAGCGGTGTAGATGATCATACCAGACTCCCACGGACATCCGGCCTGGCTc                          >  1:833851/1‑69 (MQ=255)

                   aCATCGTGTGCAAAGCGGTGTAGATGATCATACCa                                                     >  1:205948/1‑35 (MQ=255)

                   aCATCGTCTGCAAAGCGGTGTAGATGATCATACCa                                                     >  1:877537/1‑35 (MQ=255)

                   aCATCGTCTGCAAAGCGGTGTAGATGATCATACCa                                                     >  1:670080/1‑35 (MQ=255)

                   aCATCGTCTGCAAAGCGGTGTAGATGATCATACCa                                                     >  1:3010975/1‑35 (MQ=255)

                   aCATCGTCTGCAAAGCGGTGTAGATGATCATACCa                                                     >  1:3052353/1‑35 (MQ=255)

                       cggcTGCAAAGCGGTGTAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGAt               <  1:728186/66‑1 (MQ=255)

                       cGTCTGCAAAGCGGTGTAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGAt               <  1:2846438/69‑1 (MQ=255)

                       cGTCTGCAAAGCGGTGTAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGAt               <  1:3234478/69‑1 (MQ=255)

                       cGTCTGCAAAGCGGTGTAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGAt               <  1:3208410/69‑1 (MQ=255)

                       cGTCTGCAAAGCGGTGTAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGAt               <  1:2364851/69‑1 (MQ=255)

                       cGTCTGCAAAGCGGTGTAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGAt               <  1:2382322/69‑1 (MQ=255)

                       cGTCTGCAAAGCGGTGTAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGAt               <  1:2617935/69‑1 (MQ=255)

                       cGTCTGCAAAGCGGTGTAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGAt               <  1:2017468/69‑1 (MQ=255)

                       cGTCTGCAAAGCGGTGTAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGAt               <  1:2972305/69‑1 (MQ=255)

                       cGTCTGCAAAGCGGTGTAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGAt               <  1:2970133/69‑1 (MQ=255)

                       cGTCTGCAAAGCGGTGTAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGAt               <  1:2260729/69‑1 (MQ=255)

                       cGTCTGCAAAGCGGTGTAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGAt               <  1:3342/69‑1 (MQ=255)

                       cGTCTGCAAAGCGGTGTAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGAt               <  1:415282/69‑1 (MQ=255)

                       cGTCTGCAAAGCGGTGTAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGAt               <  1:1921998/69‑1 (MQ=255)

                       cGTCTGCAAAGCGGTGTAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGAt               <  1:1907782/69‑1 (MQ=255)

                       cGTCTGCAAAGCGGTGTAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGAt               <  1:456562/69‑1 (MQ=255)

                       cGTCTGCAAAGCGGTGTAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGAt               <  1:172185/69‑1 (MQ=255)

                       cGTCTGCAAAGCGGTGTAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGAt               <  1:1602605/69‑1 (MQ=255)

                       cGTCTGCAAAGCGGTGTAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGAt               <  1:1058221/69‑1 (MQ=255)

                       cGTCTGCAAAGCGGTGTAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGAt               <  1:1015074/69‑1 (MQ=255)

                        gTCTGCAAAGCGGTGTAGATGATCATACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGAt               <  1:3158317/68‑1 (MQ=255)

                         tCTGCAAAGCGGTGTAGATTATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGAt               <  1:2912631/67‑1 (MQ=255)

                             cAAAGCGGTGTAGATGATCATACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGc          >  1:1036825/1‑68 (MQ=255)

                             cAAAGCGGTGTAGATGATCATACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGc          >  1:2460586/1‑68 (MQ=255)

                                    gtgtAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  >  1:2803202/1‑69 (MQ=255)

                                    gtgtAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  >  1:922000/1‑69 (MQ=255)

                                    gtgtAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  >  1:1085845/1‑69 (MQ=255)

                                    gtgtAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  >  1:1178701/1‑69 (MQ=255)

                                    gtgtAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  >  1:780121/1‑69 (MQ=255)

                                    gtgtAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  >  1:1411476/1‑69 (MQ=255)

                                    gtgtAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  >  1:606229/1‑69 (MQ=255)

                                    gtgtAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  >  1:443642/1‑69 (MQ=255)

                                    gtgtAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  >  1:4251/1‑69 (MQ=255)

                                    gtgtAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  >  1:2016765/1‑69 (MQ=255)

                                    gtgtAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  >  1:2277401/1‑69 (MQ=255)

                                    gtgtAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  >  1:2616955/1‑69 (MQ=255)

                                    gtgtAGATGATCGTGCCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  >  1:3137765/1‑69 (MQ=255)

                                    gtgtAGATGATCATACGAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  <  1:2929339/69‑1 (MQ=255)

                                    gtgtAGATGATCATACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  <  1:58126/69‑1 (MQ=255)

                                    gtgtAGATGATCATACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  <  1:2307262/69‑1 (MQ=255)

                                    gtgtAGATGATCATACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  <  1:705869/69‑1 (MQ=255)

                                    gtgtAGATGATCATACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  <  1:153910/69‑1 (MQ=255)

                                    gtgtAGATGATCATACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  <  1:1891920/69‑1 (MQ=255)

                                    gtgtAGATGATCATACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  <  1:313543/69‑1 (MQ=255)

                                    gtgtAGATGATCATACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  <  1:1254275/69‑1 (MQ=255)

                                    gtgtAGATGATCATACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  <  1:3097276/69‑1 (MQ=255)

                                    gtgtAGATGATCATACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  <  1:872803/69‑1 (MQ=255)

                                    gtgtAGATGATCATACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  <  1:3229817/69‑1 (MQ=255)

                                    gtgtAGATGATCATACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  <  1:894899/69‑1 (MQ=255)

                                    gtgtAGATGATCATACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  <  1:2254206/69‑1 (MQ=255)

                                     tgtAGATGATCATACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTa  <  1:1790853/68‑1 (MQ=255)

TGCAAAGTAGTCAGGAATTACATCGTCTGCAAAGCGGTGTAGATGATCATACCAGACTCCCACGGACATCCGGCCTGGCTCGTCATACCGATAACGCCGAAGCTA  >  minE/1050785‑1050889

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