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	2,593,801	T→C	31.3%	intergenic (‑72/+1069)	slp ← / ← arsC	outer membrane lipoprotein/arsenate reductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,593,801	0	T	C	31.3%	120.1 / 70.5	138	intergenic (‑72/+1069)	slp/arsC	outer membrane lipoprotein/arsenate reductase
Reads supporting (aligned to +/- strand): ref base T (31/63); new base C (22/21); total (53/85)
Fisher's exact test for biased strand distribution p-value = 5.84e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

Only 100 of 138 total aligned reads displayed.

ATCCTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCTGATAGTAACGTAAACCTGTCTGATGTTTATATCCTTTCTGTTTAGGTGA  >  minE/2593736‑2593859

aTCCTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:933260/68‑1 (MQ=255)

aTCCTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:2349087/68‑1 (MQ=255)

aTCCTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:2680949/68‑1 (MQ=255)

aTCCTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:2163383/68‑1 (MQ=255)

aTCCTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:2141104/68‑1 (MQ=255)

aTCCTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:3166883/68‑1 (MQ=255)

aTCCTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:3296739/68‑1 (MQ=255)

aTCCTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:1904757/68‑1 (MQ=255)

aTCCTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:1796559/68‑1 (MQ=255)

aTCCTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:1718936/68‑1 (MQ=255)

aTCCTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:506460/68‑1 (MQ=255)

aTCCTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:589447/68‑1 (MQ=255)

aTCCTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:620921/68‑1 (MQ=255)

aTCCTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:1412522/68‑1 (MQ=255)

aTCCTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:881656/68‑1 (MQ=255)

aTCCTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:632725/68‑1 (MQ=255)

aTCCTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:729284/68‑1 (MQ=255)

aTCCTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:674900/68‑1 (MQ=255)

  ccTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:3388351/66‑1 (MQ=255)

   cTTATCAACAAATATTAAAACCATAATGGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:3045302/65‑1 (MQ=255)

   cTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:180615/65‑1 (MQ=255)

   cTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:3030235/65‑1 (MQ=255)

   cTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          >  1:782240/1‑65 (MQ=255)

   cTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:809635/65‑1 (MQ=255)

        caacaaATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCt                                                   <  1:2535957/67‑1 (MQ=255)

        caacaaATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCt                                                   <  1:636264/67‑1 (MQ=255)

        caacaaATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCt                                                   <  1:1822177/67‑1 (MQ=255)

        caacaaATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCt                                                   <  1:3157730/67‑1 (MQ=255)

        caacaaATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCt                                                   <  1:2157439/67‑1 (MQ=255)

        caacaaATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCTg                                                  <  1:1668220/68‑1 (MQ=255)

        caacaaATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCTg                                                  <  1:1453417/68‑1 (MQ=255)

         aacaaATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCt                                                   <  1:539780/66‑1 (MQ=255)

         aacaaATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCTGa                                                 <  1:2709779/68‑1 (MQ=255)

         aacaaATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCTGa                                                 <  1:913419/68‑1 (MQ=255)

         aacaaATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCTGa                                                 <  1:190506/68‑1 (MQ=255)

         aacaaATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCTGa                                                 <  1:1871258/68‑1 (MQ=255)

          acaaATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:1777348/58‑1 (MQ=255)

            aaaTATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCTGATAGt                                             <  1:916574/69‑1 (MQ=255)

            aaaTATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCTGATAGt                                             <  1:2452609/69‑1 (MQ=255)

             aaTATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGCGATTTGCCTGATAGTa                                            >  1:378997/1‑69 (MQ=255)

             aaTATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGCGATATGc                                                     >  1:3090898/1‑60 (MQ=255)

             aaTATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGCGATATGc                                                     >  1:3315198/1‑60 (MQ=255)

             aaTATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGCGATATGc                                                     >  1:1024767/1‑60 (MQ=255)

             aaTATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGCGATATGc                                                     >  1:1134277/1‑60 (MQ=255)

             aaTATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGCGATATGCCTGATAGTa                                            >  1:98709/1‑69 (MQ=255)

             aaTATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGCGATATGCCTGATAGTa                                            >  1:3258740/1‑69 (MQ=255)

             aaTATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGCGATATGCCTGATAGTa                                            >  1:739487/1‑69 (MQ=255)

             aaTATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGCGATATGCCTGATAGTa                                            >  1:2150267/1‑69 (MQ=255)

             aaTATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGCGATATGCCTGATAGTa                                            >  1:3425022/1‑69 (MQ=255)

             aaTATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGCGATATGCCTGATAGTa                                            >  1:737335/1‑69 (MQ=255)

             aaTATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGCGATATGCCTGATAGTa                                            >  1:2799640/1‑69 (MQ=255)

             aaTATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGCGATATGCCTGATAGTa                                            >  1:1042098/1‑69 (MQ=255)

             aaTATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGCGATATGCCTGATAGTa                                            >  1:1628698/1‑69 (MQ=255)

             aaTATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGCGATATGCCTGATAGTa                                            >  1:1336239/1‑69 (MQ=255)

                         ataataGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCTGATAGTAACGTAAACCTga                                >  1:128141/1‑68 (MQ=255)

                         ataataGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCTGATAGTAACGTAAACCTga                                >  1:2356763/1‑68 (MQ=255)

                         ataataGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCTGATAGTAACGTAAACCTga                                >  1:2022579/1‑68 (MQ=255)

                           aataGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          >  1:2319314/1‑41 (MQ=255)

                           aataGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          >  1:1273077/1‑41 (MQ=255)

