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	1,933,276	G→A	38.0%	F389F (TTC→TTT)	lysS ←	lysine tRNA synthetase, constitutive

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,933,276	0	G	A	38.0%	114.1 / 125.3	129	F389F (TTC→TTT)	lysS	lysine tRNA synthetase, constitutive
Reads supporting (aligned to +/- strand): ref base G (35/45); new base A (30/19); total (65/64)
Fisher's exact test for biased strand distribution p-value = 6.98e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 135 total aligned reads displayed.

GTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACC  >  minE/1933211‑1933344

gtgATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGt                                                                 >  1:4739304/1‑71 (MQ=255)

 tgATTTCCGGGTTAACGTCGTTACGACGCGCAAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTc                                                                >  1:4597413/1‑71 (MQ=255)

 tgATTTCCGGGTTAACATCATTACGGCGTGCCAGCGGGGACACTTCTGCCGGATATTCCGTAATAAAGGtt                                                                <  1:310383/71‑2 (MQ=255)

        cGGGTTAACGTCGTTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGaa                                                         >  1:239370/1‑71 (MQ=255)

           gTTAACGTCGTTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAAt                                                        >  1:5534655/1‑69 (MQ=255)

           gTTAACATCATTACGGCGTGCCAGCGGGGACACTTCTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCa                                                      <  1:5486266/71‑1 (MQ=255)

            ttAACGTCGTTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAg                                                     <  1:5676097/71‑1 (MQ=255)

            ttAACATCATTACGGCGTGCCAGCGGGGACACTTCTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAg                                                     <  1:2243293/71‑1 (MQ=255)

              aaCGTCGTTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGa                                                    <  1:1599594/70‑1 (MQ=255)

              aaCATCATTACGGCGTGCCAGCGGGGACACTTCTGCCGGATATTCCGTAATAAAGGTTGGCTGaa                                                         >  1:5617751/1‑65 (MQ=255)

              aaCATCATTACGGCGTGCCAGCGGGGACACTTCTGCCGGATATTCCGTAATAAAGGTTGGCTGaa                                                         >  1:1530850/1‑65 (MQ=255)

              aaCATCATTACGGCGTGCCAGCGGGGACACTTCTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGAt                                                   >  1:4055516/1‑71 (MQ=255)

                cgtcgtTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATg                                                                      <  1:2597515/50‑1 (MQ=255)

                cgtcgtTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATg                                                                      <  1:3767432/50‑1 (MQ=255)

                  tcattACGGCGTGCCAGCGGGGACACTTCTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGa                                                    >  1:5360930/4‑66 (MQ=255)

                  tcattACGGCGTGCCAGCGGGGACACTTCTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGAtg                                                  <  1:2922824/65‑1 (MQ=255)

                    gtTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCtt                                             >  1:2449454/1‑71 (MQ=255)

                    gtTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCtt                                             <  1:3358170/71‑1 (MQ=255)

                    attACGGCGTGCCAGCGGGGACACTTCTGCCGGATATTCCGTAATAAAg                                                                   >  1:580606/2‑49 (MQ=19)

                    attACGGCGTGCCAGCGGGGACACTTCTGCCGGATATTCCGTAATAAAg                                                                   >  1:4785117/2‑49 (MQ=19)

                    attACGGCGTGCCAGCGGGGACACTTCTGCCGGATATTCCGTAATAAAGGtt                                                                >  1:2834892/2‑51 (MQ=19)

                    attACGGCGTGCCAGCGGGGACACTTCTGCCGGATATTCCGTAATAAAGGtt                                                                >  1:4030066/2‑51 (MQ=19)

                     ttACGGCGTGCCAGCGGGGACACTTCTGCCGGATATTCCGTAATaaa                                                                    <  1:2350342/47‑1 (MQ=19)

                     ttACGGCGTGCCAGCGGGGACACTTCTGCCGGATATTCCGTAATAAAGGttg                                                               <  1:3570228/52‑3 (MQ=19)

                     ttACGGCGTGCCAGCGGGGACACTTCTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTc                                            >  1:2088010/1‑71 (MQ=255)

                      tACGGCGTGCCAGCGGGGACACTTCTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCa                                                      <  1:40475/60‑1 (MQ=255)

                         gacgCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGcc                                        <  1:3442001/71‑1 (MQ=255)

                           cgcgCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCAc                                      <  1:2829183/71‑1 (MQ=255)

                            gcgcCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAAt                                                        <  1:5121648/52‑1 (MQ=255)

                               ccAGCGGGGACACTTCTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCActtca                                  >  1:5224330/1‑70 (MQ=255)

                               ccAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCActtct                                  >  1:243279/1‑71 (MQ=255)

                                cAGCGGGGACACTTCTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCtt                                             <  1:366448/59‑1 (MQ=255)

                                  gCGGGGACACTTCTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCActtcata                                >  1:4625207/1‑67 (MQ=255)

                                  gCGGAGAAACTTCTGCCGGATATTCAGTAATGAAgg                                                                  >  1:2318334/1‑36 (MQ=255)

                                  gCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCg                               <  1:934750/71‑1 (MQ=255)

                                   cGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGcc                                        <  1:336913/61‑1 (MQ=255)

                                     gagaAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCAc                                      >  1:2806325/1‑61 (MQ=255)

                                     gagaAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCAc                                      >  1:3008522/1‑61 (MQ=255)

                                       gaAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGc                                               <  1:1816081/50‑1 (MQ=255)

