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 1,933,189 A→G 48.2% I418I (ATT→ATC)  lysS ← lysine tRNA synthetase, constitutive

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,933,1890AG48.2% 3.5 / 145.6 108I418I (ATT→ATC) lysSlysine tRNA synthetase, constitutive
Reads supporting (aligned to +/- strand):  ref base A (30/26);  new base G (21/31);  total (51/57)
Fisher's exact test for biased strand distribution p-value = 1.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.57e-01

Only 100 of 117 total aligned reads displayed.

AGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGGAGAAAC  >  minE/1933121‑1933254
                                                                    |                                                                 
aGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAAt                                                                 <  1:43334/71‑1 (MQ=255)
aGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAAt                                                                 <  1:4794449/71‑1 (MQ=255)
 ggAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAAt                                                                 >  1:406378/1‑70 (MQ=255)
  gAAACGTTCAGCCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGACCACCGATg                                                                <  1:2011664/70‑1 (MQ=255)
  gAAACGTTCAGCCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGACCACCGATg                                                                <  1:2241059/70‑1 (MQ=255)
    aGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATgaag                                                             <  1:391826/71‑1 (MQ=255)
    aGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATgaag                                                             <  1:1850030/71‑1 (MQ=255)
     gCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATgaag                                                             >  1:4574801/1‑70 (MQ=255)
        ttGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACt                                                         <  1:5328050/71‑1 (MQ=255)
          gcgcCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCaa                                                                  >  1:1466576/1‑60 (MQ=255)
          cagcCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGACCACCGATga                                                               >  1:4404693/3‑63 (MQ=255)
          cagcCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGACCACCGATGAAGAATTc                                                        >  1:1032166/3‑70 (MQ=255)
          cagcCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGACCACCGATGAAGAATTc                                                        >  1:4696600/3‑70 (MQ=255)
           agcCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGACCACCGATGAAGAATTCaa                                                      <  1:3293834/70‑1 (MQ=255)
           agcCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGACCACCGATGAAGAATTCaa                                                      <  1:4362054/70‑1 (MQ=255)
           agcCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGACCACCGATGAAGAATTCaa                                                      <  1:4686757/70‑1 (MQ=255)
           agcCTGATCTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGACCACCGATGAAGAATTCa                                                       <  1:3045636/69‑1 (MQ=255)
            gcCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCa                                                       >  1:300300/1‑69 (MQ=255)
             ccTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATga                                                               <  1:4215128/60‑1 (MQ=255)
             ccTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATga                                                               <  1:2214339/60‑1 (MQ=255)
             ccTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATg                                                                <  1:1356268/59‑1 (MQ=255)
              cTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGc                                                   >  1:1817262/1‑71 (MQ=255)
                gATCTTCTGCGTCGTTTAATTCGCTAAAACCATTAACGATTTCACGACCACCGATGAAGAATTCAAAACgg                                                 >  1:579612/1‑71 (MQ=255)
                 aTCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGt                                                >  1:5260041/1‑71 (MQ=255)
                   cTTCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGACCACCGATGAAGAATTCAAAACGGTc                                               >  1:162298/1‑70 (MQ=255)
                   cTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCt                                              >  1:83250/1‑71 (MQ=255)
                    ttCTGCGTCGTTTAATTCGCTAAAACCATTACCGATTTCACGACCACCGATGAAGAATTCAAAACGGTcgg                                             >  1:5093520/1‑69 (MQ=255)
                    ttCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCaa                                                                  >  1:2649409/1‑50 (MQ=255)
                      ccGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGt                                                <  1:3795329/66‑1 (MQ=255)
                      ccGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCtgt                                            <  1:148358/70‑1 (MQ=255)
                      ccGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCt                                              <  1:181014/68‑1 (MQ=255)
