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
A1 F28 I2 R2	356	55.1	4139924	95.4%	3949487	63.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	4,553,062	T→C	G32G (GGT→GGC)	fimG →	minor component of type 1 fimbriae

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	4,553,062	0	T	C	77.5%	214.8 / 58.1	102	G32G (GGT→GGC)	fimG	minor component of type 1 fimbriae
Reads supporting (aligned to +/- strand): ref base T (23/0); new base C (46/33); total (69/33)
Fisher's exact test for biased strand distribution p-value = 3.26e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

Only 100 of 102 total aligned reads displayed.

GGCGGCAATATTGGCGCTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGTAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGATCTCGGCGA  >  W3110S.gb/4552996‑4553121

ggcggcAATATTGGCGCTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGTAAgg                                                         >  1:1429606/1‑71 (MQ=255)

ggcggcAATATTGGCGCTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGTAAgg                                                         >  1:4046208/1‑71 (MQ=255)

ggcggcAATATTGGCGCTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGTAAgg                                                         >  1:3757778/1‑71 (MQ=255)

ggcggcAATATTGGCGCTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGCAAgg                                                         >  1:1094647/1‑71 (MQ=255)

ggcggcAATATTGGCGCTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGCAAgg                                                         >  1:1155682/1‑71 (MQ=255)

ggcggcAATATTGGCGCTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGCAAgg                                                         >  1:698398/1‑71 (MQ=255)

ggcggcAATATTGGCGCTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGCAAgg                                                         >  1:4084960/1‑71 (MQ=255)

          ttGGCGCTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCa                                                >  1:1063189/1‑70 (MQ=255)

          ttGGCGCTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCa                                                >  1:2723267/1‑70 (MQ=255)

          ttGGCGCTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCa                                                >  1:52834/1‑70 (MQ=255)

          ttGGCGCTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCa                                                >  1:2722877/1‑70 (MQ=255)

                cTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGCAATGTCGTCGCCAAACCgtg                                         <  1:1096277/71‑1 (MQ=255)

                cTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCgtg                                         <  1:324970/71‑1 (MQ=255)

                cTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCgtg                                         <  1:922223/71‑1 (MQ=255)

                cTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCgtg                                         <  1:2385105/71‑1 (MQ=255)

                cTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCgtg                                         <  1:2344345/71‑1 (MQ=255)

                cTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCgtg                                         <  1:2336483/71‑1 (MQ=255)

                cTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCgtg                                         <  1:1916633/71‑1 (MQ=255)

                cTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCgtg                                         <  1:2019655/71‑1 (MQ=255)

                cTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCgtg                                         <  1:3420386/71‑1 (MQ=255)

                cTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCgtg                                         <  1:1605467/71‑1 (MQ=255)

                cTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCgtg                                         <  1:3590273/71‑1 (MQ=255)

                cTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCgtg                                         <  1:3990410/71‑1 (MQ=255)

                cTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCgtg                                         <  1:1388453/71‑1 (MQ=255)

                cTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCgtg                                         <  1:544033/71‑1 (MQ=255)

                                  cAGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCaa                       >  1:3912556/1‑71 (MQ=255)

                                  cAGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCaa                       >  1:886638/1‑71 (MQ=255)

                                  cAGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCaa                       >  1:2126979/1‑71 (MQ=255)

                                  cAGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCaa                       >  1:2620454/1‑71 (MQ=255)

                                  cAGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCaa                       >  1:120749/1‑71 (MQ=255)

                                   aGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGtt                                  <  1:3173000/59‑1 (MQ=255)

                                   aGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGtt                                  <  1:2702708/59‑1 (MQ=255)

                                   aGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGtt                                  <  1:273199/59‑1 (MQ=255)

                                   aGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGtt                                  <  1:2746353/59‑1 (MQ=255)

                                   aGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGtt                                  <  1:217523/59‑1 (MQ=255)

                                   aGGCAGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGtt                                  <  1:227120/59‑1 (MQ=255)

