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	2,402,524	T→C	47.5%	P169P (CCA→CCG)	yigA ←	conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,402,524	0	T	C	47.5%	2.5 / 70.7	80	P169P (CCA→CCG)	yigA	conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (25/17); new base C (19/19); total (44/36)
Fisher's exact test for biased strand distribution p-value = 5.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.50e-01

GCTTCCCAGCATCGACATCGCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATACGCAGCGGTTCGAAAG  >  minE/2402458‑2402591

gCTTCCCAGCATCGACATCGCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTgg                                                                   >  1:2915594/1‑69 (MQ=255)

gCTTCCCAGCATCGACATCGCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTgg                                                                   >  1:2691743/1‑69 (MQ=255)

gCTTCCCAGCATCGACATCGCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTgg                                                                   >  1:81156/1‑69 (MQ=255)

gCTTCCCAGCATCGACATCGCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTgg                                                                   >  1:3165313/1‑69 (MQ=255)

gCTTCCCAGCATCGACATCGCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTgg                                                                   >  1:1428393/1‑69 (MQ=255)

gCTTCCCAGCATCGACATCGCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTgg                                                                   >  1:2664035/1‑69 (MQ=255)

gCTTCCCAGCATCGACATCGCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTg                                                                    >  1:750594/1‑68 (MQ=255)

             gACATCGCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCgg                                                       >  1:116341/1‑68 (MQ=255)

                 tCGCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCaa                                                  <  1:1898439/69‑1 (MQ=255)

                 tCGCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCaa                                                  <  1:2983381/69‑1 (MQ=255)

                 tCGCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCaa                                                  <  1:3386992/69‑1 (MQ=255)

                 tCGCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCaa                                                  <  1:2548415/69‑1 (MQ=255)

                 tCGCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCaa                                                  <  1:886515/69‑1 (MQ=255)

                  cGCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCaa                                                  <  1:1368072/68‑1 (MQ=255)

                   gacACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCaa                                                  >  1:545640/3‑67 (MQ=255)

                   gCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCg                                                               >  1:2771542/1‑54 (MQ=255)

                   gCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCaa                                                  >  1:1529161/1‑67 (MQ=255)

                   gCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCaa                                                  >  1:2374878/1‑67 (MQ=255)

                   gCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCaa                                                  >  1:2620933/1‑67 (MQ=255)

                   gCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCAAGa                                                <  1:696159/69‑1 (MQ=255)

                   gCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCAAGa                                                <  1:2166183/69‑1 (MQ=255)

                   gCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCAAGa                                                <  1:3241764/69‑1 (MQ=255)

                   gCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCAAGa                                                <  1:1242588/69‑1 (MQ=255)

                     cACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCAAGAt                                               <  1:2848550/68‑1 (MQ=255)

                      agcGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAg                                                          >  1:269278/3‑56 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAg                                                          >  1:2439624/1‑56 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAg                                                          >  1:2044565/1‑56 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAg                                                          >  1:2034754/1‑56 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAg                                                          >  1:199082/1‑56 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAg                                                          >  1:2444093/1‑56 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAg                                                          >  1:2715107/1‑56 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAg                                                          >  1:2236698/1‑56 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAg                                                          >  1:1012949/1‑56 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAg                                                          >  1:2864639/1‑56 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAg                                                          >  1:936995/1‑56 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAg                                                          >  1:1183426/1‑56 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAg                                                          >  1:1333344/1‑56 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAg                                                          >  1:1406309/1‑56 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAg                                                          >  1:149562/1‑56 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAg                                                          >  1:1529328/1‑56 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAg                                                          >  1:1654855/1‑56 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAg                                                          >  1:1876663/1‑56 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAGCGGTCCCAGATAg                                             <  1:3132581/69‑1 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAGCGGTCCCAGATAg                                             <  1:326670/69‑1 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAGCGGTCCCAGATAg                                             <  1:3001559/69‑1 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAGCGGTCCCAGATAg                                             <  1:3280810/69‑1 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAGCGGTCCCAGATAg                                             <  1:2976770/69‑1 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAGCGGTCCCAGATAg                                             <  1:6275/69‑1 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAGCGGTCCCAGATAg                                             <  1:2745041/69‑1 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAGCGGTCCCAGATAg                                             <  1:1016910/69‑1 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAGCGGTCCCAGATAg                                             <  1:1743404/69‑1 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAGCGGTCCCAGATAg                                             <  1:2191674/69‑1 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAGCGGTCCCAGATAg                                             <  1:1363101/69‑1 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAGCGGTCCCAGATAg                                             <  1:198239/69‑1 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAGCGGTCCCAGATAg                                             <  1:1225449/69‑1 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAGCGGTCCCAGATAg                                             <  1:1203386/69‑1 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAGCGGTCCCAGATAg                                             <  1:1826923/69‑1 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGCCCGTTAAGCGGTCCCAGATAg                                             <  1:1473532/69‑1 (MQ=255)

