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
A5 F21 I0 R2	316	65.6	5147759	97.4%	5013917	60.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	3,253,271	C→T	43.3%	V99V (GTC→GTT)	yhaK →	predicted pirin‑related protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,253,271	0	C	T	43.3%	28.5 / 74.9	60	V99V (GTC→GTT)	yhaK	predicted pirin‑related protein
Reads supporting (aligned to +/- strand): ref base C (11/23); new base T (13/13); total (24/36)
Fisher's exact test for biased strand distribution p-value = 1.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.47e-01

GATAGCGAAGGCAATCATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCTTTGGCTGGACGCCTG  >  W3110S.gb/3253203‑3253339

gATAGCGAAGGCAATCATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAg                                                                    <  1:3152185/71‑1 (MQ=255)

 aTAGCGAAGGCAATCATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTATACCCAGCCGGGTGTCAGc                                                                   >  1:3465324/1‑71 (MQ=255)

  tAGCGAAGGCAATCATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCt                                                                  <  1:3675461/71‑1 (MQ=255)

   aGCGAAGGCAATCATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTTAGCta                                                                 >  1:3895582/1‑71 (MQ=255)

   aGCGAAGGCAATCATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCta                                                                 >  1:4449110/1‑71 (MQ=255)

    gCGAAGGCAATCATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTTAGCtat                                                                <  1:4101146/71‑1 (MQ=255)

          gCAATCATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTTAGCTATAGCGaa                                                          <  1:4024458/71‑1 (MQ=255)

            aaTCATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTTAGCTATAGCGAac                                                         <  1:629582/70‑1 (MQ=255)

             aTCATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCTGGTGTTAGCTATAGCGAacac                                                       <  1:4442714/71‑1 (MQ=255)

             aTCATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTTAGCTATAGCGAacac                                                       <  1:3143676/71‑1 (MQ=255)

             aTCATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTTAGCTATAGCGAacac                                                       <  1:2872744/71‑1 (MQ=255)

              tCATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTTAGCTATAGCGAacac                                                       >  1:631920/1‑70 (MQ=255)

               cATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTTAGCTATAGCGAAcaca                                                      >  1:3095294/1‑70 (MQ=255)

               cATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTTAGCTATAGCGAACACaa                                                     >  1:3616134/1‑71 (MQ=255)

                   ttCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTTAGCTATAGCGAAcaca                                                      <  1:4907763/66‑1 (MQ=255)

                    tCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGc                                                                   >  1:393834/1‑52 (MQ=255)

                      aGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGc                                              <  1:4149307/71‑1 (MQ=255)

                       ggCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTTAGCTATAGCGAACACAATCTCAGCa                                             <  1:2934563/71‑1 (MQ=255)

                        gCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCaa                                            <  1:3639901/71‑1 (MQ=255)

                              gcCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACa                                       >  1:906049/1‑70 (MQ=255)

                                cGGAGAGGCGTTGCTGCTCTCTACCCTGCCGGGTGTTAGCTATAGCGAACACAATCTCAGCGAAGACAAAc                                    <  1:1507273/71‑1 (MQ=255)

                                 ggAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCaaa                                           <  1:2930704/63‑1 (MQ=255)

                                   agagGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGa                                         >  1:1399645/1‑63 (MQ=255)

                                    gagGCGTTGCTGCTCTCTACCCAGCCGGGTGTTAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGt                                 >  1:3762232/1‑70 (MQ=255)

                                         gTTGCTGCTCTCTACCCAGCCGGGTGTTAGCTATAGCGaa                                                          >  1:3760504/1‑40 (MQ=255)

                                         gTTGCTGCTCTCTACCCAGCCGGGTGTTAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAAcgc                           >  1:3099214/1‑71 (MQ=255)

                                         gTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACaaa                                     >  1:1007497/1‑61 (MQ=255)

                                          ttGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAAcaca                                                      <  1:4555067/43‑1 (MQ=255)

                                          ttGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAAcgcg                          <  1:4714300/71‑1 (MQ=255)

                                          ttGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAAcgcg                          <  1:1561291/71‑1 (MQ=255)

                                          ttGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAAcgcg                          <  1:1174306/71‑1 (MQ=255)

                                            gctgctCTCTACCCAGCCGGGTGTTAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGaa                        >  1:1160802/1‑71 (MQ=255)

                                            gctgctCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGa                         <  1:5115308/70‑1 (MQ=255)

                                             ctgctCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAAt                       >  1:2664929/1‑71 (MQ=255)

                                                ctctctACCCAGCCGGGTGTTAGCTATAGCGAACACAATCTCAGCAAAGACAAAc                                    >  1:3620793/1‑55 (MQ=255)

                                                ctctctACCCAGCCGGGTGTTAGCTATAGCGAACACAATCTCAGCAAAGACAAAc                                    >  1:822019/1‑55 (MQ=255)

                                                ctctctACCCAGCCGGGTGTTAGCTATAGCGAACACAATCTCAGCAAAGACAAAc                                    >  1:4939484/1‑55 (MQ=255)

                                                ctctctACCCAGCCGGGTGTTAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGc                     <  1:90831/70‑1 (MQ=255)

                                                ctctctACCCAGCCGGGTGTTAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGc                     <  1:1992865/70‑1 (MQ=255)

                                                ctctctACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCa                                             <  1:216652/46‑1 (MQ=255)

                                                ctctctACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGc                     <  1:4598734/70‑1 (MQ=255)

                                                ctctctACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGc                     <  1:4375532/70‑1 (MQ=255)

                                                   tctACCCAGCCGGGTGTTAGCTATAGAGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAg                   <  1:1684063/69‑1 (MQ=255)

                                                   tctACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAAcgcg                          <  1:669849/62‑1 (MQ=255)

                                                    ctACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAAcgc                           >  1:2360765/1‑60 (MQ=255)

                                                    ctACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAAcgc                           >  1:3249859/1‑60 (MQ=255)

                                                    ctACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCtt                >  1:3622919/1‑71 (MQ=255)

                                                      aCCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAAcgcg                          <  1:4271941/59‑1 (MQ=255)

                                                       cccAGCCGGGTGTTAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCttt               <  1:3147467/69‑1 (MQ=255)

                                                       cccAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCttt               <  1:2986910/69‑1 (MQ=255)

                                                       cccAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCTTTg              <  1:2441251/70‑1 (MQ=255)

                                                       cccAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCTTTg              <  1:4365577/70‑1 (MQ=255)

                                                              gggTGTTAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCTTTGGCTGGACg      >  1:4691117/1‑71 (MQ=255)

                                                              gggTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCTTTGGCTGGACg      <  1:1786641/71‑1 (MQ=255)

                                                                 tgtTAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCTTTGGCTGGACGCCt   >  1:1778225/1‑71 (MQ=255)

                                                                  gtCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGtt                                <  1:3654156/41‑1 (MQ=255)

                                                                  gtCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGtt                                <  1:68356/41‑1 (MQ=255)

                                                                  gtCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCTTTGGCTGGACGCCTg  >  1:278911/1‑71 (MQ=255)

                                                                   tCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCg                                  <  1:768456/38‑1 (MQ=255)

                                                                   tCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTa                               <  1:3447647/41‑1 (MQ=255)

GATAGCGAAGGCAATCATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCTTTGGCTGGACGCCTG  >  W3110S.gb/3253203‑3253339

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