                                       gaAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGAt                          <  1:1459244/71‑1 (MQ=255)

                                       gaAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGAt                          <  1:1602002/71‑1 (MQ=255)

                                        aaaCTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGAtc                         <  1:3332629/71‑1 (MQ=255)

                                         caCTTCTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGa                                                    >  1:4206593/2‑43 (MQ=25)

                                         aaCTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGAtct                        >  1:4452494/1‑71 (MQ=255)

                                          aCTTCTGCCGGATATTCCGTAATAAAGGTTGGCTGaa                                                         >  1:686656/1‑37 (MQ=25)

                                          aCTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGAtctc                       >  1:3067115/1‑71 (MQ=255)

                                           cTTCTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGc                                               <  1:2199425/46‑1 (MQ=37)

                                           cTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAg                            <  1:125500/65‑1 (MQ=255)

                                            ttCTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGc                                               <  1:4661222/45‑1 (MQ=38)

                                            ttCTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCaaa                             >  1:4159003/1‑63 (MQ=255)

                                            ttCTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGAtctctg                     >  1:1675878/1‑69 (MQ=255)

                                            ttCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGa                                                    >  1:2596696/1‑40 (MQ=255)

                                            ttCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGAt                                                   >  1:3007052/1‑41 (MQ=255)

                                            ttCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCgg                     >  1:659157/1‑71 (MQ=255)

                                            ttCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGAGCTTCTGCCACTTCTTCGAAGATCTCgg                     >  1:2016147/1‑71 (MQ=255)

                                             tCTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCtt                                             >  1:1080521/1‑46 (MQ=255)

                                             tCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGAt                          >  1:3369534/1‑65 (MQ=255)

                                             tCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGAt                          >  1:2316289/1‑65 (MQ=255)

                                              cTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGAt                                                   >  1:2297552/1‑39 (MQ=37)

                                              cTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGAt                                                   >  1:4871786/1‑39 (MQ=37)

                                              cTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGAt                                                   >  1:1123035/1‑39 (MQ=37)

                                              cTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGt                    >  1:1264060/1‑70 (MQ=255)

                                                 ccGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAAc                 <  1:5257695/70‑1 (MQ=255)

                                                 ccGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAAc                 <  1:2198002/70‑1 (MQ=255)

                                                 ccGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAAc                 <  1:4175604/70‑1 (MQ=255)

                                                 ccGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAAc                 <  1:3331715/70‑1 (MQ=255)

                                                 ccGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAAc                 <  1:5251145/70‑1 (MQ=255)

                                                 ccGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACg                <  1:2950561/71‑1 (MQ=255)

                                                  cGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGAcaa               <  1:3572823/71‑3 (MQ=255)

                                                  cGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGAcaa               <  1:3931061/71‑3 (MQ=255)

                                                  cGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGAcaa               <  1:1224416/71‑3 (MQ=255)

                                                  cGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa               <  1:688790/71‑1 (MQ=255)

                                                   ggATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAAt              <  1:2151697/71‑1 (MQ=255)

                                                   ggATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGAt              <  1:4125749/71‑1 (MQ=255)

                                                     atatTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATAc            <  1:1503976/71‑1 (MQ=255)

                                                     atatTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATAc            >  1:5397678/1‑71 (MQ=255)

                                                         tCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGa                              <  1:2718328/49‑1 (MQ=255)

                                                         tCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGa                              <  1:5684663/49‑1 (MQ=255)

                                                         tCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGcc        >  1:3587386/1‑71 (MQ=255)

                                                         tCAGTAATGAAGGTCGGATGAATCAGATGTGCTTCTGCCACTTCTTCGa                              <  1:3886211/49‑1 (MQ=255)

                                                          ccgTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTcc        >  1:880591/3‑70 (MQ=255)

                                                          ccgTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTcc        >  1:228746/3‑70 (MQ=255)

                                                          cAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCg                      >  1:4408036/1‑56 (MQ=255)

                                                          cAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGcc        >  1:1606530/1‑70 (MQ=255)

                                                           cgTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTccc       <  1:5349380/69‑1 (MQ=255)

                                                           cgTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTcc        >  1:4073074/2‑69 (MQ=255)

                                                           aGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCa      <  1:3773351/71‑1 (MQ=255)

                                                             taataaAGGTTGGCTGAATCAGATGTGCTTCTGCCACttcatca                               <  1:2489814/44‑2 (MQ=37)

                                                             taataaAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCaac    <  1:2622100/71‑3 (MQ=255)

                                                              aaTGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAg                            <  1:3744015/46‑1 (MQ=255)

                                                              aaTGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGa    <  1:3029277/70‑1 (MQ=255)

                                                              aaTGAAGCTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAc   >  1:3738040/1‑71 (MQ=255)

                                                               aTGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAcc  >  1:5092796/1‑71 (MQ=255)

                                                               aTGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAcc  >  1:2666226/1‑71 (MQ=255)

                                                               aTGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAcc  >  1:3130815/1‑71 (MQ=255)

                                                                tGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGAtc                         <  1:4082040/47‑1 (MQ=255)

                                                                tGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa               <  1:171847/57‑1 (MQ=255)

                                                                tGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa               <  1:4639703/57‑1 (MQ=255)

                                                                tGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa               <  1:3930688/57‑1 (MQ=255)

                                                                tGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa               <  1:1088435/57‑1 (MQ=255)

GTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACC  >  minE/1933211‑1933344

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