                                       aGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCaa                       >  1:3610980/1‑66 (MQ=255)

                                       aGCCGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCaa                       >  1:376170/1‑66 (MQ=255)

                                          cGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACgg               <  1:2557017/71‑1 (MQ=255)

                                          cGATGTCACCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACgg               <  1:2802694/71‑1 (MQ=255)

                                           gATGTCACCATCACGGTGAACGGTAAGGTCGTCGCCAAACCGTGTACGGTTTccac                             >  1:2830120/1‑56 (MQ=255)

                                           gATGTCACCATCACGGTGAACGGTAAGGTCGTCGCCAAACCGTGTACGGTTTccac                             >  1:1419612/1‑56 (MQ=255)

                                           gATGTCACCATCACGGTGAACGGTAAGGTCGTCGCCAAACCGTGTACGGTTTccac                             >  1:2964405/1‑56 (MQ=255)

                                           gATGTCACCATCACGGTGAACGGTAAGGTCGTCGCCAAACCGTGTACGGTTTccac                             >  1:3029712/1‑56 (MQ=255)

                                           gATGTCACCATCACGGTGAACGGTAAGGTCGTCGCCAAACCGTGTACGGTTTccac                             >  1:2706758/1‑56 (MQ=255)

                                           gATGTCACCATCACGGTGAACGGTAAGGTCGTCGCCAAACCGTGTACGGTTTccac                             >  1:3093095/1‑56 (MQ=255)

                                           gATGTCACCATCACGGTGAACGGTAAGGTCGTCGCCAAACCGTGTACGGTTTccac                             >  1:2687792/1‑56 (MQ=255)

                                           gATGTCACCATCACGGTGAACGGTAAGGTCGTCGCCAAACCGTGTACGGTTTccac                             >  1:4089153/1‑56 (MQ=255)

                                           gATGTCACCATCACGGTGAACGGTAAGGTCGTCGCCAAACCGTGTACGGTTTccac                             >  1:392795/1‑56 (MQ=255)

                                           gATGTCACCATCACGGTGAACGGTAAGGTCGTCGCCAAACCGTGTACGGTTTccac                             >  1:3890170/1‑56 (MQ=255)

                                           gATGTCACCATCACGGTGAACGGTAAGGTCGTCGCCAAACCGTGTACGGTTTccac                             >  1:1424896/1‑56 (MQ=255)

                                           gATGTCACCATCACGGTGAACGGTAAGGTCGTCGCCAAACCGTGTACGGTTTccac                             >  1:2034687/1‑56 (MQ=255)

                                           gATGTCACCATCACGGTGAACGGTAAGGTCGTCGCCAAACCGTGTACGGTTTccac                             >  1:250841/1‑56 (MQ=255)

                                           gATGTCACCATCACGGTGAACGGTAAGGTCGTCGCCAAACCGTGTACGGTTTccac                             >  1:2100882/1‑56 (MQ=255)

                                           gATGTCACCATCACGGTGAACGGTAAGGTCGTCGCCAAACCGTGTACGGTTTccac                             >  1:2166326/1‑56 (MQ=255)

                                           gATGTCACCATCACGGTGAACGGTAAGGTCGTCGCCAAACCGTGTACGGTTTccac                             >  1:2240118/1‑56 (MQ=255)

                                           gATGTCACCATCACCGTGAACGGTAAGGTCGTCGCCAAACCGTGTACGGTTTccac                             >  1:1946579/1‑56 (MQ=255)

                                                 aCCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGAtct        >  1:1369193/1‑71 (MQ=255)

                                                 aCCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGAtct        >  1:2542669/1‑71 (MQ=255)

                                                 aCCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGAtct        >  1:3116107/1‑71 (MQ=255)

                                                 aCCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGAtct        >  1:1181384/1‑71 (MQ=255)

                                                 aCCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGAtct        >  1:2837027/1‑71 (MQ=255)

                                                 aCCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGAtct        >  1:2819753/1‑71 (MQ=255)

                                                 aCCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGAtct        >  1:2318079/1‑71 (MQ=255)