                       cgcgTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCtgtg                                           <  1:5053157/70‑1 (MQ=255)
                         cgTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGAtt                                        <  1:1958619/71‑1 (MQ=255)
                            cATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTc                                               <  1:1971917/61‑1 (MQ=255)
                             aTTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAAt                                                                 <  1:2417751/42‑1 (MQ=255)
                             aTTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTcc                                     <  1:1360530/70‑1 (MQ=255)
                              ttCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCaa                                                                  <  1:4072196/40‑1 (MQ=255)
                              ttCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCaa                                                                  <  1:687521/40‑1 (MQ=255)
                               tCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCggg                                  >  1:4314297/1‑71 (MQ=255)
                                 aGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGt                                 >  1:5368628/1‑70 (MQ=255)
                                 aGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGt                                 >  1:3826387/1‑70 (MQ=255)
                                  attCGCTAAAACCATTACCGATTTCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGtt                                <  1:4205209/68‑1 (MQ=255)
                                   ttCGCTAAAACCATTACCGATTTCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTc                                      <  1:3011458/62‑1 (MQ=255)
                                   ttCGCTAAAACCATTACCGATTTCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTaa                              >  1:1234982/2‑71 (MQ=255)
                                    tCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAAc                             >  1:3613736/1‑71 (MQ=255)
                                    tCGCTAAAACCATTACCGATTTCACGACCACCGATGAAGAATTCaa                                                      <  1:3771975/46‑1 (MQ=255)
                                     cGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCg                                    >  1:2196321/1‑63 (MQ=255)
                                     cGCTAAAACCATTACCGATTTCACGACCACCGATgaaga                                                            >  1:451785/1‑39 (MQ=37)
                                     cGCTAAAACCATTACCGATTTCACGACCACCGATgaaga                                                            >  1:5382863/1‑39 (MQ=37)
                                     cGCTAAAACCATTACCGATTTCACGACCACCGATGAAGAATTCaaaa                                                    >  1:4452849/1‑46 (MQ=255)
                                      gCTAAAGCCGTTACCGATTTCACGACCACCAATga                                                               >  1:3170531/1‑35 (MQ=255)
                                      gCTAAAGCCGTTACCGATTTCACGACCACCAATga                                                               >  1:2763212/1‑35 (MQ=255)
                                      gCTAAAACCATTACCGATTTTACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAAcat                           <  1:4925232/71‑3 (MQ=255)
                                      gCTAAAACCATTACCGATTTCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAAca                            <  1:5627787/70‑2 (MQ=255)
                                         aaaaCCATTACCGATTTCACGACCACCGATGAAGAATTc                                                        <  1:4824171/39‑1 (MQ=25)
                                         aaaaCCATTACCGATTTCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAAcatcat                        >  1:2585388/1‑69 (MQ=255)
                                         aaaaCCATTACCGATTTCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAAcatcat                        >  1:2156035/1‑69 (MQ=255)
                                         aaaGCCGTTACCGATTTCACGACCACCAATgaagaa                                                           >  1:4497982/1‑36 (MQ=255)
                                         aaaGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAAcgtcgt                        >  1:5640703/1‑71 (MQ=255)
                                           aGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGc                                                   <  1:5349877/42‑1 (MQ=255)
                                            gCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTac                     >  1:2357625/1‑71 (MQ=255)
                                            gCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTac                     >  1:3650974/1‑71 (MQ=255)
                                            gCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTac                     >  1:3459425/1‑71 (MQ=255)
                                            gCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTac                     >  1:1998655/1‑71 (MQ=255)
                                              cattACCGATTTCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAACATCATTacgg                   <  1:217585/69‑2 (MQ=255)
                                                ttAGCGATTTCACGACCACCGATGAAGAATTCAAAACg                                                  <  1:5633858/38‑1 (MQ=25)
                                                ttACCGATTTCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAAcatcat                        <  1:4769723/64‑3 (MQ=255)
