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 F1 I0 R1	2892	75.3	5698161	66.1%	3766484	59.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,933,744	G→A	21.1%	D233D (GAC→GAT)	lysS ←	lysine tRNA synthetase, constitutive

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,933,744	0	G	A	21.1%	247.4 / 57.0	123	D233D (GAC→GAT)	lysS	lysine tRNA synthetase, constitutive
Reads supporting (aligned to +/- strand): ref base G (35/62); new base A (17/9); total (52/71)
Fisher's exact test for biased strand distribution p-value = 1.29e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.90e-01

Only 100 of 124 total aligned reads displayed.

CGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAGGGATCACCTGCATC  >  minE/1933674‑1933813

cGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATg                                                                       >  1:2840604/1‑71 (MQ=255)

    tACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTc                                                                     >  1:4741747/1‑69 (MQ=255)

      cacGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTc                                                                     >  1:5660354/1‑67 (MQ=255)

       acGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGAt                                                                <  1:2723919/71‑1 (MQ=255)

        cGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCgaga                                                                 <  1:3263218/69‑1 (MQ=255)

         gCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATcc                                                              <  1:3558803/71‑1 (MQ=255)

         gCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATcc                                                              <  1:925502/71‑1 (MQ=255)

          cTCGAAGCCACCAACCACCTGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCa                                                             <  1:2373747/71‑1 (MQ=255)

             gAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAg                                                            <  1:1307289/69‑1 (MQ=255)

               aGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGcgcg                                                        >  1:3754388/1‑71 (MQ=255)

               aGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGcgcg                                                        >  1:97304/1‑71 (MQ=255)

                gCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGt                                                       >  1:1466483/1‑71 (MQ=255)

                gCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGt                                                       <  1:530615/71‑1 (MQ=255)

                gCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGt                                                       <  1:5160679/71‑1 (MQ=255)

                 ccaccaACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCga                                                                   <  1:307660/58‑1 (MQ=255)

                 ccaccaACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCga                                                                   <  1:2140913/58‑1 (MQ=255)

                   accaaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAt                                                    <  1:1891689/71‑1 (MQ=255)

                     caaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAtgg                                                  <  1:5127902/71‑1 (MQ=255)

                     caaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATACAGCGCGTTAtgg                                                  <  1:2083800/71‑1 (MQ=255)

                      aaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAgc                                                           >  1:1710353/1‑61 (MQ=255)

                      aaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAgc                                                           >  1:3788737/1‑61 (MQ=255)

                      aaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAtggt                                                 >  1:768292/1‑71 (MQ=255)

                       accaccAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAtggtg                                                <  1:4447946/71‑1 (MQ=255)

                       accaccAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAtgg                                                  >  1:1444606/1‑69 (MQ=255)

                       acaaccaGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTatgatg                                                >  1:4548195/4‑71 (MQ=255)

                       acaaccaGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTatgatg                                                >  1:4321830/4‑71 (MQ=255)

                        caaccaGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTAtgatgg                                               >  1:1068133/3‑71 (MQ=255)

                          accaGACGTTTCAGATACAGCTCCGGTGCGATACGCAGATACATATCTAAATCCAGAGCATTATgatggg                                              >  1:415251/1‑70 (MQ=255)

                          accaGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATgatgggt                                             <  1:2784532/71‑1 (MQ=255)

                          accaGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATgatggg                                              >  1:829866/1‑70 (MQ=255)

                          accaGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATggtgggt                                             <  1:3568469/71‑1 (MQ=255)

                          accaGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATggtgggt                                             >  1:5677978/1‑71 (MQ=255)

                           ccaGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATgatgggt                                             >  1:1133008/1‑70 (MQ=255)

                           ccaGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATgatgggt                                             >  1:739177/1‑70 (MQ=255)

                            caGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGcgcg                                                        <  1:1430205/58‑1 (MQ=255)

                             aGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGa                                           >  1:1790977/1‑70 (MQ=255)

                              gACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATGATGGGTAAt                                          >  1:3131719/1‑70 (MQ=255)

                              gACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATa                                         <  1:585195/71‑1 (MQ=255)

                              gACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATa                                         <  1:3421319/71‑1 (MQ=255)

                                 gCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAAc                                      >  1:5113055/1‑71 (MQ=255)

                                 gCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAAc                                      <  1:4374755/71‑1 (MQ=255)

                                     gAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACgg                                    <  1:4481914/69‑1 (MQ=255)

                                     gAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACgg                                    <  1:5619305/69‑1 (MQ=255)

                                     gAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACgg                                    <  1:743625/69‑1 (MQ=255)

                                      agatACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATGATGGGTAATAAACGGGcg                                 <  1:4996120/68‑1 (MQ=255)

                                        gTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAt                                                    <  1:752053/50‑1 (MQ=255)

                                        atACAGCTCCGGCGCGATACGCATATACATATCTAAATCCAGAGCATTAt                                                    <  1:280149/49‑1 (MQ=255)

                                        atACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTAt                                                    <  1:4654202/49‑1 (MQ=255)

                                        atACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATGATGGGTAATAAACGGGcgag                               >  1:2999489/2‑69 (MQ=255)

