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	2,859,346	C→T	40.6%	S91S (AGC→AGT)	mutL →	methyl‑directed mismatch repair protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,859,346	0	C	T	40.6%	23.1 / 39.1	59	S91S (AGC→AGT)	mutL	methyl‑directed mismatch repair protein
Reads supporting (aligned to +/- strand): ref base C (13/22); new base T (18/6); total (31/28)
Fisher's exact test for biased strand distribution p-value = 7.44e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.77e-01

GTCATGCCACCAGTAAAATCGCCTCTCTGGACGATCTCGAAGCCATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCACTTCA  >  minE/2859294‑2859409

gTCATGCCACCAGTAAAATCGCCTCTCTGGACGATCTCGAAGCCATTATCAGTCTGGGCTTTCGCGGTg                                                 <  1:109382/69‑1 (MQ=255)

gTCATGCCACCAGTAAAATCGCCTCTCTGGACGATCTCGAAGCCATTATCAGTCTGGGCTTTCGCGGTg                                                 <  1:2859753/69‑1 (MQ=255)

gTCATGCCACCAGTAAAATCGCCTCTCTGGACGATCTCGAAGCCATTATCAGTCTGGGCTTTCGCGGTg                                                 <  1:1813651/69‑1 (MQ=255)

gTCATGCCACCAGTAAAATCGCCTCTCTGGACGATCTCGAAGCCATTATCAGTCTGGGCTTTCGCGGTg                                                 <  1:167439/69‑1 (MQ=255)

gTCATGCCACCAGTAAAATCGCCTCTCTGGACGATCTCGAAGCCATTATCAGTCTGGGCTTTCGCGGTg                                                 <  1:477559/69‑1 (MQ=255)

 tCATGCCACCAGTAAAATCGCCTCTCTGGACGATCTCGAAGCCATTATCAGTCTGGGCTTTCGCGGTg                                                 <  1:2847263/68‑1 (MQ=255)

  cATGCCACCAGTAAAATCGCCTCTCTGGACGATCTCGAAGCCATTATCAGCCTGGGCTTTCGCGGTGa                                                <  1:2716746/68‑1 (MQ=255)

  cATGCCACCAGTAAAATCGCCTCTCTGGACGATCTCGAAGCCATTATCAGCCTGGGCTTTCGCGGTGa                                                <  1:2293717/68‑1 (MQ=255)

  cATGCCACCAGTAAAATCGCCTCTCTGGACGATCTCGAAGCCATTATCAGCCTGGGCTTTCGCGGTGAg                                               >  1:1385042/1‑69 (MQ=255)

            gTAAAATCGCCTCTCTGGACGATCTCGAAGCCATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCg                                      >  1:1268085/1‑68 (MQ=255)

            gTAAAATCGCCTCTCTGGACGATCTCGAAGCCATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCg                                      >  1:3007808/1‑68 (MQ=255)

            gTAAAATCGCCTCTCTGGACGATCTCGAAGCCATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCg                                      >  1:1926160/1‑68 (MQ=255)

            gTAAAATCGCCTCTCTGGACGATCTCGAAGCCATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCg                                      >  1:1582871/1‑68 (MQ=255)

            gTAAAATCGCCTCTCTGGACGATCTCGAAGCCATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCg                                      >  1:1069780/1‑68 (MQ=255)

            gTAAAATCGCCTCTCTGGACGATCTCGAAGCCATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCg                                      >  1:896506/1‑68 (MQ=255)

               aaaTCGCCTCTCTGGACGATCTCGAAGCCATTATCAGCCTGGGCTTTCGCGGTGAGgcgc                                           >  1:1446340/1‑60 (MQ=255)

                           tGGACGATCTCGAAGCCATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGt                        <  1:1647570/67‑1 (MQ=255)

                                   ctcGAAGCCATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTg              >  1:1242402/1‑69 (MQ=255)

                                   ctcGAAGCCATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTg              >  1:1910635/1‑69 (MQ=255)

