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	1,498,221	T→C	60.9%	K541K (AAA→AAG)	nuoC ←	NADH:ubiquinone oxidoreductase, chain C,D

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,498,221	0	T	C	60.9%	23.6 / 31.5	51	K541K (AAA→AAG)	nuoC	NADH:ubiquinone oxidoreductase, chain C,D
Reads supporting (aligned to +/- strand): ref base T (6/14); new base C (20/11); total (26/25)
Fisher's exact test for biased strand distribution p-value = 2.27e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGAACACGGGTGCGGTAACTCATGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCTTTGGTCGCCTCAATCATCTGGAAAGATTCATTGGCAGGCATCACCGGACCCCACGACACTTGCAGGA  >  minE/1498159‑1498288

cGAACACGGGTGCGGTAACTCATGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCTTTGGTc                                                               >  1:3279031/1‑69 (MQ=255)

cGAACACGGGTGCGGTAACTCATGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCTTTGGTc                                                               >  1:3290751/1‑69 (MQ=255)

cGAACACGGGTGCGGTAACTCATGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCTTTGGTc                                                               >  1:459509/1‑69 (MQ=255)

cGAACACGGGTGCGGTAACTCATGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCTTTGGTc                                                               >  1:1548999/1‑69 (MQ=255)

        ggTGCGGTAACTCATGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCTTTGGTCGCCTCAat                                                       <  1:3189673/69‑1 (MQ=255)

        ggTGCGGTAACTCATGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCTTTGGTCGCCTCAat                                                       <  1:233447/69‑1 (MQ=255)

        ggTGCGGTAACTCATGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCTTTGGTCGCCTCAat                                                       <  1:3283261/69‑1 (MQ=255)

        ggTGCGGTAACTCATGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCTTTGGTCGCCTCAat                                                       <  1:35375/69‑1 (MQ=255)

              gTAACTCATGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCTTTGGTCGCCTCAATCATCt                                                  >  1:2632614/1‑68 (MQ=255)

                     aTGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCCTTGGTCGcc                                                            >  1:3243695/1‑51 (MQ=255)

                     aTGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCCTTGGTCGcc                                                            >  1:2545452/1‑51 (MQ=255)

                     aTGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCCTTGGTCGcc                                                            >  1:2413264/1‑51 (MQ=255)

                     aTGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCCTTGGTCGcc                                                            >  1:2128443/1‑51 (MQ=255)

                     aTGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCCTTGGTCGcc                                                            >  1:3280777/1‑51 (MQ=255)

                     aTGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCCTTGGTCGcc                                                            >  1:2238692/1‑51 (MQ=255)

                     aTGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCCTTGGTCGcc                                                            >  1:2945594/1‑51 (MQ=255)

                     aTGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCCTTGGTCGcc                                                            >  1:2194994/1‑51 (MQ=255)

                     aTGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCCTTGGTCGcc                                                            >  1:2922336/1‑51 (MQ=255)

                     aTGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCCTTGGTCGcc                                                            >  1:1840153/1‑51 (MQ=255)

                     aTGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCCTTGGTCGcc                                                            >  1:470001/1‑51 (MQ=255)

                     aTGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCCTTGGTCGcc                                                            >  1:1671261/1‑51 (MQ=255)

                     aTGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCCTTGGTCGcc                                                            >  1:543283/1‑51 (MQ=255)

                     aTGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCCTTGGTCGcc                                                            >  1:548708/1‑51 (MQ=255)

                     aTGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCCTTGGTCGcc                                                            >  1:1356928/1‑51 (MQ=255)

                     aTGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCCTTGGTCGcc                                                            >  1:134511/1‑51 (MQ=255)

                     aTGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCCTTGGTCGcc                                                            >  1:920058/1‑51 (MQ=255)

                     aTGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCCTTGGTCGcc                                                            >  1:1152201/1‑51 (MQ=255)

                     aTGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCCTTGGTCGcc                                                            >  1:1059223/1‑51 (MQ=255)

                     aTGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCCTTGGTCGc                                                             >  1:3212001/1‑50 (MQ=255)

                       ggTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCTTTGGTCGCCTCAATCATCTGGAAAGAtt                                         <  1:1281257/68‑1 (MQ=255)

                        gTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCTTTGGTCGCCTCAATCATCTGGAAAGATTCa                                       >  1:872391/1‑69 (MQ=255)

                          gctgcCGTCGCTGGTCAGGTAGTAACTGTTGATCCCTTTGGTCGCCTCAATCATCTGGAAAGATTCAtt                                     <  1:996985/69‑1 (MQ=255)

                                gTCGCTGGTCAGGTAGTAACTGTTGATCCCTTTGGTCGCCTCAATCATCTGGAAAGATTCATTggcagg                               <  1:937296/69‑1 (MQ=255)

                                gTCGCTGGTCAGGTAGTAACTGTTGATCCCTTTGGTCGCCTCAATCATCTGGAAAGATTCATTggcagg                               <  1:1943508/69‑1 (MQ=255)

