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	1,933,714	G→A	34.8%	Y243Y (TAC→TAT)	lysS ←	lysine tRNA synthetase, constitutive

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,933,714	0	G	A	34.8%	120.7 / 99.9	115	Y243Y (TAC→TAT)	lysS	lysine tRNA synthetase, constitutive
Reads supporting (aligned to +/- strand): ref base G (36/39); new base A (29/11); total (65/50)
Fisher's exact test for biased strand distribution p-value = 1.73e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.44e-01

Only 100 of 117 total aligned reads displayed.

CCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGG  >  minE/1933646‑1933779

ccTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATa                                                                 <  1:4856855/71‑1 (MQ=255)

 cTTCGTTACGGAAGTTTCGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTAc                                                                <  1:3647018/71‑1 (MQ=255)

 cTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTAc                                                                <  1:187276/71‑1 (MQ=255)

  ttCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGtg                                                                 >  1:1564411/1‑68 (MQ=255)

  ttCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTa                                                                 >  1:604968/1‑69 (MQ=255)

  ttCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATa                                                                 >  1:2430177/1‑69 (MQ=255)

    cattACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAgc                                                             >  1:4430100/3‑70 (MQ=255)

    cGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAgg                                                                   >  1:1963701/1‑65 (MQ=255)

     attACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAgg                                                             <  1:5207271/69‑2 (MQ=255)

     attACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAgc                                                             <  1:1080444/69‑2 (MQ=255)

     attACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAgc                                                             <  1:2252117/69‑2 (MQ=255)

        aCGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTcc                                                          >  1:5351536/1‑70 (MQ=255)

        aCGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCg                                                         >  1:5008196/1‑71 (MQ=255)

        aCGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTcc                                                          <  1:2260078/70‑1 (MQ=255)

        aCGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCg                                                         >  1:3371058/1‑71 (MQ=255)

            aaGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATa                                                                 >  1:4202604/1‑59 (MQ=255)

            aaGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATa                                                                 >  1:5596705/1‑59 (MQ=255)

            aaGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATa                                                                 >  1:5252360/1‑59 (MQ=255)

            aaGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATa                                                                 >  1:917003/1‑59 (MQ=255)

            aaGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAg                                                              >  1:1566166/1‑62 (MQ=255)

            aaGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGgcgc                                                     <  1:288199/71‑1 (MQ=255)

            aaGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGgcgc                                                     <  1:2875600/71‑1 (MQ=255)

            aaGTTACGGTTGATTTCGAATACACGCTCGAAGCCA‑CAACCACCAGACGCTTGAGGTACAg                                                              >  1:1682360/1‑61 (MQ=255)

              gTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGa                                                   <  1:4795269/71‑1 (MQ=255)

                tACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATa                                                 >  1:2469760/1‑71 (MQ=255)

                 aCGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATAc                                                >  1:4862806/1‑71 (MQ=255)

                 aCGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGgcgc                                                     >  1:5387034/1‑66 (MQ=255)

                  cGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATACg                                               >  1:4656395/1‑71 (MQ=255)

                   ggTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACG‑TTCAGATACAGCTCCGGCGCGATACGCa                                             <  1:201603/71‑1 (MQ=255)

                   ggTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGc                                              <  1:3248809/71‑1 (MQ=255)

                   ggTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGc                                              <  1:3931902/71‑1 (MQ=255)

                   ggTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGc                                              <  1:5289292/71‑1 (MQ=255)

                   ggTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGc                                              <  1:1084355/71‑1 (MQ=255)

                     ttGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATACGCa                                             <  1:665385/70‑1 (MQ=255)

                       gATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAg                                                              >  1:481697/1‑51 (MQ=255)

                        aTTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATa                                         <  1:4404712/71‑1 (MQ=255)

                          ttCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACa                                       >  1:2757169/1‑71 (MQ=255)

                           tCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACa                                       >  1:490592/1‑70 (MQ=255)

                           tCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACa                                       >  1:3019741/1‑70 (MQ=255)

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

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

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

                                    cGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTAc                                        >  1:1057842/1‑60 (MQ=255)

                                    cGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTAc                                        >  1:2671457/1‑60 (MQ=255)

                                    cGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTAc                                        >  1:2664894/1‑60 (MQ=255)

                                    cGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTAc                                        >  1:1303601/1‑60 (MQ=255)

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

                                    cGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATc                             <  1:2306737/71‑1 (MQ=255)

                                    cGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATc                             <  1:5599401/71‑1 (MQ=255)

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

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

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

                                      cTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGc                                              >  1:2788999/1‑52 (MQ=255)

                                      cTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGc                                              >  1:1380682/1‑52 (MQ=255)

                                      cTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGc                                              >  1:1373156/1‑52 (MQ=255)

                                      cTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACaa                                      >  1:362631/1‑59 (MQ=255)

                                       tCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTc                                                           <  1:1940562/38‑1 (MQ=255)

                                       tCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTc                                                           <  1:4190127/38‑1 (MQ=255)

                                        cGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACa                                       >  1:935990/1‑57 (MQ=255)

                                         gAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCg                                  <  1:446745/61‑1 (MQ=255)

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

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

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

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

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

                                              caccaACCACCAGACGCTTGAGGTACAGTTCCGgcgc                                                     >  1:2939465/1‑37 (MQ=255)

                                              caccaACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTa                                         >  1:252778/1‑49 (MQ=255)

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

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

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

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

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

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

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

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

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

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

                                                     caccaGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCga                                 >  1:1355163/1‑50 (MQ=255)

                                                     aaccaGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACa                                       >  1:287815/2‑44 (MQ=19)

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

                                                      accaGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACGTATCTAAATCCAGAGCATTATgatggg            >  1:3721280/1‑70 (MQ=255)

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

                                                      accaGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATgatggg            >  1:3398683/1‑70 (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)

                                                       ccaGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATgatggg            >  1:4618509/1‑69 (MQ=255)

                                                       ccaGACGCTTGAGGTACAGTTCTGGCGCGAAACGCAGGTACa                                       >  1:5536718/1‑42 (MQ=38)

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

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

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

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

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

                                                           aCGTTTCAGATACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATGATGGGtaataa      <  1:1714656/71‑1 (MQ=255)

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

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

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

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

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

CCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGG  >  minE/1933646‑1933779

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