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
A6 F21 I0 R1	2169	63.0	3952800	76.2%	3012033	62.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	775,547	C→T	31.2%	T390T (ACC→ACT)	icd →	isocitrate dehydrogenase, specific for NADP+

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	775,547	0	C	T	31.2%	106.3 / 59.4	77	T390T (ACC→ACT)	icd	isocitrate dehydrogenase, specific for NADP+
Reads supporting (aligned to +/- strand): ref base C (20/33); new base T (15/9); total (35/42)
Fisher's exact test for biased strand distribution p-value = 5.17e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCAT  >  minE/775481‑775615

ttGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATg                                                                  <  1:2920408/71‑1 (MQ=255)

 tGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGa                                                                 >  1:889719/1‑71 (MQ=255)

   gACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACt                                                               <  1:1054709/71‑1 (MQ=255)

     ctgAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTc                                                             >  1:226522/3‑71 (MQ=255)

     ccGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc                                                             <  1:3111728/71‑1 (MQ=255)

      cGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc                                                             >  1:1353041/1‑70 (MQ=255)

      cGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCg                                                            <  1:587455/71‑1 (MQ=255)

      cGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCg                                                            <  1:2441030/71‑1 (MQ=255)

        aaGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGaa                                                          >  1:583720/1‑70 (MQ=255)

         aGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGc                                                         <  1:775697/71‑1 (MQ=255)

           cGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTa                                                                    <  1:378070/58‑1 (MQ=25)

             gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                                     <  1:353651/71‑1 (MQ=255)

               tGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTa                                                                    >  1:318741/1‑54 (MQ=21)

               tGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTc                                                             >  1:3342495/1‑61 (MQ=25)

               tGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTc                                                      <  1:1910208/68‑1 (MQ=255)

                    tgaTTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCg                                                            <  1:3498612/55‑1 (MQ=37)

                      aTTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGaa                                                          >  1:1201966/1‑56 (MQ=37)

                      aTTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGatggaagg                                            <  1:1574197/71‑1 (MQ=255)

                      aTTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggatg                                             <  1:1831267/70‑1 (MQ=255)

                       ttGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggatg                                             <  1:78720/69‑1 (MQ=255)

                       ttGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGatggatgg                                            >  1:791662/1‑70 (MQ=255)

                        tGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGgcg                                          >  1:3834562/1‑71 (MQ=255)

                         gTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGgcgc                                         >  1:1879414/1‑71 (MQ=255)

                          ttAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc                                                             <  1:1183662/50‑1 (MQ=255)

                          ttAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTc                                                             <  1:628191/50‑1 (MQ=255)

                            aaaGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCt                                        >  1:3218581/1‑69 (MQ=255)

                             aaGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatgga                                               <  1:3441921/61‑1 (MQ=255)

                             aaGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGgcg                                          >  1:3685146/1‑66 (MQ=255)

                             aaGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                     <  1:1086468/71‑1 (MQ=255)

                              aGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAAc                                    >  1:3298736/1‑71 (MQ=255)

                              aGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAAc                                    >  1:2512575/1‑71 (MQ=255)

                               ggTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGgcg                                          <  1:641740/64‑1 (MQ=37)

                                gTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGAc                                                                <  1:3422754/41‑1 (MQ=255)

                                  aTGGAAGGCGCAATCAATGCCAAGACCGTAACTTAt                                                                   >  1:2493804/1‑36 (MQ=12)

                                   tGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAgctgct                                >  1:927540/1‑70 (MQ=255)

                                   tGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAgctgct                                >  1:1951607/1‑70 (MQ=255)

                                   tGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                                     <  1:2883345/49‑1 (MQ=255)

                                   tGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCt                                                     <  1:111813/49‑1 (MQ=255)

                                     gAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTaag                                     >  1:2782698/1‑62 (MQ=25)

                                     gAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaa                             <  1:3383689/71‑1 (MQ=255)

                                      aaGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGaaa                            <  1:1973873/71‑1 (MQ=255)

                                       aGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGc                                                         >  1:3752277/1‑41 (MQ=255)

                                       aGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAAt                           <  1:2825124/71‑1 (MQ=255)

                                        ggCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat                                              <  1:1168006/51‑1 (MQ=255)

                                           gcAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatgg                                                <  1:829444/46‑1 (MQ=255)

                                            cAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgct                                <  1:3923229/61‑1 (MQ=255)

                                            cAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCa                      <  1:609243/71‑1 (MQ=255)

                                             aaTCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGtt                        >  1:1902623/1‑68 (MQ=255)

                                             aaTCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCag                     <  1:2405367/71‑1 (MQ=255)

                                             aaTCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGaa                             <  1:69330/63‑1 (MQ=255)

                                             aaTCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGtt                        >  1:1630890/1‑68 (MQ=255)

                                               tCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGctgctg                               <  1:1482909/59‑1 (MQ=21)

                                               tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTc                                                      >  1:1562840/1‑36 (MQ=255)

                                               tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGgcg                                          <  1:3213237/48‑1 (MQ=255)

                                               tCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGgcg                                          <  1:3909858/48‑1 (MQ=255)

                                                 aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGtt                 <  1:3935588/71‑1 (MQ=255)

                                                 aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGtt                 >  1:3619381/1‑71 (MQ=255)

                                                 aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGtt                 <  1:1002922/71‑1 (MQ=255)

                                                   cgcgAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTg               >  1:2955554/1‑71 (MQ=255)

                                                      gAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAAc                                    <  1:1034313/47‑1 (MQ=255)

                                                      gAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTg            <  1:827144/71‑1 (MQ=255)

                                                       aagaCCGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTg            >  1:2896146/4‑70 (MQ=255)

                                                       aaaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgctg                               <  1:2124752/51‑1 (MQ=255)

                                                       aaaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgctg                               <  1:736547/51‑1 (MQ=255)

                                                        aaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActg                                  >  1:1563463/1‑47 (MQ=255)

                                                        aaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActg                                  >  1:2736213/1‑47 (MQ=255)

                                                        aaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGt             >  1:2134509/1‑68 (MQ=255)

                                                        aaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAc          <  1:2238057/71‑1 (MQ=255)

                                                        aaaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAc          <  1:1276596/71‑1 (MQ=255)

                                                         aaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgct                                >  1:3602388/1‑48 (MQ=255)

                                                         aaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgct                                >  1:3597981/1‑48 (MQ=255)

                                                         aaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgc                                 >  1:3114004/1‑47 (MQ=255)

                                                          aCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                     >  1:2726813/1‑42 (MQ=255)

                                                           ccGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGAcgcg       <  1:540875/71‑1 (MQ=255)

                                                            cGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCa                      >  1:2369195/1‑55 (MQ=255)

                                                            cGTAACTTATGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAagcg       >  1:1092867/1‑70 (MQ=255)

                                                                aCCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatcat  >  1:3354160/1‑71 (MQ=255)

                                                                  cTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGa      <  1:1127717/65‑1 (MQ=255)

TTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCAT  >  minE/775481‑775615

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