                                gTCGCTGGTCAGGTAGTAACTGTTGATCCCTTTGGTCGCCTCAATCATCTGGAAAGATTCATTggcagg                               <  1:2189139/69‑1 (MQ=255)

                                gTCGCTGGTCAGGTAGTAACTGTTGATCCCTTTGGTCGCCTCAATCATCTGGAAAGATTCATTggcagg                               <  1:2253009/69‑1 (MQ=255)

                                   gCTGGTCAGGTAGTAACTGTTGATCCCTTTGGTCGCCTCAATCATCTGGAAAGATTCATTggcaggca                             <  1:2381354/68‑1 (MQ=255)

                                     tGGTCAGGTAGTAACTGTTGATCCCTTTGGTCGCCTCAATCATCTGGAAAGATTCATTGGCAGGCATc                           <  1:2782615/68‑1 (MQ=255)

                                     tGGTCAGGTAGTAACTGTTGATCCCTTTGGTCGCCTCAATCATCTGGAAAGATTCATTGGCAGGCATc                           <  1:1000087/68‑1 (MQ=255)

                                         cAGGTAGTAACTGTTGATCCCTTTGGTCGCCTCAATCATCTGGAAAGATTCATTGGCAGGCATc                           <  1:2285805/64‑1 (MQ=255)

                                                  aCTGTTGATCCCCTTGGTCGCCTCAACCATCTGGAAGGATTCATTGGCAGGCATCACCGGAccc                  <  1:2831490/64‑1 (MQ=255)

                                                  aCTGTTGATCCCCTTGGTCGCCTCAACCATCTGGAAGGATTCATTGGCAGGCATCACCGGAccc                  <  1:3288888/64‑1 (MQ=255)

                                                  aCTGTTGATCCCCTTGGTCGCCTCAACCATCTGGAAGGATTCATTGGCAGGCATCACCGGAccc                  <  1:1157604/64‑1 (MQ=255)

                                                  aCTGTTGATCCCCTTGGTCGCCTCAACCATCTGGAAGGATTCATTGGCAGGCATCACCGGAccc                  <  1:90913/64‑1 (MQ=255)

                                                  aCTGTTGATCCCCTTGGTCGCCTCAACCATCTGGAAGGATTCATTGGCAGGCATCACCGGAccc                  <  1:139287/64‑1 (MQ=255)

                                                  aCTGTTGATCCCCTTGGTCGCCTCAACCATCTGGAAGGATTCATTGGCAGGCATCACCGGAccc                  <  1:718315/64‑1 (MQ=255)

                                                  aCTGTTGATCCCCTTGGTCGCCTCAACCATCTGGAAGGATTCATTGGCAGGCATCACCGGAccc                  <  1:1727856/64‑1 (MQ=255)

                                                  aCTGTTGATCCCCTTGGTCGCCTCAACCATCTGGAAGGATTCATTGGCAGGCATCACCGGAccc                  <  1:468078/64‑1 (MQ=255)

                                                  aCTGTTGATCCCCTTGGTCGCCTCAACCATCTGGAAGGATTCATTGGCAGGCATCACCGGAccc                  <  1:1880788/64‑1 (MQ=255)

                                                  aCTGTTGATCCCCTTGGTCGCCTCAACCATCTGGAAGGATTCATTGGCAGGCATCACCGGAccc                  <  1:2652748/64‑1 (MQ=255)

                                                   cTGTTGATCCCCTTGGTCGCCTCAACCATCTGGAAGGATTCATTGGCAGGCATCACCGGAccc                  <  1:469988/63‑1 (MQ=255)

                                                              tttGGTCGCCTCAATCATCTGGAAAGATTCATTGGCAGGCATCACCGGACCCCACGACACTTGCAGGa  <  1:499200/68‑1 (MQ=255)

                                                              tttGGTCGCCTCAATCATCTGGAAAGATTCATTGGCAGGCATCACCGGACCCCACGACACTTGCAGGa  <  1:1611719/68‑1 (MQ=255)

                                                              tttGGTCGCCTCAATCATCTGGAAAGATTCATTGGCAGGCATCACCGGACCCCACGACACTTGCAGGa  <  1:1560417/68‑1 (MQ=255)

                                                              tttGGTCGCCTCAATCATCTGGAAAGATTCATTGGCAGGCATCACCGGACCCCACGACACTTGCAGGa  <  1:736018/68‑1 (MQ=255)

                                                              tttGGTCGCCTCAATCATCTGGAAAGATTCATTGGCAGGCATCACCGGACCCCACGACACTTGCAGGa  <  1:871184/68‑1 (MQ=255)

                                                              tttGGTCGCCTCAATCATCTGGAAAGATTCATTGGCAGGCATCACCGGACCCCACGACACTTGCAGGa  <  1:2699369/68‑1 (MQ=255)

CGAACACGGGTGCGGTAACTCATGGTGCTGCCGTCGCTGGTCAGGTAGTAACTGTTGATCCCTTTGGTCGCCTCAATCATCTGGAAAGATTCATTGGCAGGCATCACCGGACCCCACGACACTTGCAGGA  >  minE/1498159‑1498288

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