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
A2 F3 I0 R2 232 76.3 4135488 90.9% 3759158 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 430,231 G→A 22.7% D280N (GAC→AAC)  glnS → glutamyl‑tRNA synthetase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE430,2310GA22.7% 181.9 / 50.3 88D280N (GAC→AAC) glnSglutamyl‑tRNA synthetase
Reads supporting (aligned to +/- strand):  ref base G (31/37);  new base A (5/15);  total (36/52)
Fisher's exact test for biased strand distribution p-value = 1.25e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.52e-01

ATGAGTTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGCGTCGTCGTGGTTAC  >  minE/430163‑430299
                                                                    |                                                                    
aTGAGTTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGa                                                                     >  1:3070751/1‑70 (MQ=255)
aTGAGTTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGAGTAAGTTGAACCTGCTGGTGACCGa                                                                     >  1:3820384/1‑70 (MQ=255)
 tGAGTTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGAc                                                                    >  1:2698624/1‑70 (MQ=255)
 tGAGTTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGAc                                                                    >  1:3234110/1‑70 (MQ=255)
 tGAGTTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGAc                                                                    >  1:164399/1‑70 (MQ=255)
 tGAGTTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGAc                                                                    >  1:1617395/1‑70 (MQ=255)
   aGTTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAg                                                                 <  1:3585333/71‑1 (MQ=255)
      tctcGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCAc                                                              >  1:199840/1‑71 (MQ=255)
      tctcGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCAc                                                              >  1:1487029/1‑71 (MQ=255)
       ctcGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCAc                                                              <  1:2482038/70‑1 (MQ=255)
       ctcGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACg                                                             >  1:1123244/1‑71 (MQ=255)
       ctcGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACg                                                             >  1:1905228/1‑71 (MQ=255)
       ctcGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACg                                                             >  1:3540049/1‑71 (MQ=255)
       ctcGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACg                                                             >  1:1598772/1‑71 (MQ=255)
       ctcGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACg                                                             >  1:782073/1‑71 (MQ=255)
       ctcGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACg                                                             >  1:3686209/1‑71 (MQ=255)
       ctcGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACg                                                             >  1:2739567/1‑71 (MQ=255)
         cgcgCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGtt                                                           >  1:2695475/1‑71 (MQ=255)
         cgcgCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGtt                                                           >  1:2782496/1‑71 (MQ=255)
          gcgcCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTg                                                          <  1:3885613/71‑1 (MQ=255)
          gcgcCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTg                                                          <  1:2644521/71‑1 (MQ=255)
          gcgcCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTg                                                          <  1:1702910/71‑1 (MQ=255)
           cgcCTGAATCTGGTATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACg                                                             >  1:2986738/1‑67 (MQ=255)
           cgcCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACg                                                             >  1:3967876/1‑67 (MQ=255)
           cgcCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACg                                                             >  1:713581/1‑67 (MQ=255)
           cgcCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACg                                                             >  1:1133556/1‑67 (MQ=255)
           cgcCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGa                                                         <  1:375523/71‑1 (MQ=255)
           cgcCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGa                                                         <  1:3313866/71‑1 (MQ=255)
            gcCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAg                                                                 <  1:3631095/62‑1 (MQ=255)
             ccTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAg                                                       <  1:1929805/71‑1 (MQ=255)
              cTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAg                                                       <  1:1300377/70‑1 (MQ=255)
               tGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGc                                                     >  1:1201918/1‑71 (MQ=255)
                  aTCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTgg                                                  <  1:1682529/71‑1 (MQ=255)
                    cTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTgg                                                  <  1:2749300/69‑1 (MQ=255)
                    cTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTgg                                                  <  1:2628717/69‑1 (MQ=255)
                     tGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGAt                                               >  1:2866314/1‑71 (MQ=255)
                     tGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGAt                                               >  1:941887/1‑71 (MQ=255)
                     tGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGAt                                               >  1:99427/1‑71 (MQ=255)
                     tGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGAt                                               >  1:1200109/1‑71 (MQ=255)
                     tGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGAt                                               >  1:3619924/1‑71 (MQ=255)
                     tGGAATACACCGTGATGTCCAAGCGTAAGTTGAACATGCTGGTGACCGACAAGCACGTTGAAGGCTGGGAt                                               >  1:2040718/1‑71 (MQ=255)
                       gAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGAt                                               <  1:251617/69‑1 (MQ=255)
                       gAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGAt                                               <  1:2267379/69‑1 (MQ=255)
                             acCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCcgcg                                       <  1:877734/71‑1 (MQ=255)
                             acCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCcgcg                                       <  1:1507966/71‑1 (MQ=255)
                              ccGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAg                                                                 <  1:1766863/44‑1 (MQ=255)
