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	2,832,168	T→A	47.5%	intergenic (‑94/‑182)	yjeH ← / → groS	predicted transporter/Cpn10 chaperonin GroES, small subunit of GroESL

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,832,168	0	T	A	47.5%	3.2 / 71.5	61	intergenic (‑94/‑182)	yjeH/groS	predicted transporter/Cpn10 chaperonin GroES, small subunit of GroESL
Reads supporting (aligned to +/- strand): ref base T (20/12); new base A (15/14); total (35/26)
Fisher's exact test for biased strand distribution p-value = 4.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTAGCACAATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAATTTTTTTTCT  >  minE/2832128‑2832232

gTAGCACAATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGaaa                                                         <  1:440754/50‑1 (MQ=255)

gTAGCACAATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGaaa                                                         <  1:1976005/50‑1 (MQ=255)

gTAGCACAATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGaaa                                                         <  1:3032788/50‑1 (MQ=255)

gTAGCACAATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGaaa                                                         <  1:1177166/50‑1 (MQ=255)

gTAGCACAATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGaaa                                                         <  1:2885413/50‑1 (MQ=255)

gTAGCACAATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGaaa                                                         <  1:515396/50‑1 (MQ=255)

gTAGCACAATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGaaa                                                         <  1:2045724/50‑1 (MQ=255)

gTAGCACAATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGaaa                                                         <  1:2147813/50‑1 (MQ=255)

gTAGCACAATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGaaa                                                         <  1:891190/50‑1 (MQ=255)

gTAGCACAATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGaaa                                                         <  1:553746/50‑1 (MQ=255)

gTAGCACAATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGaaa                                                         <  1:2267007/50‑1 (MQ=255)

gTAGCACAATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGaaa                                                         <  1:2183915/50‑1 (MQ=255)

     acaATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGAAATGTGAGGt                                                 >  1:2342474/1‑53 (MQ=255)

     acaATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGAAATGTGAGGTg                                                >  1:2410930/1‑54 (MQ=255)

     acaATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGAAATGTGAGGTg                                                >  1:2019314/1‑54 (MQ=255)

     acaATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGAAATGTGAGGTg                                                >  1:2221464/1‑54 (MQ=255)

     acaATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGAAATGTGAGGTg                                                >  1:2585921/1‑54 (MQ=255)

     acaATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGAAATGTGAGGTg                                                >  1:329319/1‑54 (MQ=255)

     acaATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGAAATGTGAGGTg                                                >  1:427510/1‑54 (MQ=255)

     acaATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGAAATGTGAGGTg                                                >  1:1927638/1‑54 (MQ=255)

     acaATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGAAATGTGAGGTg                                                >  1:182637/1‑54 (MQ=255)

     acaATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGAAATGTGAGGTg                                                >  1:668011/1‑54 (MQ=255)

     acaATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGAAATGTGAGGTg                                                >  1:921099/1‑54 (MQ=255)

     acaATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGAAATGTGAGGTg                                                >  1:808368/1‑54 (MQ=255)

     acaATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGAAATGTGAGGTg                                                >  1:891566/1‑54 (MQ=255)

     acaATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGAAATGTGAGGTg                                                >  1:1676395/1‑54 (MQ=255)

                           gtgATGAAGAAATAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGaa            >  1:2646810/3‑68 (MQ=255)

                           gtgATGAAGAAATAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAAt           >  1:1023589/3‑69 (MQ=255)

                           gtgATGAAGAAATAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAAt           >  1:3415329/3‑69 (MQ=255)

                           gtgATGAAGAAATAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAAt           >  1:1104689/3‑69 (MQ=255)

                           gtgATGAAGAAATAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAAt           >  1:484666/3‑69 (MQ=255)

                           gtgATGAAGAAATAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAAt           >  1:3227657/3‑69 (MQ=255)

                           gtgATGAAGAAATAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAAt           >  1:3063425/3‑69 (MQ=255)

                           gtgATGAAGAAATAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAAt           >  1:1299479/3‑69 (MQ=255)

                           gtgATGAAGAAATAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAAt           >  1:2799098/3‑69 (MQ=255)

                           gtgATGAAGAAATAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAAt           >  1:267782/3‑69 (MQ=255)

                           gtgATGAAGAAATAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAAt           >  1:1564824/3‑69 (MQ=255)

                           gtgATGAAGAAATAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAAt           >  1:2391406/3‑69 (MQ=255)

                           gtgATGAAGAAATAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAAt           >  1:2361402/3‑69 (MQ=255)

                           gtgATGAAGAAATAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAAt           >  1:2269275/3‑69 (MQ=255)

                           gtgATGAAGAAATAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAAt           >  1:1934275/3‑69 (MQ=255)

                                gaagaaATTGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAAtttttt      >  1:2675993/1‑69 (MQ=255)

                                gaagaaATTGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAAtttttt      >  1:1803363/1‑69 (MQ=255)

                                gaagaaATTGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAAttttt       >  1:633924/1‑68 (MQ=255)

                                gaagaaATTCCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAAttttt       >  1:1550129/1‑68 (MQ=255)

                                 aagaaATTGCGATGAAATGTGAGGTGAATCAGGGtttt                                    >  1:1989984/1‑38 (MQ=255)

                                 aagaaATTGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAAttttttt     >  1:502768/1‑69 (MQ=255)

                                    aaaTAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAATTTtttttct  <  1:973764/69‑1 (MQ=255)

                                    aaaTAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAATTTtttttct  <  1:3428065/69‑1 (MQ=255)

                                    aaaTAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAATTTtttttct  <  1:3394286/69‑1 (MQ=255)

                                    aaaTAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAATTTtttttct  <  1:3345237/69‑1 (MQ=255)

                                    aaaTAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAATTTtttttct  <  1:2922021/69‑1 (MQ=255)

                                    aaaTAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAATTTtttttct  <  1:2773027/69‑1 (MQ=255)

                                    aaaTAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAATTTtttttct  <  1:2287437/69‑1 (MQ=255)

                                    aaaTAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAATTTtttttct  <  1:2166882/69‑1 (MQ=255)

                                    aaaTAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAATTTtttttct  <  1:1707271/69‑1 (MQ=255)

                                    aaaTAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAATTTtttttct  <  1:16924/69‑1 (MQ=255)

                                    aaaTAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAATTTtttttct  <  1:1172457/69‑1 (MQ=255)

                                    aaaTAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAATTTtttttct  <  1:1143572/69‑1 (MQ=255)

                                    aaaTAGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAATTTtttttct  <  1:1050129/69‑1 (MQ=255)

                                    aaaTAGCGATGAAATGGGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAATTTtttttct  <  1:1817250/69‑1 (MQ=255)

GTAGCACAATCAGATTCGCTTATGACGGCGATGAAGAAATTGCGATGAAATGTGAGGTGAATCAGGGTTTTCACCCGATTTTGTGCTGATCAGAATTTTTTTTCT  >  minE/2832128‑2832232

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