                                                ttACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGAttt                                       >  1:1390382/1‑49 (MQ=255)
                                                 tACCGATTTCACGACCACCGATGAAGAATTCAAAACGGTCGGTGa                                          >  1:3099723/1‑45 (MQ=255)
                                                 tACCGATTTCACGACCACCGATGAAGAATTCAAAACGGTCGGTGa                                          >  1:5626423/1‑45 (MQ=255)
                                                 gaCCGATTTCACGACCACCGATGAAGAATTCAAAACGGTCGGTGa                                          >  1:5177432/2‑45 (MQ=255)
                                                  aCCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGAt                                         >  1:3840602/1‑45 (MQ=255)
                                                  aCCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGAcgcg               >  1:1279968/1‑71 (MQ=255)
                                                      aTTTCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAAcatcat                        >  1:1087368/1‑56 (MQ=255)
                                                      aTTTCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAACATCATTACGGCGTGCCAg           <  1:784231/71‑1 (MQ=255)
                                                      aTTTCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAACATCATTACGGCGTGCCAg           <  1:5034452/71‑1 (MQ=255)
                                                      aTTTCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAACATCATTACGGCGTGCCAg           <  1:5182046/71‑1 (MQ=255)
                                                      aTTTCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAACATCATTACGGCGTGCCAg           >  1:610317/1‑71 (MQ=255)
                                                      aTTTCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAACATCATTACGGCGTGCCAg           <  1:4415099/71‑1 (MQ=255)
                                                      aTTTCACGACCACCAATGAAGAACTCAAAGCGGTCtgtg                                           <  1:5181708/39‑1 (MQ=255)
                                                       tttCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAACATCATTacggcgtg               <  1:4017068/66‑3 (MQ=255)
                                                       tttCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAACATCATTACGGCGTGCCAGc          <  1:114508/71‑1 (MQ=255)
                                                       tttCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAACATCATTACGGCGTGCCAGc          <  1:4345069/71‑1 (MQ=255)
                                                       tttCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGc          <  1:1902831/71‑1 (MQ=255)
                                                       tttCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGc          <  1:2494489/71‑1 (MQ=255)
                                                        ttCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAAc                             >  1:1764189/1‑51 (MQ=255)
                                                        ttCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAAc                             >  1:170271/1‑51 (MQ=255)
                                                         tCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAACATCATTACGGCGTGcc             >  1:3604451/1‑66 (MQ=255)
                                                         tCACGACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAACATCATTACGGCGTGCCAGCg         <  1:2327593/70‑1 (MQ=255)
                                                          cACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCg         <  1:1954216/69‑1 (MQ=255)
                                                           aCGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAAcgtcgt                        >  1:4191302/1‑53 (MQ=255)
                                                            cGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGGCAGCGgag      >  1:4861846/1‑70 (MQ=255)
                                                            cGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGgag      >  1:2485440/1‑70 (MQ=255)
                                                             gACCACCGATGAAGAATTCAAAACGGTCGGTGATTTCCGGGTTAACATCATTACGGCTTGCCAGCGgggac    <  1:4978718/71‑2 (MQ=255)
                                                              accaccAATGAAGAACTCTAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTac                     <  1:5526757/53‑1 (MQ=255)
                                                               ccaccaATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGGAGAAAc  >  1:1245625/1‑71 (MQ=255)
                                                               ccaccaATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGGAGAAAc  >  1:1928819/1‑71 (MQ=255)
                                                                 accaATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGGAGaa    <  1:5295457/67‑1 (MQ=255)
                                                                    aaTGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGcc             >  1:5497285/1‑55 (MQ=255)
                                                                    aaTGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGcc             >  1:3819135/1‑55 (MQ=255)
                                                                    |                                                                 
AGGAAGCGTTGCGCCTGATCTTCCGCGTCATTCAGCTCGCTAAAGCCGTTACCGATTTCACGACCACCAATGAAGAACTCAAAGCGGTCTGTGATTTCCGGGTTAACGTCGTTACGACGCGCCAGCGGAGAAAC  >  minE/1933121‑1933254

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