                                        atACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATGATGGGTAATAAACGGGcgag                               >  1:5531915/2‑69 (MQ=255)

                                        atACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATGATGGGTAATAAACGGGcgag                               >  1:4868777/2‑69 (MQ=255)

                                         tACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGAcgcg                               >  1:1524639/1‑70 (MQ=255)

                                         tACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGAcgcg                               >  1:5297841/1‑70 (MQ=255)

                                          aCAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAtgg                                                  >  1:1514538/1‑50 (MQ=255)

                                          aCAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGAcgcg                               >  1:4957127/1‑69 (MQ=255)

                                           cAGTTCCGGTGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCa                             <  1:2054571/70‑1 (MQ=255)

                                           cAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCa                                                             <  1:5547392/38‑1 (MQ=255)

                                           cAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAg                            <  1:2744063/71‑1 (MQ=255)

                                           cAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATGATGGGTAATAAACGGGCGAGCa                             <  1:1520136/70‑1 (MQ=255)

                                           cAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATGATGGGTAATAAACGGGCGAGCa                             <  1:3098146/70‑1 (MQ=255)

                                             gTTCCGGCGCGATACGCAGGTACATGTCGAGATCCa                                                             <  1:5223067/36‑1 (MQ=255)

                                             gTTCCGGCGCGATACGCAGGTACATGTCGAGATCCa                                                             <  1:2269693/36‑1 (MQ=255)

                                             gTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCg                          >  1:2763614/1‑71 (MQ=255)

                                             gTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCg                          <  1:1366105/71‑1 (MQ=255)

                                              ttCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATa                                         <  1:3277419/55‑1 (MQ=255)

                                              ctCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATGATGGGTAATAAACGGGCGAGCa                             <  1:2434266/66‑1 (MQ=255)

                                               tCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCgg                         >  1:3631966/1‑70 (MQ=255)

                                               tCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCgg                         >  1:1682187/1‑70 (MQ=255)

                                                ccGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGc                        <  1:3232740/70‑1 (MQ=255)

                                                ccGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATGATGGGTAATAAACGGGCGAGCAga                           >  1:2668014/1‑66 (MQ=255)

                                                 cGGCGCGATTCGCAGGTACATGTCGAGATCCAGCGCGt                                                       <  1:1514816/38‑1 (MQ=255)

                                                 cGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGt                                                       <  1:4096482/38‑1 (MQ=255)

                                                 cGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCAc                      >  1:37593/1‑71 (MQ=255)

                                                 cGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATGATGGGTAATAAACGGGcga                                <  1:4585500/61‑2 (MQ=255)

                                                   gcgcGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGAc                                  <  1:2283399/57‑1 (MQ=255)

                                                    cgcgATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGCTAAACGGACGCGCAGCGGCACCGc                   <  1:5365137/71‑1 (MQ=255)

                                                       gATACGCAGGTACATGTCGAGATCCAGCGCGTTAt                                                    <  1:2186273/35‑1 (MQ=255)

                                                       gATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAg                <  1:1631914/71‑1 (MQ=255)

                                                       gATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAg                <  1:1173550/71‑1 (MQ=255)

                                                       gATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAg                <  1:1766010/71‑1 (MQ=255)

                                                        aTACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACg                                     <  1:2549212/49‑1 (MQ=255)

                                                        aTACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACg                                     <  1:886589/49‑1 (MQ=255)

                                                        aTACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAgg               >  1:4510568/1‑71 (MQ=255)

                                                        aTACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAgg               >  1:4463565/1‑71 (MQ=255)

                                                        aTACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAgg               >  1:3536593/1‑71 (MQ=255)

                                                         tACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGa                                           >  1:5393793/1‑42 (MQ=255)

                                                         tACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGa                                           >  1:4060995/1‑42 (MQ=255)

                                                         tACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGcc                  <  1:3841223/67‑1 (MQ=255)

                                                         tACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAggg              <  1:182418/71‑1 (MQ=255)

                                                           cGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCa                 >  1:2929089/1‑66 (MQ=255)

                                                           cGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAGGGa             <  1:3943651/70‑1 (MQ=255)

                                                            gCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCa                       <  1:211022/59‑1 (MQ=255)

                                                             cAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAGGGATCa          <  1:2229378/71‑1 (MQ=255)

                                                               ggTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACg                                     <  1:167878/42‑1 (MQ=255)

                                                                gTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAGGGATCACCt       <  1:2411358/71‑1 (MQ=255)

                                                                 tACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACgcgc                              <  1:4856365/47‑1 (MQ=255)

                                                                   cATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAAc                                      <  1:196368/37‑1 (MQ=255)

                                                                    aTGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAGGGATCACCTGcat   >  1:3289528/1‑71 (MQ=255)

                                                                    aTGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAGGGATCACCTGca    >  1:5083439/1‑70 (MQ=255)

                                                                     tGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGAcgcg                               <  1:1338097/42‑1 (MQ=255)

CGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGGACGCGCAGCGGCACCGCCAGGGATCACCTGCATC  >  minE/1933674‑1933813

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