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	454,400	T→C	59.3%	I229V (ATA→GTA) ‡	ybgH ←	predicted transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	454,400	0	T	C	59.3%	20.7 / 35.5	54	I229V (ATA→GTA) ‡	ybgH	predicted transporter
Reads supporting (aligned to +/- strand): ref base T (14/8); new base C (15/17); total (29/25)
Fisher's exact test for biased strand distribution p-value = 2.74e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.41e-01

CACCCAGGCCAATAATAGTCGCGACAATTAAGGCGTATACCGACCACTCTTTCCAGAACAGTATGGTAATCAGTGCAGGCGTTGCCACCAGCAGAACCAGCAGCCATCCCCAGTTC  >  minE/454337‑454452

cacCCAGGCCAATAATAGTCGCGACAATTAAGGCGTATACCGACCACTCTTTCCAGAACAGTATGGTa                                                  >  1:2728650/1‑68 (MQ=255)

   caaGGCCTATGATCGTCGCGACAATCAAGGCGTATACCGACCACTCTTTCCAGAACAACACGGTAATc                                               >  1:2857698/3‑68 (MQ=255)

   caaGGCCAATGATCGTCGCGACAATCAAGGCGTATACCGACCACTCTTTCCAGAACAACACGGTAATc                                               >  1:1660317/3‑68 (MQ=255)

   caaGGCCAATGATCGTCGCGACAATCAAGGCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCa                                              >  1:2607446/3‑69 (MQ=255)

   caaGGCCAATGATCGTCGCGACAATCAAGGCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCa                                              >  1:975894/3‑69 (MQ=255)

   caaGGCCAATGATCGTCGCGACAATCAAGGCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCa                                              >  1:879712/3‑69 (MQ=255)

   caaGGCCAATGATCGTCGCGACAATCAAGGCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCa                                              >  1:42198/3‑69 (MQ=255)

   caaGGCCAATGATCGTCGCGACAATCAAGGCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCa                                              >  1:3421437/3‑69 (MQ=255)

   caaGGCCAATGATCGTCGCGACAATCAAGGCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCa                                              >  1:3295695/3‑69 (MQ=255)

   caaGGCCAATGATCGTCGCGACAATCAAGGCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCa                                              >  1:3293186/3‑69 (MQ=255)

   caaGGCCAATGATCGTCGCGACAATCAAGGCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCa                                              >  1:2668114/3‑69 (MQ=255)

   caaGGCCAATGATCGTCGCGACAATCAAGGCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCa                                              >  1:2379245/3‑69 (MQ=255)

   caaGGCCAATGATCGTCGCGACAATCAAGGCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCa                                              >  1:2192829/3‑69 (MQ=255)

   caaGGCCAATGATCGTCGCGACAATCAAGGCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCa                                              >  1:2152570/3‑69 (MQ=255)

   caaGGCCAATGATCGTCGCGACAATCAAGGCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCa                                              >  1:2076288/3‑69 (MQ=255)

   caaGGCCAATGATCGTCGCGACAATCAAGGCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCa                                              >  1:1724260/3‑69 (MQ=255)

           ataataGTCGCGACAATTAAGGCGTATACCGACCACTCTTTCCAGAACAGTATGGTAATCAGTGCAGGc                                      >  1:2161534/1‑69 (MQ=255)

             aataGTCGCGACAATTAAGGCGTATACCGACCACTCTTTCCAGAACAGTATGGTAATCAGTGCAGGCGt                                    >  1:2070760/1‑69 (MQ=255)

              ataGTCGCGACAATTAAGGCGTATACCGACCACTCTTTCCAGAACAGTATGGTAATCAGTGCAGGCGtt                                   >  1:1107618/1‑69 (MQ=255)

              ataGTCGCGACAATTAAGGCGTATACCGACCACTCTTTCCAGAACAGTATGGTAATCAGTGCAGGCGtt                                   >  1:146954/1‑69 (MQ=255)

                         aaTTAAGGCGTATACCGACCACTCTTTCCAGAACAGTATGGTAATCAGTGCAGGCGTTGCCACcagcag                        <  1:2872229/69‑1 (MQ=255)

                         aaTTAAGGCGTATACCGACCACTCTTTCCAGAACAGTATGGTAATCAGTGCAGGCGTTGCCACcagcag                        <  1:2952178/69‑1 (MQ=255)

                         aaTTAAGGCGTATACCGACCACTCTTTCCAGAACAGTATGGTAATCAGTGCAGGCGTTGCCACcagcag                        <  1:3196137/69‑1 (MQ=255)

                         aaTTAAGGCGTATACCGACCACTCTTTCCAGAACAGTATGGTAATCAGTGCAGGCGTTGCCACcagcag                        <  1:3201945/69‑1 (MQ=255)

                         aaTTAAGGCGTATACCGACCACTCTTTCCAGAACAGTATGGTAATCAGTGCAGGCGTTGCCACcagcag                        <  1:2646529/69‑1 (MQ=255)

                         aaTTAAGGCGTATACCGACCACTCTTTCCAGAACAGTATGGTAATCAGTGCAGGCGTTGCCACcagcag                        <  1:2293593/69‑1 (MQ=255)