                           aataGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          >  1:2419515/1‑41 (MQ=255)

                           aataGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          >  1:138320/1‑41 (MQ=255)

                            ataGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:1083868/40‑1 (MQ=255)

                            ataGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGa                                                          <  1:2738500/40‑1 (MQ=255)

                            ataGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCTGATAGTAACGTAAAc                                    >  1:1995090/1‑62 (MQ=255)

                            ataGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCTGATAGTAACGTAAACCTGTCTg                             >  1:1586/1‑69 (MQ=255)

                            ataGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCTGATAGTAACGTAAACCTGTCTg                             >  1:634309/1‑69 (MQ=255)

                                 tatTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCTGATAGTAACGTAAACCTGTCTGATGtt                        <  1:2883905/69‑1 (MQ=255)

                                 tatTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCTGATAGTAACGTAAACCTGTCTGATGtt                        <  1:3244021/69‑1 (MQ=255)

                                  atTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCt                                                   >  1:3291173/1‑41 (MQ=255)

                                  atTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCt                                                   >  1:3209235/1‑41 (MQ=255)

                                  atTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCt                                                   >  1:2536884/1‑41 (MQ=255)

                                  atTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCt                                                   >  1:423283/1‑41 (MQ=255)

                                  atTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCTGATAGTAACGTAAACCTGTCTGATGtt                        <  1:1237041/68‑1 (MQ=255)

                                  atTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCTGATAGTAACGTAAACCTGTCTGATGtt                        >  1:2575182/1‑68 (MQ=255)

                                   tttCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCTGATAGTAACGTAAACCTGTCTGATGTTta                      <  1:672786/69‑1 (MQ=255)

                                     tCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCt                                                   >  1:414190/1‑38 (MQ=255)

                                     tCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCt                                                   >  1:1008226/1‑38 (MQ=255)

                                     tCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCt                                                   >  1:487257/1‑38 (MQ=255)

                                     tCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCt                                                   >  1:2742607/1‑38 (MQ=255)

                                     tCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCt                                                   >  1:2809747/1‑38 (MQ=255)

                                     tCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCt                                                   >  1:346442/1‑38 (MQ=255)

                                     tCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCt                                                   >  1:2196642/1‑38 (MQ=255)

                                     tCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCt                                                   >  1:3416989/1‑38 (MQ=255)

                                     tCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCt                                                   >  1:2069985/1‑38 (MQ=255)

                                     tCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCt                                                   >  1:186390/1‑38 (MQ=255)

                                     tCTTTATAGTTTTCATCTGATTCTGAGGTGATAAGCCt                                                   >  1:2559181/1‑38 (MQ=255)

                                     tCTTTATAGTTTTCATCTGATTCTGAGGCGATATGCCTGATAGTAACGTAAACCTGTc                               <  1:1810246/58‑1 (MQ=255)

                                     tCTTTATAGTTTTCATCTGATTCTGAGGCGATATGCCTGATAGTAACGTAAACCTGTc                               <  1:1469581/58‑1 (MQ=255)

                                     tCTTTATAGTTTTCATCTGATTCTGAGGCGATATGCCTGATAGTAACGTAAACCTGTc                               <  1:484277/58‑1 (MQ=255)

                                     tCTTTATAGTTTTCATCTGATTCTGAGGCGATATGCCTGATAGTAACGTAAACCTGTc                               <  1:436966/58‑1 (MQ=255)

                                     tCTTTATAGTTTTCATCTGATTCTGAGGCGATATGCCTGATAGTAACGTAAACCTGTc                               <  1:177453/58‑1 (MQ=255)

                                     tCTTTATAGTTTTCATCTGATTCTGAGGCGATATGCCTGATAGTAACGTAAACCTGTc                               <  1:3336231/58‑1 (MQ=255)

                                     tCTTTATAGTTTTCATCTGATTCTGAGGCGATATGCCTGATAGTAACGTAAACCTGTc                               <  1:2147383/58‑1 (MQ=255)

                                     tCTTTATAGTTTTCATCTGATTCTGAGGCGATATGCCTGATAGTAACGTAAACCTGTc                               <  1:2985072/58‑1 (MQ=255)

                                     tCTTTATAGTTTTCATCTGATTCTGAGGCGATATGCCTGATAGTAACGTAAACCTGTc                               <  1:2714007/58‑1 (MQ=255)

                                     tCTTTATAGTTTTCATCTGATTCTGAGGCGATATGCCTGATAGTAACGTAAACCTGTc                               <  1:2281881/58‑1 (MQ=255)

                                     tCTTTATAGTTTTCATCTGATTCTGAGGCGATATGCCTGATAGTAACGTAAACCTGTc                               <  1:2465228/58‑1 (MQ=255)

                                         tataGTTTTCATCTGATTCTGAGGCGATATGCCTGATAGTAACGTAAACCTGTc                               <  1:2377421/54‑1 (MQ=255)

                                                          tCTGAGGTGATATGCCTGATAGTAACGTAAACCTGTCTGATGTTTATATCCTTTCTGTTTAGGTGa  <  1:1599508/66‑1 (MQ=255)

                                                          tCTGAGGTGATATGCCTGATAGTAACGTAAACCTGTCTGATGTTTATATCCTTTCTGTTTAGGTGa  <  1:1152601/66‑1 (MQ=255)

ATCCTTATCAACAAATATTAAAACCATAATAGATATTTCTTTATAGTTTTCATCTGATTCTGAGGTGATATGCCTGATAGTAACGTAAACCTGTCTGATGTTTATATCCTTTCTGTTTAGGTGA  >  minE/2593736‑2593859

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A