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 1,933,711 G→C 35.9% L244L (CTC→CTG)  lysS ← lysine tRNA synthetase, constitutive

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,933,7110GC35.9% 111.2 / 115.2 117L244L (CTC→CTG) lysSlysine tRNA synthetase, constitutive
Reads supporting (aligned to +/- strand):  ref base G (38/37);  new base C (29/13);  total (67/50)
Fisher's exact test for biased strand distribution p-value = 7.90e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.44e-01

Only 100 of 121 total aligned reads displayed.

AAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGG  >  minE/1933641‑1933779
                                                                      |                                                                    
aaaTACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTg                                                                      <  1:4666974/71‑1 (MQ=255)
 aaTACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGa                                                                     <  1:2298181/71‑1 (MQ=255)
   tACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAga                                                                   <  1:5118977/71‑2 (MQ=255)
   tACCTTCATTACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAga                                                                   <  1:260610/71‑2 (MQ=255)
     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)
         cattACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAgc                                                             >  1:4430100/3‑70 (MQ=255)
         cGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAgg                                                                   >  1:1963701/1‑65 (MQ=255)
          attACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAgg                                                             <  1:5207271/69‑2 (MQ=255)
          attACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAgc                                                             <  1:2252117/69‑2 (MQ=255)
          attACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAgc                                                             <  1:1080444/69‑2 (MQ=255)
          attACGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTA‑AACCAGACGTTTCAGATACAGCTc                                                           >  1:2459265/2‑71 (MQ=255)
             aCGGAAGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTcc                                                          >  1:5351536/1‑70 (MQ=255)
             aCGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAg                                                                    >  1:421668/1‑60 (MQ=255)
             aCGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTcc                                                          <  1:2260078/70‑1 (MQ=255)
             aCGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCg                                                         >  1:3371058/1‑71 (MQ=255)
                 aaGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATa                                                                 >  1:5252360/1‑59 (MQ=255)
                 aaGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATa                                                                 >  1:917003/1‑59 (MQ=255)
                 aaGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATa                                                                 >  1:2971219/1‑59 (MQ=255)
                 aaGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATa                                                                 >  1:4202604/1‑59 (MQ=255)
                 aaGTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATa                                                                 >  1:5596705/1‑59 (MQ=255)
                 aaGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAg                                                              >  1:1566166/1‑62 (MQ=255)
                 aaGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGgcgc                                                     <  1:288199/71‑1 (MQ=255)
                 aaGTTACGGTTGATTTCGAATACACGCTCGAAGCCA‑CAACCACCAGACGCTTGAGGTACAg                                                              >  1:1682360/1‑61 (MQ=255)
                   gTTACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGa                                                   <  1:4795269/71‑1 (MQ=255)
                     tACGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATa                                                 >  1:2469760/1‑71 (MQ=255)
                      aCGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATa                                                 >  1:4185953/1‑70 (MQ=255)
                      aCGGTTGATTTCGAATACCCGTTCAAAACCGCCTACAACCAGACGTTTCAGATACAGCTCCGGCGCGATAc                                                >  1:4862806/1‑71 (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                                              <  1:5289292/71‑1 (MQ=255)
                        ggTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGc                                              <  1:1084355/71‑1 (MQ=255)
                        ggTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGc                                              <  1:3931902/71‑1 (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)
                                 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)
                                         cGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTAc                                        >  1:1057842/1‑60 (MQ=255)
                                         cGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTAc                                        >  1:2664894/1‑60 (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                                                           <  1:4190127/38‑1 (MQ=255)
                                             cGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACa                                       >  1:935990/1‑57 (MQ=255)
                                              gAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCg                                  <  1:446745/61‑1 (MQ=255)
                                              gAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAg                          <  1:1307289/69‑1 (MQ=255)
                                                aGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGcgcg                      >  1:3754388/1‑71 (MQ=255)
                                                 gCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGt                     >  1:1466483/1‑71 (MQ=255)
                                                 gCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGt                     <  1:530615/71‑1 (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)
                                                    accaaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAt                  >  1:2121995/1‑71 (MQ=255)
                                                      caaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAtgg                <  1:5127902/71‑1 (MQ=255)
                                                      caaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATACAGCGCGTTAtgg                <  1:2083800/71‑1 (MQ=255)
                                                       aaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGa                                                   >  1:5087035/1‑35 (MQ=255)
                                                       aaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGATACg                                               <  1:1845592/39‑1 (MQ=255)
                                                       aaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGATACg                                               <  1:149809/39‑1 (MQ=255)
                                                       aaccaCCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAgc                         >  1:3788737/1‑61 (MQ=255)
                                                        accaccAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTAtggtg              <  1:4447946/71‑1 (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)
                                                           accaGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACGTATCTAAATCCAGAGCATTATgatggg            >  1:3721280/1‑70 (MQ=255)
                                                           accaGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATgatgggt           <  1:2784532/71‑1 (MQ=255)
                                                           accaGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATgatggg            >  1:3398683/1‑70 (MQ=255)
                                                           accaGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATgatggg            >  1:829866/1‑70 (MQ=255)
                                                           accaGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATggtgggt           <  1:3568469/71‑1 (MQ=255)
                                                            ccaGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATgatgggt           >  1:739177/1‑70 (MQ=255)
                                                            ccaGACGTTTCAGATACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATgatgggt           >  1:1133008/1‑70 (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       <  1:585195/71‑1 (MQ=255)
                                                               gACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATa       <  1:3421319/71‑1 (MQ=255)
                                                                aCGTTTCAGATACAGCTCCGGCGCGATACGCAGATACATATCTAAATCCAGAGCATTATGATGGGtaataa      <  1:1714656/71‑1 (MQ=255)
                                                                  gCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAAc    >  1:5113055/1‑71 (MQ=255)
                                                                  gCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAAc    <  1:4374755/71‑1 (MQ=255)
                                                                      gAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACgg  <  1:5619305/69‑1 (MQ=255)
                                                                      gAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACgg  <  1:743625/69‑1 (MQ=255)
                                                                      |                                                                    
AAATACCTTCGTTACGGAAGTTACGGTTGATTTCGAATACACGCTCGAAGCCACCAACCACCAGACGCTTGAGGTACAGTTCCGGCGCGATACGCAGGTACATGTCGAGATCCAGCGCGTTATGGTGGGTGATAAACGG  >  minE/1933641‑1933779

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