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	775,571	T→A	34.5%	D398E (GAT→GAA)	icd →	isocitrate dehydrogenase, specific for NADP+

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	775,571	0	T	A	34.5%	61.0 / 53.2	55	D398E (GAT→GAA)	icd	isocitrate dehydrogenase, specific for NADP+
Reads supporting (aligned to +/- strand): ref base T (17/19); new base A (14/5); total (31/24)
Fisher's exact test for biased strand distribution p-value = 8.72e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.41e-01

ATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTT  >  minE/775503‑775638

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)

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

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

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

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

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

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

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

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

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

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

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

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

                  ggCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTgatggat                                                                     <  1:1168006/51‑1 (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)

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

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

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

                           aaCGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGtt                                        <  1:3935588/71‑1 (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                                                      <  1:736547/51‑1 (MQ=255)

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

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

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

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

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

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

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

                                   aaCCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAActgct                                                       >  1:3602388/1‑48 (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)

                                             tATGACTTCGAGCGTCTGATGGATGGCGGTAAACTGCTGAAATGtt                                               >  1:1893457/1‑46 (MQ=255)

                                             tATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCg                       >  1:1698382/1‑70 (MQ=255)

                                             tATGACTTCGAACGTCTGATGGAAGGCGCTAAgctgct                                                       >  1:1527449/1‑38 (MQ=25)

                                              aTGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGa                      >  1:2398538/1‑70 (MQ=255)

                                               tGACTTCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGaa                     >  1:2320314/1‑70 (MQ=255)

                                                 aCTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaaaa                   <  1:950675/70‑1 (MQ=255)

                                                    tCGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATg               >  1:932792/1‑71 (MQ=255)

                                                     cGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAagc                               >  1:1887323/1‑54 (MQ=255)

                                                     cGAACGTCTGATGGAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACAt                <  1:3071595/69‑1 (MQ=255)

                                                                tggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGt   <  1:3379597/71‑1 (MQ=255)

                                                                 ggatggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGtt  >  1:1691546/1‑71 (MQ=255)

                                                                    tggCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGa                      >  1:788489/1‑48 (MQ=255)

ATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAGTT  >  minE/775503‑775638

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