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	2,389,320	T→C	6.7%	N358S (AAC→AGC)	yfbK ←	conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,389,320	0	T	C	6.7%	253.8 / 8.6	90	N358S (AAC→AGC)	yfbK	conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (47/37); new base C (2/4); total (49/41)
Fisher's exact test for biased strand distribution p-value = 4.06e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.53e-01

AGAGAGGGTATCAATGTAGCTGTAGTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACACCAGACTCCCGCTGTTTTTTGAC  >  W3110S.gb/2389253‑2389384

agagagGGTATCAATGTAGCTGTAGTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGt                                                               <  1:394037/71‑1 (MQ=255)

agagagGGTATCAATGTAGCTGTAGTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGt                                                               <  1:3757946/71‑1 (MQ=255)

   gagGGTATCAATGTAGCTGTAGTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAAt                                                            <  1:3571586/71‑1 (MQ=255)

   gagGGTATCAATGTAGCTGTAGTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAAt                                                            <  1:392039/71‑1 (MQ=255)

    agGGTATCAATGTAGCTGTAGTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGCTGTAAtt                                                           >  1:2884769/1‑71 (MQ=255)

      ggTATCAATGTAGCTGTAGTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGc                                                         <  1:1261602/71‑1 (MQ=255)

        tATCAATGTAGCTGTAGTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGc                                                         <  1:1417757/69‑1 (MQ=255)

         aTCAATGTAGCTGTAGTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTAt                                                      >  1:1488686/1‑71 (MQ=255)

          tCAATGTAGCTGTAGTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGtt                                                                 >  1:4071957/1‑59 (MQ=255)

          tCAATGTAGCTGTAGTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGtt                                                                 >  1:5098175/1‑59 (MQ=255)

          tCAATGTAGCTGTAGTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGt                                                               <  1:4677510/61‑1 (MQ=255)

          tCAATGTAGCTGTAGTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGt                                                               <  1:1392979/61‑1 (MQ=255)

          tCAATGTAGCTGTAGTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGt                                                               <  1:3599607/61‑1 (MQ=255)

           cAATGTAGCTGTAGTTGCCGTTAGCAACATCGGCAATTCGCACCATCATTGCCTCGtt                                                                 >  1:1506158/1‑58 (MQ=255)

            aaTGTAGCTGTAGTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTcc                                                   >  1:2292503/1‑71 (MQ=255)

            aaTGTAGCTGTAGTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTcc                                                   >  1:725866/1‑71 (MQ=255)

            aaTGTAGCTGTAGTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTcc                                                   >  1:4068158/1‑71 (MQ=255)

            aaTGTAGCTGTAGTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTcc                                                   >  1:4149921/1‑71 (MQ=255)

               gTAGCTGTAGTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGCTGTAATTGCTATTCCCCa                                                >  1:3997411/1‑71 (MQ=255)

                   cTGTAGTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGc                                             >  1:1138892/1‑70 (MQ=255)

                        gTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCa                                                >  1:535573/1‑62 (MQ=255)

                        gTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCa                                                >  1:568262/1‑62 (MQ=255)

                        gTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCa                                                >  1:3484983/1‑62 (MQ=255)

                         ttGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGc                                                         <  1:3021804/52‑1 (MQ=255)

                         ttGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGc                                                         <  1:290790/52‑1 (MQ=255)

                         ttGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGc                                                         <  1:283635/52‑1 (MQ=255)

                          tGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTc                                     >  1:2587517/1‑71 (MQ=255)

                           gCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCt                                                        >  1:1590728/1‑51 (MQ=255)

                           gCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCa                                                >  1:4856618/1‑59 (MQ=255)

                           gCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTc                                     <  1:2698156/70‑1 (MQ=255)

                           gCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTc                                     <  1:4038803/70‑1 (MQ=255)

                           gCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTc                                     >  1:2910379/1‑70 (MQ=255)

                           gCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTc                                     >  1:1659910/1‑70 (MQ=255)

                           gCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTc                                     >  1:3323940/1‑70 (MQ=255)

                           gCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTc                                     <  1:2235075/70‑1 (MQ=255)

                            ccGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTaa                                                             >  1:4468035/1‑45 (MQ=255)

                            ccGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGa                                   <  1:2041755/71‑1 (MQ=255)

                             cGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTaa                                                             >  1:4725047/1‑44 (MQ=255)

                             cGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTaa                                                             >  1:3729442/1‑44 (MQ=255)

                              gTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACa                                 <  1:1567436/71‑1 (MQ=255)

                              gTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACa                                 <  1:2982334/71‑1 (MQ=255)

                               ttACCAACATCGGCAATTCGCACCATCATTGCCTCGCTGTAATTGCTAtt                                                     <  1:4231989/50‑1 (MQ=255)

                               ttACCAACATCGGCAATTAGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGa                                   >  1:2699113/1‑68 (MQ=255)

                                 aCCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACaga                               <  1:1699475/70‑1 (MQ=255)

                                  ccAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACagag                              <  1:2000974/70‑1 (MQ=255)

                                    aaCATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTAt                                                      >  1:1728975/1‑44 (MQ=255)