                          aTTAAGGCGTATACCGACCACTCTTTCCAGAACAGTATGGTAATCAGTGCAGGCGTTGCCACcagcag                        <  1:1066857/68‑1 (MQ=255)

                          aTTAAGGCGTATACCGACCACTCTTTCCAGAACAGTATGGTAATCAGTGCAGGCGTTGCCACcagcag                        <  1:1828369/68‑1 (MQ=255)

                                gCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCAGCGCAGGCGTTGCCACCAGCAGAACcagt                 <  1:3341195/69‑2 (MQ=255)

                                gCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCAGCGCAGGCGTTGCCACCAGCAGAACcagt                 <  1:1222724/69‑2 (MQ=255)

                                gCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCAGCGCAGGCGTTGCCACCAGCAGAACcagt                 <  1:595986/69‑2 (MQ=255)

                                gCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCAGCGCAGGCGTTGCCACCAGCAGAACcagt                 <  1:808512/69‑2 (MQ=255)

                                gCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCAGCGCAGGCGTTGCCACCAGCAGAACcagt                 <  1:3226697/69‑2 (MQ=255)

                                gCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCAGCGCAGGCGTTGCCACCAGCAGAACcagt                 <  1:824803/69‑2 (MQ=255)

                                gCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCAGCGCAGGCGTTGCCACCAGCAGAACcagt                 <  1:3015070/69‑2 (MQ=255)

                                gCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCAGCGCAGGCGTTGCCACCAGCAGAACcagt                 <  1:2133056/69‑2 (MQ=255)

                                gCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCAGCGCAGGCGTTGCCACCAGCAGAACcagt                 <  1:2834712/69‑2 (MQ=255)

                                gCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCAGCGCAGGCGTTGCCACCAGCAGAACcagt                 <  1:2733192/69‑2 (MQ=255)

                                gCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCAGCGCAGGCGTTGCCACCAGCAGAACcagt                 <  1:1681625/69‑2 (MQ=255)

                                gCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCAGCGCAGGCGTTGCCACCAGCAGAACcagt                 <  1:1556829/69‑2 (MQ=255)

                                gCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCAGCGCAGGCGTTGCCACCAGCAGAACcagt                 <  1:2528603/69‑2 (MQ=255)

                                gCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCAGCGCAGGCGTTGCCACCAGCAGAACcagt                 <  1:1744830/69‑2 (MQ=255)

                                gCGTATACCGACCACTCTTTCCAGAACAACACGGTAATCAGCGCAGGCGTTGCCACCAGCAGAACcagt                 <  1:2320205/69‑2 (MQ=255)

                                gCGTATACCGACCACTCTTTCCAGAACAACACGGTAATAAGCGCAGGCGTTGCCACCAGCAGAACcagt                 <  1:3397119/69‑2 (MQ=255)

                                       ccGACCACTCTTTCCAGAACAGTATGGTAATCAGTGCAGGCGTTGc                                 >  1:1354727/1‑46 (MQ=255)

                                       ccGACCACTCTTTCCAGAACAGTATGGTAATCAGTGCAGGCGTTGCCACCAGCAGAACCAGCAGCCATc          >  1:2696777/1‑69 (MQ=255)

                                       ccGACCACTCTTTCCAGAACAGTATGGTAATCAGTGCAGGCGTTGCCACCAGCAGAACCAGCAGCCATc          >  1:2457747/1‑69 (MQ=255)

                                             aCTCTTTCCAGAACAACACGGTAATCAGCGCAGGCGTTGCCACCAGCAGAACcagt                 <  1:816197/56‑2 (MQ=255)

                                               tctTTCCAGAACAGTATGGTAATCAGTGCAGGCGTTGCCACCAGCAGAACCAGCAGCCATCCCCAGTTc  >  1:1082697/1‑69 (MQ=255)

                                               tctTTCCAGAACAGTATGGTAATCAGTGCAGGCGTTGCCACCAGCAGAACCAGCAGCCATCCCCAGTTc  >  1:909364/1‑69 (MQ=255)

                                               tctTTCCAGAACAGTATGGTAATCAGTGCAGGCGTTGCCACCAGCAGAACCAGCAGCCATCCCCAGTTc  >  1:2266879/1‑69 (MQ=255)

                                               tctTTCCAGAACAGTATGGTAATCAGTGCAGGCGTTGCCACCAGCAGAACCAGCAGCCATCCCCAGTTc  >  1:1314598/1‑69 (MQ=255)

                                                ctTTCCAGAACAGTATGGTAATCAGTGCAGGCGTTGCCACCAGCAGAACCAGCAGCCATCCCCAGTTc  >  1:1899027/1‑68 (MQ=255)

                                                ctTTCCAGAACAGTATGGTAATCAGTGCAGGCGTTGCCACCAGCAGAACCAGCAGCCATCCCCAGTTc  >  1:2551637/1‑68 (MQ=255)

CACCCAGGCCAATAATAGTCGCGACAATTAAGGCGTATACCGACCACTCTTTCCAGAACAGTATGGTAATCAGTGCAGGCGTTGCCACCAGCAGAACCAGCAGCCATCCCCAGTTC  >  minE/454337‑454452

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