                              ccGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCAACAAg                                                                 <  1:3411872/44‑1 (MQ=255)
                                 tGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGa                                                >  1:3230389/1‑58 (MQ=255)
                                 tGATGTCAAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCAc                                                              <  1:1653387/44‑1 (MQ=255)
                                      tCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAg                                                                 <  1:1480883/36‑1 (MQ=255)
                                      tCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAg                                                                 <  1:960530/36‑1 (MQ=255)
                                      tCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAg                                                                 <  1:3729735/36‑1 (MQ=255)
                                      tCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAg                                                                 <  1:113166/36‑1 (MQ=255)
                                            cGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTgg                                                  <  1:1929215/45‑1 (MQ=255)
                                            cGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTgg                                                  <  1:384605/45‑1 (MQ=255)
                                            cGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTgg                                                  <  1:1337184/45‑1 (MQ=255)
                                            cGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTgg                                                  <  1:3913245/45‑1 (MQ=255)
                                            cGTAAGTTCAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTgg                                                  <  1:570854/45‑1 (MQ=255)
                                              tAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGa                                                >  1:3526483/1‑45 (MQ=255)
                                              tAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGa                                                >  1:896031/1‑45 (MQ=255)
                                              tAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGa                                                >  1:2946231/1‑45 (MQ=255)
                                              tAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCcgcg                                       <  1:2985418/54‑1 (MQ=255)
                                              tAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCcgcg                                       <  1:42650/54‑1 (MQ=255)
                                                  ttGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGATGACCcgcg                                       <  1:2988993/50‑1 (MQ=255)
                                                  ttGAACCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGATGACCcgcg                                       <  1:2861703/50‑1 (MQ=255)
                                                   tGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTg                 >  1:2029248/1‑71 (MQ=255)
                                                   tGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTg                 >  1:4023718/1‑71 (MQ=255)
                                                     aaCCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCcgcg                                       <  1:3103567/47‑1 (MQ=255)
                                                     aaCCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCcgcg                                       <  1:217746/47‑1 (MQ=255)
                                                     aaCCTGCTGGTGACCAACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCg                                <  1:908896/54‑1 (MQ=255)
                                                      aCCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGcgt              <  1:713277/71‑1 (MQ=255)
                                                      aCCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGcgt              <  1:3732661/71‑1 (MQ=255)
                                                      aCCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGcgt              <  1:703356/71‑1 (MQ=255)
                                                       ccTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGcgtc             <  1:2699117/71‑1 (MQ=255)
                                                        ctgctgGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTc                        <  1:3685585/59‑1 (MQ=255)
                                                        ctgctgGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTc                        <  1:1215211/59‑1 (MQ=255)
                                                         tgctgGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGcgtcgt           >  1:3491634/1‑71 (MQ=255)
                                                              gTGACCAACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTTcgtcgtcgt        <  1:3746049/69‑1 (MQ=255)
                                                              gTGACCAACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGcgtcgtcgt        <  1:4133021/69‑1 (MQ=255)
                                                              gTGACCAACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGcgtcgtcgt        <  1:1378755/69‑1 (MQ=255)
                                                               tGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGCGTCGTCGTGGt     <  1:3558771/71‑1 (MQ=255)
                                                               tGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGCGTCGTCGTGGt     <  1:1681245/71‑1 (MQ=255)
                                                               tGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGCGTCGTCGTGGt     <  1:1761495/71‑1 (MQ=255)
                                                               tGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGCGTCGTCGTGGt     <  1:1980420/71‑1 (MQ=255)
                                                               tGACCAACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGCGTCGTCGTGGt     <  1:1308100/71‑1 (MQ=255)
                                                                gACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGCGTCGTCGTGGt     >  1:3856797/1‑70 (MQ=255)
                                                                  ccGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGCGTCGTCGTGGTTac  <  1:1670609/71‑1 (MQ=255)
                                                                  ccGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGCGTCGTCGTGGTTac  <  1:107559/71‑1 (MQ=255)
                                                                    gACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGCGTCGTCGTGGTTa   <  1:742465/68‑1 (MQ=255)
                                                                    gACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGCGTCGTCGTGGTTa   <  1:85028/68‑1 (MQ=255)
                                                                    |                                                                    
ATGAGTTCTCGCGCCTGAATCTGGAATACACCGTGATGTCCAAGCGTAAGTTGAACCTGCTGGTGACCGACAAGCACGTTGAAGGCTGGGATGACCCGCGTATGCCGACCATTTCCGGTCTGCGTCGTCGTGGTTAC  >  minE/430163‑430299

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