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	1,445,416	A→G	70.7%	D655D (GAT→GAC)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,445,416	0	A	G	70.7%	63.4 / 26.3	65	D655D (GAT→GAC)	rcsC	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
Reads supporting (aligned to +/- strand): ref base A (13/6); new base G (20/25); total (33/32)
Fisher's exact test for biased strand distribution p-value = 1.04e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.22e-01

GTAAACTGGCTGCCCATTCCCGGTTCTGAATCTACCGAGATATCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCGGTCCCCTGGAAAT  >  minE/1445375‑1445480

gTAAACTGGCTGCCCATTCCCGGTTCTGAATCTACCGAGAT‑GCCCCGTCCATCATGCTGATCAGttttt                                      <  1:1092088/69‑1 (MQ=255)

 tAAACTGGCTGCCCATTCCCGGTTCTGAATCTACCGAGATGTCGCCGTCCATCATGCTGATCAGttttt                                      <  1:1662996/69‑1 (MQ=255)

 tAAACTGGCTGCCCATTCCCGGTTCTGAATCTACCGAGATGTCGCCGTCCATCATGCTGATCAGttttt                                      <  1:1985803/69‑1 (MQ=255)

 tAAACTGGCTGCCCATTCCCGGTTCTGAATCTACCGAGATGTCGCCGTCCATCATGCTGATCAGttttt                                      <  1:1311779/69‑1 (MQ=255)

 tAAACTGGCTGCCCATTCCCGGTTCTGAATCTACCGAGATGTCGCCGTCCATCATGCTGATCAGttttt                                      <  1:2413047/69‑1 (MQ=255)

 tAAACTGGCTGCCCATTCCCGGTTCTGAATCTACCGAGATGTCGCCGTCCATCATGCTGATCAGttttt                                      <  1:2485128/69‑1 (MQ=255)

 tAAACTGGCTGCCCATTCCCGGTTCTGAATCTACCGAGATGTCGCCGTCCATCATGCTGATCAGttttt                                      <  1:3057713/69‑1 (MQ=255)

 tAAACTGGCTGCCCATTCCCGGTTCTGAATCTACCGAGATGTCGCCGTCCATCATGCTGATCAGttttt                                      <  1:1012326/69‑1 (MQ=255)

 tAAACTGGCTGCCCATTCCCGGTTCTGAATCTACCGAGATGTCGCCGTCCATCATGCTGATCAGttttt                                      <  1:2869081/69‑1 (MQ=255)

  aaaCTGGCTGCCCATTCCCGGTTCTGAATCTACCGAGATATCGCCGTCcat                                                       >  1:2725259/1‑51 (MQ=255)

  aaaCTGGCTGCCCATTCCCGGTTCTGAATCTACCGAGATATCGCCGTCcat                                                       >  1:303694/1‑51 (MQ=255)

  aaaCTGGCTGCCCATTCCCGGTTCTGAATCTACCGAGATATCGCCGTCcat                                                       >  1:2866454/1‑51 (MQ=255)

  aaaCTGGCTGCCCATTCCCGGTTCTGAATCTACCGAGATATCGCCGTCcat                                                       >  1:2918360/1‑51 (MQ=255)

  aaaCTGGCTGCCCATTCCCGGTTCTGAATCTACCGAGATATCGCCGTCcat                                                       >  1:3344465/1‑51 (MQ=255)

  aaaCTGGCTGCCCATTCCCGGTTCTGAATCTACCGAGATATCGCCGTCcat                                                       >  1:297285/1‑51 (MQ=255)

  aaaCTGGCTGCCCATTCCCGGTTCTGAATCTACCGAGATATCGCCGTCcat                                                       >  1:3367032/1‑51 (MQ=255)

               aTTCCCGGTTCTGAATCTACCGAGATATCGCCGTCCATGATGCTGATCAg                                           <  1:3027949/50‑1 (MQ=255)

                  cccGGTTCTGAATCTACCGAGATATCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGccaga                        >  1:1980579/1‑66 (MQ=255)

                  cccGGTTCTGAATCTACCGAGATATCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGccaga                        >  1:1442445/1‑66 (MQ=255)

                  cccGGTTCTGAATCTACCGAGATATCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGccaga                        >  1:2115537/1‑66 (MQ=255)

                        tCTGAATCTACCGAGATATCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCg               >  1:1912097/1‑69 (MQ=255)

                        tCTGAATCTACCGAGATATCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCg               >  1:3323047/1‑69 (MQ=255)

                        tCTGAATCTACCGAGATATCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCg               >  1:3101644/1‑69 (MQ=255)

                                   cGAGATGTCGCCGTCCATCATGCTGATCAGttttt                                      <  1:2091267/35‑1 (MQ=255)

                                     agaTGTCGCCGTCCATCATTCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTcc           <  1:117279/60‑1 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTcc           <  1:2099521/60‑1 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTcc           <  1:1214378/60‑1 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTcc           <  1:2798629/60‑1 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTcc           <  1:1206609/60‑1 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTcc           <  1:122930/60‑1 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTcc           <  1:1232976/60‑1 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTcc           <  1:1167173/60‑1 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTcc           <  1:129129/60‑1 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTcc           <  1:3239913/60‑1 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTcc           <  1:1493801/60‑1 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTcc           <  1:1981432/60‑1 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTcc           <  1:433293/60‑1 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTcc           <  1:1770541/60‑1 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTcc           <  1:3370533/60‑1 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTcc           <  1:3429381/60‑1 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTCCCCTGGaagt  >  1:3396730/1‑67 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTCCCCTGGaagt  >  1:947967/1‑67 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTCCCCTGGaagt  >  1:689303/1‑67 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTCCCCTGGaagt  >  1:3031890/1‑67 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTCCCCTGGaagt  >  1:447936/1‑67 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTCCCCTGGaagt  >  1:3258170/1‑67 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTCCCCTGGaagt  >  1:2988392/1‑67 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTCCCCTGGaagt  >  1:2572795/1‑67 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTCCCCTGGaagt  >  1:2510476/1‑67 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTCCCCTGGaagt  >  1:2184313/1‑67 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTCCCCTGGaagt  >  1:2132491/1‑67 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTCCCCTGGaagt  >  1:1256618/1‑67 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTCCCCTGGaagt  >  1:155698/1‑67 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTCCCCTGGaagt  >  1:1940991/1‑67 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTCCCCTGGaagt  >  1:176970/1‑67 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTCCCCTGGaagt  >  1:1658471/1‑67 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTCCCCTGGaagt  >  1:1647124/1‑67 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTCCCCTGGaag   >  1:12253/1‑67 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTCCCCTGGaag   >  1:674549/1‑67 (MQ=255)

                                     agaTGTCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCAGTCCCCTGGaa    >  1:652851/1‑67 (MQ=255)

                                     agaTATCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCGGTCCCCTGGAAAt  <  1:1998596/69‑1 (MQ=255)

                                     agaTATCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCGGTCCCCTGGAAAt  <  1:2063475/69‑1 (MQ=255)

                                     agaTATCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCGGTCCCCTGGAAAt  <  1:2486571/69‑1 (MQ=255)

                                     agaTATCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCGGTCCCCTGGAAAt  <  1:1229136/69‑1 (MQ=255)

                                     agaTATCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCGGTCCCCTGGAAAt  <  1:2578417/69‑1 (MQ=255)

GTAAACTGGCTGCCCATTCCCGGTTCTGAATCTACCGAGATATCGCCGTCCATCATGCTGATCAGTTTTTCACAAATCGCCAGACCCAGACCGGTCCCCTGGAAAT  >  minE/1445375‑1445480

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