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	2,387,114	G→A	34.6%	L142L (CTG→TTG)	yigM ←	predicted inner membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,387,114	0	G	A	34.6%	55.3 / 39.9	75	L142L (CTG→TTG)	yigM	predicted inner membrane protein
Reads supporting (aligned to +/- strand): ref base G (33/16); new base A (17/9); total (50/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.80e-01

TCCATCAGGCGTTTGTAACCCACCATGCCAATGGCAAAAGTGATATTGGAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATCCCGGCACCAATCACC  >  minE/2387050‑2387175

tCCATCAGGCGTTTGTAACCCACCATGCCAATGGCAAAAGTGATATTGGAGAGTTGCACCAGCAGCaa                                                            >  1:2546024/1‑68 (MQ=255)

      aGGCGTTTGTAACCCACCATGCCAATGGCGAAAGTGATATTGGAGAGTTGCACCAGCAGCAAGCCAg                                                       >  1:2813846/1‑67 (MQ=255)

      aGGCGTTTGTAACCCACCATGCCAATGGCAAAAGTGATATTGGAGAGTTGCACCAGCAGCAAGCCAg                                                       >  1:3152145/1‑67 (MQ=255)

      aGGCGTTTGTAACCCACCATGCCAATGGCAAAAGTGATATTGGAGAGTTGCACCAGCAGCAAGCCAg                                                       >  1:2834663/1‑67 (MQ=255)

      aGGCGTTTGTAACCCACCATGCCAATGGCAAAAGTGATATTGGAGAGTTGCACCAGCAGCAAGCCAg                                                       >  1:2761875/1‑67 (MQ=255)

      aGGCGTTTGTAACCCACCATGCCAATGGCAAAAGTGATATTGGAGAGTTGCACCAGCAGCAAGCCAg                                                       >  1:1739601/1‑67 (MQ=255)

      aGGCGTTTGTAACCCA‑CATGCCAATGGCAAAAGTGATATTGGAGAGTTGCCCCAGCAGCAAGCCAg                                                       >  1:2886674/1‑66 (MQ=255)

                      ccaTGCCAATGGCAAAAGTGATATTGGAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGa                                     <  1:751668/69‑1 (MQ=255)

                      ccaTGCCAATGGCAAAAGTGATATTGGAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGa                                     <  1:1176843/69‑1 (MQ=255)

                      ccaTGCCAATGGCAAAAGTGATATTGGAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGa                                     <  1:3342979/69‑1 (MQ=255)

                      ccaTGCCAATGGCAAAAGTGATATTGGAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGa                                     <  1:3092486/69‑1 (MQ=255)

                      ccaTGCCAATGGCAAAAGTGATATTGGAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGa                                     <  1:3088422/69‑1 (MQ=255)

                      ccaTGCCAATGGCAAAAGTGATATTGGAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGa                                     <  1:2924671/69‑1 (MQ=255)

                        aTGCCAATGGCAAAAGTGATATTGGAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGa                                     <  1:2349188/67‑1 (MQ=255)

                          ggcAATGGCAAAAGTGATGTTGGAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTg                                 <  1:472285/67‑1 (MQ=255)

                          gCCAATGGCAAAAGTGATATTGGAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTg                                 <  1:1101945/69‑1 (MQ=255)

                           ccAATGGCAAAAGTGATATTGGGGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTg                                 >  1:1907723/1‑68 (MQ=255)

                           ccAATGGCAAAAGTGATATTGGAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCt                                  >  1:528101/1‑67 (MQ=255)

                           ccAATGGCAAAAGTGATATTGGAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTg                                 >  1:1504033/1‑68 (MQ=255)

                           ccAATGGCAAAAGTGATATTGGAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTg                                 >  1:2159386/1‑68 (MQ=255)

                           ccAATGGCAAAAGTGATATTGGAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTg                                 >  1:1579256/1‑68 (MQ=255)

                                 gCAAAAGTGATATTGGAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATa                           >  1:171865/1‑68 (MQ=255)

                                 gCAAAAGTGATATTGGAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATa                           >  1:872971/1‑68 (MQ=255)

                                 gCAAAAGTGATATTGGAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATa                           >  1:1526984/1‑68 (MQ=255)

                                         gATATTGGAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGaataat                  <  1:911875/69‑1 (MQ=255)

                                         gATATTGGAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGaataat                  <  1:1483837/69‑1 (MQ=255)

                                         gATATTGGAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGaataat                  <  1:3006200/69‑1 (MQ=255)

                                          atatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATc                 <  1:181761/69‑1 (MQ=255)

                                          atatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATc                 <  1:451156/69‑1 (MQ=255)

                                          atatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATc                 <  1:2660901/69‑1 (MQ=255)

