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	1,480,522	T→C	56.7%	I108I (ATT→ATC)	glpA →	sn‑glycerol‑3‑phosphate dehydrogenase (anaerobic), large subunit, FAD/NAD(P)‑binding

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,480,522	0	T	C	56.7%	13.2 / 38.1	53	I108I (ATT→ATC)	glpA	sn‑glycerol‑3‑phosphate dehydrogenase (anaerobic), large subunit, FAD/NAD(P)‑binding
Reads supporting (aligned to +/- strand): ref base T (5/18); new base C (19/11); total (24/29)
Fisher's exact test for biased strand distribution p-value = 4.87e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCCTGTTTATCACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGATCAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGA  >  minE/1480470‑1480587

gCCTGTTTATCACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGaagaag                                                   <  1:1301710/69‑1 (MQ=255)

gCCTGTTTATCACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGaagaag                                                   <  1:2710896/69‑1 (MQ=255)

gCCTGTTTATCACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGaagaag                                                   <  1:2261670/69‑1 (MQ=255)

       tATCACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAggg                                              <  1:3056230/67‑1 (MQ=255)

       tATCACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAggg                                              <  1:3005215/67‑1 (MQ=255)

       tATCACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAggg                                              <  1:2823377/67‑1 (MQ=255)

          cACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGATCAg                                         >  1:933748/1‑69 (MQ=255)

          cACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGATCAg                                         >  1:2243984/1‑69 (MQ=255)

          cACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGATCAg                                         >  1:1551428/1‑69 (MQ=255)

                    gAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGATCAGCGCAGAAGCt                               <  1:1632214/69‑1 (MQ=255)

                    gAAGATGACCTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCAACGCAGAAGcc                               <  1:2804656/69‑2 (MQ=255)

                    gAAGATGACCTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCAACGCAGAAGcc                               <  1:828088/69‑2 (MQ=255)

                    gAAGATGACCTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCAACGCAGAAGcc                               <  1:2729872/69‑2 (MQ=255)

                    gAAGATGACCTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCAACGCAGAAGcc                               <  1:1461251/69‑2 (MQ=255)

                    gAAGATGACCTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCAACGCAGAAGcc                               <  1:2579502/69‑2 (MQ=255)

                    gAAGATGACCTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCAACGCAGAAGcc                               <  1:2324507/69‑2 (MQ=255)

                    gAAGATGACCTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCAACGCAGAAGcc                               <  1:3124961/69‑2 (MQ=255)

                    gAAGATGACCTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCAACGCAGAAGcc                               <  1:2126830/69‑2 (MQ=255)

                    gAAGATGACCTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCAACGCAGAAGcc                               <  1:427199/69‑2 (MQ=255)

                    gAAGATGACCTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCAACGCAGAAGcc                               <  1:398817/69‑2 (MQ=255)

                    gAAGATGACCTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCAAAGCAGAAGcc                               <  1:100225/69‑2 (MQ=255)

                     aaGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGATCAGCGCAGAAGCta                              <  1:357411/69‑1 (MQ=255)

                     aaGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGATCAGCGCAGAAGCta                              <  1:1921632/69‑1 (MQ=255)

                      aGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGATCAGCGCAGAAGCtat                             <  1:2222678/69‑1 (MQ=255)

                      aGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGATCAGCGCAGAAGCtat                             <  1:2026802/69‑1 (MQ=255)

                           aCCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGATCAGCGCAGAAGCt                               <  1:678158/62‑1 (MQ=255)

                           aCCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGATCAGCGCAGAAGCTATAGAcc                        >  1:1910987/1‑69 (MQ=255)

                            ccTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCa                                          >  1:3426566/1‑50 (MQ=255)

                            ccTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCa                                          >  1:3359883/1‑50 (MQ=255)

                            ccTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCa                                          >  1:3265351/1‑50 (MQ=255)

                            ccTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCa                                          >  1:1010002/1‑50 (MQ=255)

                            ccTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCa                                          >  1:2936498/1‑50 (MQ=255)

                            ccTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCa                                          >  1:722697/1‑50 (MQ=255)

                            ccTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCa                                          >  1:1287354/1‑50 (MQ=255)

                            ccTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCa                                          >  1:1333594/1‑50 (MQ=255)

                            ccTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCa                                          >  1:2218497/1‑50 (MQ=255)

                            ccTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCa                                          >  1:1442206/1‑50 (MQ=255)

                            ccTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCa                                          >  1:1752243/1‑50 (MQ=255)

                            ccTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCa                                          >  1:1813205/1‑50 (MQ=255)

                            ccTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCa                                          >  1:1849966/1‑50 (MQ=255)

                            ccTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCa                                          >  1:214556/1‑50 (MQ=255)

                            ccTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCa                                          >  1:2208037/1‑50 (MQ=255)

                            ccTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCa                                          >  1:1419694/1‑50 (MQ=255)

                            ccTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCa                                          >  1:1342291/1‑50 (MQ=255)

                            ccTCTCCTTCCAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCa                                          >  1:2624157/1‑50 (MQ=255)

                            ccTCTCCTTACAGGCCACTTTTATCCGCGCCTGCGAAGAAGCAGGGATCa                                          >  1:2736136/1‑50 (MQ=255)

                              tctcCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGATCAGCGCAGAAGCTATAGACCCgc                     <  1:2238959/69‑1 (MQ=255)

                                        ggCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGATCAGCGCAGAAGCTATAGACCCGCAGCAAgcgcg           <  1:2272147/69‑1 (MQ=255)

                                            aCTTTTATTCGCGCCTGCGAAGAAGCAGGGATCAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCAtt       <  1:1141533/69‑1 (MQ=255)

                                             cTTTTATTCGCGCCTGCGAAGAAGCAGGGATCAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCAtt       <  1:214651/68‑1 (MQ=255)

                                               tttATTCGCGCCTGCGAAGAAGCAGGGATCAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTAt     >  1:50964/1‑68 (MQ=255)

                                                  aTTCGCGCCTGCGAAGAAGCAGGGATCAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGa  <  1:3198485/68‑1 (MQ=255)

                                                  aTTCGCGCCTGCGAAGAAGCAGGGATCAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGa  <  1:2834742/68‑1 (MQ=255)

GCCTGTTTATCACCCTGCCGGAAGATGACCTCTCCTTCCAGGCCACTTTTATTCGCGCCTGCGAAGAAGCAGGGATCAGCGCAGAAGCTATAGACCCGCAGCAAGCGCGCATTATCGA  >  minE/1480470‑1480587

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A