                                        aGCCATTATCAGCCTGTGCTTTCTCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCt         <  1:2775436/69‑1 (MQ=255)

                                        aGCCATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGa             <  1:3298165/65‑1 (MQ=255)

                                        aGCCATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCt         <  1:403987/69‑1 (MQ=255)

                                        aGCCATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCt         <  1:3323634/69‑1 (MQ=255)

                                        aGCCATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCt         <  1:3162531/69‑1 (MQ=255)

                                          cctttATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCa       <  1:1506164/66‑1 (MQ=255)

                                          ccATTATCAGCCTGGGCTTTCGCTGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCa       <  1:1106940/69‑1 (MQ=255)

                                          ccATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCa       <  1:2812009/69‑1 (MQ=255)

                                          ccATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCa       <  1:2622064/69‑1 (MQ=255)

                                          ccATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCa       <  1:2944222/69‑1 (MQ=255)

                                          ccATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCa       <  1:1777253/69‑1 (MQ=255)

                                          ccATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCa       <  1:2406137/69‑1 (MQ=255)

                                          ccATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCa       <  1:2117207/69‑1 (MQ=255)

                                          ccATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCa       <  1:2061357/69‑1 (MQ=255)

                                          ccATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCa       <  1:6081/69‑1 (MQ=255)

                                          ccATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCa       <  1:1781180/69‑1 (MQ=255)

                                          ccATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGATTCCCGCCTGACGCTCa       <  1:3340019/69‑1 (MQ=255)

                                             ttATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCACtt    <  1:2398249/69‑1 (MQ=255)

                                             ttATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCACtt    <  1:1168690/69‑1 (MQ=255)

                                              tATCAGTCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCACtt    >  1:972910/1‑68 (MQ=255)

                                              tATCAGTCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCACtt    >  1:479291/1‑68 (MQ=255)

                                              tATCAGTCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCACtt    >  1:2299066/1‑68 (MQ=255)

                                              tATCAGTCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCACTTc   >  1:2648606/1‑69 (MQ=255)

                                              tATCAGTCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCACTTc   >  1:2566737/1‑69 (MQ=255)

                                              tATCAGTCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCACTTc   >  1:2541413/1‑69 (MQ=255)

                                              tATCAGTCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCACTTc   >  1:680930/1‑69 (MQ=255)

                                              tATCAGTCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCACTTc   >  1:2385618/1‑69 (MQ=255)

                                              tATCAGTCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCACTTc   >  1:3306242/1‑69 (MQ=255)

                                              tATCAGTCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCACTTc   >  1:2256897/1‑69 (MQ=255)

                                              tATCAGTCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCACTTc   >  1:1926655/1‑69 (MQ=255)

                                              tATCAGTCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCACTTc   >  1:1658183/1‑69 (MQ=255)

                                              tATCAGTCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCACTTc   >  1:456752/1‑69 (MQ=255)

                                              tATCAGTCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCACTTc   >  1:1625116/1‑69 (MQ=255)

                                              tATCAGTCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCACTTc   >  1:1559067/1‑69 (MQ=255)

                                              tATCAGTCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCACTTc   >  1:578349/1‑69 (MQ=255)

                                              tATCAGTCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCACTTc   >  1:1547502/1‑69 (MQ=255)

                                              tATCAGTCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCAGCCTGACGCTCACTTc   >  1:1243175/1‑69 (MQ=255)

                                               aTCAGCCTGGGCTTTCGCGGTGAGGGGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCACTTCa  >  1:1322992/1‑69 (MQ=255)

                                               aTCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGt                             >  1:2456003/1‑42 (MQ=255)

                                               aTCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCACTTCa  >  1:2644448/1‑69 (MQ=255)

GTCATGCCACCAGTAAAATCGCCTCTCTGGACGATCTCGAAGCCATTATCAGCCTGGGCTTTCGCGGTGAGGCGCTGGCGAGTATCAGTTCGGTTTCCCGCCTGACGCTCACTTCA  >  minE/2859294‑2859409

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A