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	2,705,113	A→C	25.5%	intergenic (+37/‑70)	damX → / → dam	hypothetical protein/DNA adenine methylase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,705,113	0	A	C	25.5%	65.2 / 28.2	55	intergenic (+37/‑70)	damX/dam	hypothetical protein/DNA adenine methylase
Reads supporting (aligned to +/- strand): ref base A (31/10); new base C (7/7); total (38/17)
Fisher's exact test for biased strand distribution p-value = 9.83e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.89e-01

ACAGGCCGATCTGAAGTAATCAAGGTTATCTCCCGCAATGGTTTATCGTTGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTGTAATTAG  >  minE/2705058‑2705173

aCAGGCCGATCTGAAGTAATCAAGGTTATCTCCCGCAATGGTTTATCGTTGCGGGAGTTGCCTGAAgcg                                                 >  1:116751/1‑69 (MQ=255)

aCAGGCCGATCTGAAGTAATCAAGGTTATCTCCCGCAATGGTTTATCGTTGCGGGAGTTGCCTGAAgcg                                                 >  1:2510367/1‑69 (MQ=255)

aCAGGCCGATCTGAAGTAATCAAGGTTATCTCCCGCAATGGTTTATCGTTGCGGGAGTTGCCTGAAgcg                                                 >  1:1950025/1‑69 (MQ=255)

aCAGGCCGATCTGAAGTAATCAAGGTTATCTCCCGCAATGGTTTATCGTTGCGGGAGTTGCCTGAAgcg                                                 >  1:3067561/1‑69 (MQ=255)

   ggCCGATCTGAAGTAATCAAGGTTATCTCCCGCAATGGTTTATCGTTGCGGGAGTTGCCTGAAGCGCTg                                              <  1:2812767/69‑1 (MQ=255)

   ggCCGATCTGAAGTAATCAAGGTTATCTCCCGCAATGGTTTATCGTTGCGGGAGTTGCCTGAAGCGCTg                                              <  1:2816685/69‑1 (MQ=255)

                  aTCAAGGTTATCTCCCGCAATGGTTTATCGTTGCGGGAGTTGCCTGAAGCGCTg                                              >  1:3165157/1‑54 (MQ=255)

                  aTCAAGGTTATCTCCCGCAATGGTTTATCGTTGCGGGAGTTGCCTGAAGCGCTg                                              >  1:2869132/1‑54 (MQ=255)

                  aTCAAGGTTATCTCCCGCAATGGTTTATCGTTGCGGGAGTTGCCTGAAGCGCTg                                              >  1:2090897/1‑54 (MQ=255)

                  aTCAAGGTTATCTCCCGCAATGGTTTATCGTTGCGGGAGTTGCCTGAAGCGCTg                                              >  1:3432028/1‑54 (MQ=255)

                  aTCAAGGTTATCTCCCGCAATGGTTTATCGTTGCGGGAGTTGCCTGAAGCGCTg                                              >  1:513256/1‑54 (MQ=255)

                  aTCAAGGTTATCTCCCGCAATGGTTTATCGTTGCGGGAGTTGCCTGAAGCGCTg                                              >  1:554231/1‑54 (MQ=255)

                    cAAGGTTATCTCCCGCAATGGTTTATCGTTGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCttt                             >  1:1388621/1‑69 (MQ=255)

                    cAAGGTTATCTCCCGCAATGGTTTATCGTTGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCttt                             >  1:1285033/1‑69 (MQ=255)

                    cAAGGTTATCTCCCGCAATGGTTTATCGTTGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCttt                             >  1:2343433/1‑69 (MQ=255)

                    cAAGGTTATCTACCGCAATGGTTTATCGTTGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGc                                >  1:248935/1‑66 (MQ=255)

                             ctcCCGCAATGGTTTATCGTTGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGc                    >  1:1975114/1‑69 (MQ=255)

                             ctcCCGCAATGGTTTATCGTTGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGc                    >  1:216631/1‑69 (MQ=255)

