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	1,933,681	A→C	37.9%	R254R (CGT→CGG)	lysS ←	lysine tRNA synthetase, constitutive

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,933,681	0	A	C	37.9%	53.4 / 142.6	124	R254R (CGT→CGG)	lysS	lysine tRNA synthetase, constitutive
Reads supporting (aligned to +/- strand): ref base A (41/36); new base C (31/16); total (72/52)
Fisher's exact test for biased strand distribution p-value = 1.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

Only 100 of 127 total aligned reads displayed.

CATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGAT  >  minE/1933612‑1933751

   ggTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACg                                                                      >  1:780594/1‑69 (MQ=255)

    gTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCt                                                                    <  1:3970881/70‑1 (MQ=255)

    gTGAACTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCgtt                                                                    >  1:1080564/1‑68 (MQ=255)

     tGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCg                                                                  <  1:1146341/71‑1 (MQ=255)

       aaCTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGaa                                                                <  1:430150/71‑1 (MQ=255)

       aaCTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGaa                                                                <  1:4527674/71‑1 (MQ=255)

       aaCTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTcaa                                                                 <  1:2987779/70‑3 (MQ=255)

       aaCTCAGGATTATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTcaa                                                                 >  1:3317304/1‑68 (MQ=255)

         ctctGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGc                                                              >  1:4649937/1‑71 (MQ=255)

         ctctGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGc                                                              <  1:4084731/71‑1 (MQ=255)

         ctctGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGc                                                              <  1:5195268/71‑1 (MQ=255)

            tGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGa                                                                 <  1:4923416/65‑1 (MQ=255)

            tGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGa                                                                 <  1:4519719/65‑1 (MQ=255)

            tGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGa                                                                 <  1:675965/65‑1 (MQ=255)

            tGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGccac                                                           >  1:5437985/1‑71 (MQ=255)

            tGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGccac                                                           >  1:2777119/1‑71 (MQ=255)

            tGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTAAGGTTGATTTCGAATACACGCTCGAAGccac                                                           >  1:2157608/1‑71 (MQ=255)

             gggTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTACGAATACACGCTCGAAGccac                                                           >  1:2774212/1‑70 (MQ=255)

              ggTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAg                                                               >  1:2616005/1‑65 (MQ=255)

              ggTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGccacc                                                          <  1:4870123/70‑1 (MQ=255)

              gattATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAAccgcc                                                          >  1:4934209/3‑70 (MQ=255)

               gTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCaccaa                                                        >  1:2757253/1‑71 (MQ=255)

                ttATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAAccgccta                                                        >  1:4819371/1‑68 (MQ=255)

                ttATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAAccgccta                                                        >  1:5319967/1‑68 (MQ=255)

                ttATGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCgcctac                                                       <  1:3838952/71‑1 (MQ=255)

                  aTGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCaaaa                                                               >  1:277397/1‑60 (MQ=255)

                  aTGGCGAACAGAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCgcctacaa                                                     >  1:748797/1‑69 (MQ=255)

                   tGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGcca                                                            >  1:4435687/1‑63 (MQ=255)

                     aCGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAaccac                                                    >  1:1326860/1‑69 (MQ=255)

                      cGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAg                                                 <  1:1516433/71‑1 (MQ=255)

                         aCGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACg                                              >  1:1033978/1‑71 (MQ=255)

                          cagAAATACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACgt                                             <  1:4399028/69‑2 (MQ=255)

                            gAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGgcacc                                                          >  1:421049/1‑56 (MQ=255)

                            gAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCtt                                           >  1:2675331/1‑71 (MQ=255)

                            gAAATACCTTCATTACGGAAGTTATGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGttt                                           >  1:3821128/1‑71 (MQ=255)

                             aaaTACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCg                                                                  <  1:3268977/47‑1 (MQ=255)

                             aaaTACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGcca                                                            >  1:1239092/1‑53 (MQ=255)

                             aaaTACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGcca                                                            >  1:376949/1‑53 (MQ=255)

                             aaaTACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTg                                          <  1:4666974/71‑1 (MQ=255)

                              aaTACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGa                                         <  1:2298181/71‑1 (MQ=255)

                               aTACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGttt                                           >  1:5186520/1‑68 (MQ=255)

                                tACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAga                                       <  1:5118977/71‑2 (MQ=255)

                                  ccTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCgcctacaa                                                     >  1:3994674/1‑53 (MQ=255)

                                  ccTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTacaac                                                    >  1:1873826/1‑56 (MQ=255)

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

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

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

                                    ttCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGccacca                                                         <  1:5360544/49‑1 (MQ=255)

                                    ttCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGccacca                                                         <  1:3893942/49‑1 (MQ=255)

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

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

                                    ttCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAAcc                                                             <  1:1435071/45‑1 (MQ=25)

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

                                      cGTTACGGAAGTTACGGTTGATTTCGAATACACGCTc                                                                   >  1:5012709/1‑37 (MQ=255)

                                      cGTTACGGAAGTTACGGTTGATTTCGAATACACGCTc                                                                   >  1:2656446/1‑37 (MQ=255)

                                      cGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGcca                                                            >  1:1274171/1‑44 (MQ=255)

                                      cGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGcca                                                            >  1:1972426/1‑44 (MQ=255)

                                      cGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGcc                                                             >  1:2008424/1‑43 (MQ=255)

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

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

                                       attACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTA‑AACCAGACGTTTCAGATACAGCTc                               >  1:2459265/2‑71 (MQ=255)

                                          aCGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAAccgcc                                                          >  1:282983/1‑42 (MQ=19)

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

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

                                          aCGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAg                                        >  1:421668/1‑60 (MQ=255)

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

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

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

                                              aaGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATa                                     >  1:2971219/1‑59 (MQ=255)

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

                                              aaGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATa                                     >  1:5252360/1‑59 (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)

                                                gTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCtt                                           <  1:3189958/51‑1 (MQ=255)

                                                gTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCtt                                           <  1:515468/51‑1 (MQ=255)

                                                gTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCtt                                           <  1:4129044/51‑1 (MQ=255)

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

                                                   aCGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACgt                                             >  1:2275108/1‑45 (MQ=12)

                                                   aCGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATa                     >  1:4185953/1‑70 (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                  <  1:1084355/71‑1 (MQ=255)

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

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

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

                                                       ttGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAg                >  1:3631369/1‑71 (MQ=255)

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

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

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

                                                             tCGAATACACGCTCGAAGCCACCAACCACCAGACGCt                                            >  1:4662182/1‑37 (MQ=255)

                                                             tCGAATACACGCTCGAAGCCACCAACCACCAGACGCt                                            >  1:2582511/1‑37 (MQ=255)

                                                              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)

CATGGTGAACTCTGGGTTATGACGTACGGAAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGAT  >  minE/1933612‑1933751

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