                      aCCGATCCCACCGCTTTCGCTTCCGGTAGCACAACCAGCAGCTCCGGTCCGTTaa                                                           >  1:3046726/1‑55 (MQ=39)

                       ccGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAGCGGTCCCAGATAg                                             <  1:1175714/68‑1 (MQ=255)

                       ccGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCCGGTCCGTTAAGCGGTCCCAGATAg                                             <  1:484902/68‑1 (MQ=255)

                         gATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCAAGa                                                <  1:1466109/63‑1 (MQ=255)

                         gATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCAAGATAGTGc                                          >  1:724711/1‑69 (MQ=255)

                         gATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCAAGATAGTGc                                          >  1:1941083/1‑69 (MQ=255)

                         gATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCAAGATAGTGc                                          >  1:3263156/1‑69 (MQ=255)

                         gATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCAAGATAGTGc                                          >  1:2491497/1‑69 (MQ=255)

                             ccACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCAAGATAGTGCTGtt                                      <  1:1823258/69‑1 (MQ=255)

                             ccACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCAAGATAGTGCTGtt                                      <  1:596366/69‑1 (MQ=255)

                                               gTAGCACCACCAGCAGCTCCGGTCCGTTAAGCGGTCCCAGATAg                                             <  1:811840/44‑1 (MQ=37)

                                                 aGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAAt                   >  1:2205008/1‑68 (MQ=255)

                                                  gCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAAt                   >  1:2127209/1‑67 (MQ=255)

                                                  gCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATa                  >  1:1755278/1‑68 (MQ=255)

                                                  gCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATa                  >  1:1060014/1‑68 (MQ=255)

                                                  gCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATa                  >  1:180362/1‑68 (MQ=255)

                                                  gCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATa                  >  1:1320281/1‑68 (MQ=255)

                                                         cagcagCTCTGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATACGCAGCgg          >  1:1102608/1‑69 (MQ=255)

                                                         cagcagCTCTGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATACGCAGCg           >  1:1925800/1‑68 (MQ=255)

                                                              gcTCTGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATACGCAGCGGTTCGa     <  1:1712361/69‑1 (MQ=255)

                                                              gcTCTGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATACGCAGCGGTTCGa     <  1:1076166/69‑1 (MQ=255)

                                                              gcTCTGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATACGCAGCGGTTCGa     <  1:2970444/69‑1 (MQ=255)

                                                               ctctGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATACGCAGCGGTTCGa     <  1:501029/68‑1 (MQ=255)

                                                               ctctGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATACGCAGCGGTTCGa     <  1:710790/68‑1 (MQ=255)

                                                               cgctGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATACGCAGCGGTTCGa     <  1:1826339/66‑1 (MQ=255)

                                                                tctGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATACGCAGCGGTTCGaaa   >  1:2893956/1‑69 (MQ=255)

                                                                tctGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATACGCAGCGGTTCGaaa   >  1:804163/1‑69 (MQ=255)

                                                                tctGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATACGCAGCGGTTCGaaa   >  1:3160957/1‑69 (MQ=255)

                                                                tctGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATACGCAGCGGTTCGaaa   >  1:1239122/1‑69 (MQ=255)

                                                                tctGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATACGCAGCGGTTCGaaa   <  1:3369671/69‑1 (MQ=255)

                                                                 ctGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATACGCAGCGGTTCGAAAg  <  1:1980766/69‑1 (MQ=255)

                                                                 ctGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATACGCAGCGGTTCGAAAg  <  1:2932404/69‑1 (MQ=255)

                                                                 ctGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATACGCAGCGGTTCGAAAg  <  1:892158/69‑1 (MQ=255)

                                                                 ctGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATACGCAGCGGTTCGAAAg  <  1:1453951/69‑1 (MQ=255)

                                                                 ctGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATACGCAGCGGTTCGAAAg  <  1:94203/69‑1 (MQ=255)

GCTTCCCAGCATCGACATCGCCACCGATCCCACCGCTTTCGCTTCCGGTAGCACCACCAGCAGCTCTGGTCCGTTAAGCGGCCCAAGATAGTGCTGTTCCTGCCCCAAACGCTGAATACGCAGCGGTTCGAAAG  >  minE/2402458‑2402591

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