                                                 aCCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGAtct        >  1:3760892/1‑71 (MQ=255)

                                                 aCCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGAtct        >  1:3361568/1‑71 (MQ=255)

                                                 aCCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGAtct        >  1:1626846/1‑71 (MQ=255)

                                                 aCCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGAtct        >  1:654227/1‑71 (MQ=255)

                                                 aCCATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGAtct        >  1:2696479/1‑71 (MQ=255)

                                                   cATCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTccac                             >  1:1821004/1‑48 (MQ=255)

                                                   cATCACGGTGAAAGGCAAGGTCGTCGCCAAACCGTGTACGGTTTccac                             >  1:1285414/1‑48 (MQ=39)

                                                     tCACGGTGAACGGCAAGGTCGTCTCCAAACCGTGTACGGTTTCCACCACCAATGCCACgg               <  1:2895296/60‑1 (MQ=255)

                                                     tCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACgg               <  1:1736079/60‑1 (MQ=255)

                                                     tCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACgg               <  1:396601/60‑1 (MQ=255)

                                                     tCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACgg               <  1:101272/60‑1 (MQ=255)

                                                     tCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACgg               <  1:551387/60‑1 (MQ=255)

                                                     tCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACgg               <  1:2520130/60‑1 (MQ=255)

                                                     tCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACgg               <  1:1428562/60‑1 (MQ=255)

                                                     tCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACgg               <  1:1847148/60‑1 (MQ=255)

                                                     tCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACgg               <  1:879876/60‑1 (MQ=255)

                                                     tCACGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACgg               <  1:2026881/60‑1 (MQ=255)

                                                     tCACGGTGAACGGCAAGGTCGTCGCCAAACCGTCTACGGTTTCCACCACCAATGCCACgg               <  1:1543812/60‑1 (MQ=255)

                                                       aCGGTGAACGGTAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGATGTCGGCGa  >  1:101423/1‑71 (MQ=255)

                                                       aCGGTGAACGGTAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGATCTCGGCGa  >  1:1684154/1‑71 (MQ=255)

                                                       aCGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTcc                               >  1:3614407/1‑42 (MQ=255)

                                                       aCGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGATCTCGGCGa  >  1:319674/1‑71 (MQ=255)

                                                       aCGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGATCTCGGCGa  >  1:2034659/1‑71 (MQ=255)

                                                       aCGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGATCTCGGCGa  >  1:210870/1‑71 (MQ=255)

                                                       aCGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGATCTCGGCGa  >  1:2188793/1‑71 (MQ=255)

                                                       aCGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGATCTCGGCGa  >  1:1742160/1‑71 (MQ=255)

                                                       aCGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGATCTCGGCGa  >  1:2540006/1‑71 (MQ=255)

                                                       aCGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGATCTCGGCGa  >  1:1319750/1‑71 (MQ=255)

                                                       aCGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGATCTCGGCGa  >  1:1658824/1‑71 (MQ=255)

                                                       aCGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGATCTCGGCGa  >  1:4073195/1‑71 (MQ=255)

                                                       aCGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGATCTCGGCGa  >  1:1379501/1‑71 (MQ=255)

                                                       aCGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGATCTCGGCGa  >  1:3266804/1‑71 (MQ=255)

                                                       aCGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGATCTCGGCGa  >  1:3430874/1‑71 (MQ=255)

                                                       aCGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGATCTCGGCGa  >  1:3495348/1‑71 (MQ=255)

                                                       aCGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGATCTCGGCGa  >  1:3916450/1‑71 (MQ=255)

                                                       aCGGTGAACGGCAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCAAGGTTGATCTCGGCGa  >  1:250997/1‑71 (MQ=255)

GGCGGCAATATTGGCGCTCGCAAGTGCGACGATACAGGCAGCCGATGTCACCATCACGGTGAACGGTAAGGTCGTCGCCAAACCGTGTACGGTTTCCACCACCAATGCCACGGTTGATCTCGGCGA  >  W3110S.gb/4552996‑4553121

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