                                          atatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATc                 <  1:564299/69‑1 (MQ=255)

                                          atatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATc                 <  1:688034/69‑1 (MQ=255)

                                          atatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATc                 <  1:3131260/69‑1 (MQ=255)

                                          atatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATc                 <  1:2520192/69‑1 (MQ=255)

                                          atatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATc                 <  1:2487754/69‑1 (MQ=255)

                                          atatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATc                 <  1:1885327/69‑1 (MQ=255)

                                           tatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTc                                          >  1:3183415/1‑43 (MQ=37)

                                           tatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATcc                >  1:3334374/1‑69 (MQ=255)

                                           tatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATcc                >  1:314050/1‑69 (MQ=255)

                                           tatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATcc                >  1:1255578/1‑69 (MQ=255)

                                           tatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATcc                >  1:1265782/1‑69 (MQ=255)

                                           tatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATcc                >  1:3173761/1‑69 (MQ=255)

                                           tatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATcc                >  1:1756317/1‑69 (MQ=255)

                                           tatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATcc                >  1:2110553/1‑69 (MQ=255)

                                           tatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATcc                >  1:2788295/1‑69 (MQ=255)

                                           tatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATcc                >  1:2664744/1‑69 (MQ=255)

                                           tatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATcc                >  1:562031/1‑69 (MQ=255)

                                           tatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATcc                >  1:607291/1‑69 (MQ=255)

                                           tatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATcc                >  1:2452007/1‑69 (MQ=255)

                                           tatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATcc                >  1:2295618/1‑69 (MQ=255)

                                           tatTGGAGAGTTGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATc                 >  1:1537079/1‑68 (MQ=255)

                                           tatTGGAGAGTAGCACCAGCAATAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATcc                >  1:2171257/1‑69 (MQ=255)

                                           tatTGCAGAGTTGCACCAGCAATAAGCCAGTCCAg                                                  >  1:1233640/1‑35 (MQ=18)

                                             ttGGAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATccc               >  1:621408/1‑68 (MQ=255)

                                             ttGGAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATccc               >  1:184661/1‑68 (MQ=255)

                                               ggAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATg                                             <  1:860017/36‑1 (MQ=255)

                                               ggAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATg                                             <  1:3303805/36‑1 (MQ=255)

                                               ggAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACTTGATCATAGCGAATAATCCCGGc            >  1:1730564/1‑69 (MQ=255)

                                               ggAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATCCCgg             >  1:1548192/1‑68 (MQ=255)

                                               ggAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATCCCGGc            >  1:3301619/1‑69 (MQ=255)

                                               ggAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATCCCGGc            >  1:2294438/1‑69 (MQ=255)

                                               ggAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATCCCGGc            >  1:761796/1‑69 (MQ=255)

                                               ggAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATCCCGGc            >  1:701698/1‑69 (MQ=255)

                                               ggAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATCCCGGc            >  1:2388317/1‑69 (MQ=255)

                                               ggAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATCCCGGc            >  1:248063/1‑69 (MQ=255)

                                               ggAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATCCCGGc            >  1:2518535/1‑69 (MQ=255)

                                               ggAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATCCCGGc            >  1:1506587/1‑69 (MQ=255)

                                               ggAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATCCCGGc            >  1:1505852/1‑69 (MQ=255)

                                               ggAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATCCCGGc            >  1:3352402/1‑69 (MQ=255)

                                               ggAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATCCCGGc            >  1:2082845/1‑69 (MQ=255)

                                               ggAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATCCCGGc            >  1:1501455/1‑69 (MQ=255)

                                               ggAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATCCCGGc            >  1:3193797/1‑69 (MQ=255)

                                                      tGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATCCCGGCACCAATc     <  1:2704712/69‑1 (MQ=255)

                                                      tGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATCCCGGCACCAATc     <  1:2528625/69‑1 (MQ=255)

                                                       gCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATCCCGGCACCAATCa    >  1:1087728/1‑69 (MQ=255)

                                                           cagcagCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATCCCGGCACCAATCAcc  >  1:444281/1‑67 (MQ=255)

                                                           cagcagCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATCCCGGCACCAATCAcc  >  1:2377501/1‑67 (MQ=255)

                                                           cagcagCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATCCCGGCACCAATCAcc  >  1:3243825/1‑67 (MQ=255)

                                                           cagcagCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATCCCGGCACCAATCAcc  >  1:2253347/1‑67 (MQ=255)

TCCATCAGGCGTTTGTAACCCACCATGCCAATGGCAAAAGTGATATTGGAGAGTTGCACCAGCAGCAAGCCAGTCCAGAAATGGTCGGTGACCTGATCATAGCGAATAATCCCGGCACCAATCACC  >  minE/2387050‑2387175

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