                             ctcCCGCAATGGTTTATCGTTGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGc                    >  1:850555/1‑69 (MQ=255)

                                  gCAATGGTTTATCGTTGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGgag               <  1:174036/69‑1 (MQ=255)

                                       ggTTTATCATTGCGGGCGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTtctc                          <  1:3312246/53‑1 (MQ=39)

                                       ggTTTATCATTGCGGGCGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTtctc                          <  1:974739/53‑1 (MQ=39)

                                       ggTTTATCATTGCGGGCGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTtctc                          <  1:515939/53‑1 (MQ=39)

                                       ggTTTATCATTGCGGGCGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTtctc                          <  1:3037590/53‑1 (MQ=39)

                                       ggTTTATCATTGCGGGCGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTtctc                          <  1:524769/53‑1 (MQ=39)

                                       ggTTTATCATTGCGGGCGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTtctc                          <  1:2431657/53‑1 (MQ=39)

                                       ggTTTATCATTGCGGGCGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTtctc                          <  1:1740854/53‑1 (MQ=39)

                                        gTTTATCGTTGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGgt          >  1:2197072/1‑68 (MQ=255)

                                        gTTTATCGTTGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGgt          >  1:306898/1‑68 (MQ=255)

                                              cattGCGGGCGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTGTAAtta   >  1:850803/3‑69 (MQ=255)

                                              cattGCGGGCGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTGTAAtta   >  1:2188946/3‑69 (MQ=255)

                                              cattGCGGGCGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTGTAAtta   >  1:627914/3‑69 (MQ=255)

                                              cattGCGGGCGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTGTAAtta   >  1:1448647/3‑69 (MQ=255)

                                              cattGCGGGCGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTGTAAtta   >  1:31081/3‑69 (MQ=255)

                                              cattGCGGGCGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTGTAAtta   >  1:2451919/3‑69 (MQ=255)

                                              cattGCGGGCGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTGTAAtta   >  1:3433967/3‑69 (MQ=255)

                                               gTTGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTGTAAttag  <  1:127066/69‑1 (MQ=255)

                                               gTTGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTGTAAttag  <  1:2530712/69‑1 (MQ=255)

                                               gTTGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTGTAAttag  <  1:841816/69‑1 (MQ=255)

                                               gTTGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTGTAAttag  <  1:2051578/69‑1 (MQ=255)

                                               gTTGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTGTAAtta   <  1:2526739/68‑1 (MQ=255)

                                               gTTGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTGTAAtta   <  1:1405624/68‑1 (MQ=255)

                                               gTTGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTGTAAtta   <  1:3344029/68‑1 (MQ=255)

                                                 tGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTGTAAt     >  1:1706073/1‑64 (MQ=255)

                                                 tGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTGTAAt     >  1:1453581/1‑64 (MQ=255)

                                                 tGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTGTAAt     >  1:2171772/1‑64 (MQ=255)

                                                 tGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTGTAAt     >  1:1390795/1‑64 (MQ=255)

                                                 tGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTGTAAt     >  1:2644892/1‑64 (MQ=255)

                                                 tGCGGGAGTTGCCTGAAGAGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTGTAAt     >  1:1438184/1‑64 (MQ=255)

                                                  gCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGgttt        >  1:2312674/1‑58 (MQ=255)

                                                  gCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGgtgt        >  1:1612343/1‑60 (MQ=255)

                                                  gCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGgtgt        >  1:3300094/1‑60 (MQ=255)

                                                  gCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGgtgt        >  1:3095741/1‑60 (MQ=255)

                                                  gCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGgtgt        >  1:1869838/1‑60 (MQ=255)

                                                  gCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGgtgt        >  1:2892246/1‑60 (MQ=255)

ACAGGCCGATCTGAAGTAATCAAGGTTATCTCCCGCAATGGTTTATCGTTGCGGGAGTTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTCCACAGCCGGAGAAGGTGTAATTAG  >  minE/2705058‑2705173

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