                                    aaCATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTc                                                    >  1:2667202/1‑46 (MQ=255)

                                     aCATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAac                          <  1:162241/71‑1 (MQ=255)

                                      cATCGGCAATTCGCACCATCATTGCCTCGTTGTaa                                                             >  1:4075411/1‑35 (MQ=255)

                                      cATCGGCAATTCGCACCATCATTGCCTCGTTGTaa                                                             >  1:5045662/1‑35 (MQ=255)

                                      cATCGGCAATTCGCACCATCATTGCCTCGTTGTaa                                                             >  1:15621/1‑35 (MQ=255)

                                      cATCGGCAATTCGCACCATCATTGCCTCGTTGTaa                                                             >  1:3919014/1‑35 (MQ=255)

                                      cATCGGCAATTCGCACCATCATTGCCTCGTTGTaa                                                             >  1:2149343/1‑35 (MQ=255)

                                      cATCGGCAATTCGCACCATCATTGCCTCGTTGTaa                                                             >  1:1672657/1‑35 (MQ=255)

                                        tCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAacac                        <  1:2457330/70‑1 (MQ=255)

                                         cGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAacac                        <  1:475484/69‑1 (MQ=255)

                                         cGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACAcc                       >  1:787069/1‑70 (MQ=255)

                                         cGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACAcc                       >  1:160417/1‑70 (MQ=255)

                                           gCAATTCGCACCATCATTTCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACaga                               <  1:4595619/60‑1 (MQ=255)

                                           gCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACaga                               <  1:4334477/60‑1 (MQ=255)

                                            cAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACACCAGAc                   <  1:887881/71‑1 (MQ=255)

                                             aaTTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGt                             >  1:4874988/1‑60 (MQ=255)

                                             aaTTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGt                             >  1:1719379/1‑60 (MQ=255)

                                                tCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAac                          <  1:4474079/60‑1 (MQ=255)

                                                tCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACACCAGACTccc               >  1:4929173/1‑71 (MQ=255)

                                                tCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACACCAGACTccc               >  1:4858317/1‑71 (MQ=255)

                                                 cGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCa                                           >  1:3944781/1‑42 (MQ=255)

                                                 cGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCa                                           >  1:3918730/1‑42 (MQ=255)

                                                 cGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACACCAGACTccc               <  1:4365671/70‑1 (MQ=255)

                                                 cGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACACCAGACTCCCg              >  1:1350508/1‑71 (MQ=255)

                                                 cGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACACCAGACTCCCg              >  1:874728/1‑71 (MQ=255)

                                                   cACCATCATTGCCTCGCTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGt                             <  1:1533474/54‑1 (MQ=255)

                                                   cACCATCATTGCCTCGCTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGt                             <  1:647453/54‑1 (MQ=255)

                                                   cACCATCATTGCCTCGCTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGt                             <  1:705581/54‑1 (MQ=255)

                                                     ccATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACACCa                      <  1:1890721/59‑1 (MQ=255)

                                                     ccATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACACCAGACTCCCGCTGt          >  1:631583/1‑71 (MQ=255)

                                                      catcatTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACACCAGACTCCCGCTGtt         >  1:958716/1‑71 (MQ=255)

                                                      catcatTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACACCAGACTCCCGCTGtt         <  1:1403312/71‑1 (MQ=255)

                                                      catcatTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACACCAGACTCCCGCTGtt         >  1:1337518/1‑71 (MQ=255)

                                                      catcatTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACACCAGACTCCCGCTGt          >  1:5055218/1‑70 (MQ=255)

                                                        tcatTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGt                             <  1:285921/49‑1 (MQ=255)

                                                        tcatTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACACCa                      <  1:3908025/56‑1 (MQ=255)

                                                        tcatTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACACCAGACTCCCGCTGtttt       <  1:315595/71‑1 (MQ=255)

                                                          atTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACACCAGa                    >  1:1606889/1‑56 (MQ=255)

                                                          atTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACACCAGa                    >  1:788244/1‑56 (MQ=255)

                                                          atTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACACCAGACTCCCGCTGtttttt     <  1:2228912/71‑1 (MQ=255)

                                                            tGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACACCAGACTCCCGCTGTTTTTTGa   >  1:3434786/1‑71 (MQ=255)

                                                             gCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACACCAGACTCCCGCTGTTTTTTGAc  >  1:2865149/1‑71 (MQ=255)

                                                              ccTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGa                                   >  1:3971507/1‑37 (MQ=255)

                                                              ccTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGa                                   >  1:92600/1‑37 (MQ=255)

                                                              ccTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACACCAGACTCCCGCTGTTTTTTGAc  <  1:1249298/70‑1 (MQ=255)

                                                                tCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAacac                        <  1:4331410/46‑1 (MQ=255)

                                                                 cGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACACCa                      <  1:1550070/47‑1 (MQ=255)

AGAGAGGGTATCAATGTAGCTGTAGTTGCCGTTACCAACATCGGCAATTCGCACCATCATTGCCTCGTTGTAATTGCTATTCCCCACGCCAAACGTCGACAGAGTAACACCAGACTCCCGCTGTTTTTTGAC  >  W3110S.gb/2389253‑2389384

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