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 909,573 C→T 30.6% L584L (CTG→TTG)  ycjT → predicted hydrolase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE909,5730CT30.6% 71.0 / 36.7 49L584L (CTG→TTG) ycjTpredicted hydrolase
Reads supporting (aligned to +/- strand):  ref base C (11/23);  new base T (9/6);  total (20/29)
Fisher's exact test for biased strand distribution p-value = 1.14e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATTCACGCGCAGAAGTGAACGAGATGCAGATCCTCAAACAAGCTGATGTGGTGATGCTCAATTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAACCGCGCACTATTCAC  >  minE/909505‑909641
                                                                    |                                                                    
attCACGCGCAGAAGTGAACGAGATGCAGATCCTCAAACAAGCTGATGTGGTGATGCTCAATTACAtgctg                                                                    >  1:2490772/1‑71 (MQ=255)
   cACGCGCAGAAGTGAACGAGATGCAGATCCTCAAACAAGCTGATGTGGTGATGCTCAATTACATGCTGCCg                                                                 >  1:3670692/1‑71 (MQ=255)
              gTGAACGAGATGCAGATCCTCAAACAAGCTGATGTGGTGATGCTCAATTACATGTTGCCGGAGCAGTtct                                                       >  1:2251261/1‑70 (MQ=255)
                   cGAGATGCAGATCCTCAAACAAGCTGATGTGGTGATGCTCAATTACATGCTGCCGGAGCAGTTCTCAGCgg                                                 <  1:3507809/71‑1 (MQ=255)
                   cGAGATGCAGATCCTCAAACAAGCTGATGTGGTGATGCTCAATTACATGCTGCCGGAGCAGTTCTCAGCgg                                                 <  1:652184/71‑1 (MQ=255)
                         gCAGATCCTCAAACAAGCTGATTTGGTGATGCTCAATTACAtgc                                                                      >  1:2290651/1‑44 (MQ=255)
                         gCAGATCCTCAAACAAGCTGATGTGGTGATGCTCAATTACAtgc                                                                      >  1:911849/1‑44 (MQ=255)
                         gCAGATCCTCAAACAAGCTGATGTGGTGATGCTCAATTACAtgc                                                                      >  1:2824372/1‑44 (MQ=255)
                               ccTCAAACAAGCTGATGTGGTGATGCTCAATTACATGTTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTg                                     >  1:953986/1‑71 (MQ=255)
                               ccTCAAACAAGCTGATGTGGTGATGCTCAATTACATGTTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTg                                     >  1:495338/1‑71 (MQ=255)
                               ccTCAAACAAGCTGATGTGGTGATGCTCAATTACATGTTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTg                                     >  1:1815457/1‑71 (MQ=255)
                               ccTCAAACAAGCTGATGTGGTGATGCTCAATTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTg                                     >  1:3332786/1‑71 (MQ=255)
                                cTCAAACAAGCTGATGTGGTGATGCTCAATTACATGTTGCCGGAGCAGTtctc                                                      <  1:1023958/53‑1 (MQ=255)
                                  cAAACAAGCTGATGTGGTGATGCTCAATTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGcc                                   >  1:2030284/1‑70 (MQ=255)
                                  cAAACAAGCTGATGTGGTGATGCTCAATTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGcc                                   >  1:2222208/1‑70 (MQ=255)
                                   aaaCAAGCTGATGTGGTGATGCTCAATTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCaa                                 >  1:1598399/1‑71 (MQ=255)
                                          cTGATGTGGTGATGCTCAATTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCaa                          <  1:1132098/71‑1 (MQ=255)
                                           ttaTGTGGTGATGCTCAATTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCaa                          <  1:2193195/68‑1 (MQ=255)
                                            gATGTGGTGATGCTCAATTACATGCTGCCGGAGCAGTTCTCAGCGGCATCgtg                                          <  1:2036715/53‑1 (MQ=255)
                                                  gtgATGCTCAATTACATGCTGCCGGAGCAGTTCTCAGCGGCATCTTGTCTTGCCAATCTGCAATTTTATg                   <  1:2268812/70‑1 (MQ=255)
                                                  gtgATGCTCAATTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATg                   <  1:1310823/70‑1 (MQ=255)
                                                  gtgATGCTCAATTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGa                  <  1:311513/71‑1 (MQ=255)
                                                  gtgATGCTCAATTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGa                  <  1:2727182/71‑1 (MQ=255)
                                                  gtgATGCTCAATTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGa                  <  1:3329506/71‑1 (MQ=255)
                                                  gtgATGCTCAATCACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATg                   <  1:736158/70‑1 (MQ=255)
                                                   tgATGCTCAATTACATGTTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGc                            <  1:649237/60‑1 (MQ=255)
                                                   tgATGCTCAATTACATGTTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGc                            <  1:1584634/60‑1 (MQ=255)
                                                   tgATGCTCAATTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATg                   <  1:2127637/69‑1 (MQ=255)
                                                     aTGCTCAATTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAAcc               >  1:425954/1‑71 (MQ=255)
                                                     aTGCTCAATTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAAcc               >  1:1378149/1‑71 (MQ=255)
                                                      tGCTCAATTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAACcg              <  1:2843744/71‑1 (MQ=255)
                                                      tGCTCAATTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAACcg              <  1:1406458/71‑1 (MQ=255)
                                                        cTCAATTACATGTTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATg                   <  1:2494945/64‑1 (MQ=255)
                                                        cTCAATTACATGTTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATg                   <  1:70535/64‑1 (MQ=255)
                                                        cTCAATTACATGTTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATg                   <  1:3388296/64‑1 (MQ=255)
                                                        cTCAATTACATGCTGCCGGAGCAGTTCTCAGCGGCa                                               <  1:3710726/36‑1 (MQ=255)
                                                        cTCAATTACATGCTGCCGGAGCAGTTCTCAGCGGCa                                               <  1:515078/36‑1 (MQ=255)
                                                        cTCAATTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAACcgcg            >  1:1930131/1‑71 (MQ=255)
                                                        cTCAATTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAACcgcg            >  1:1274330/1‑71 (MQ=255)
                                                          cAATTACATGTTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAACCGCGCa          >  1:961297/1‑71 (MQ=255)
                                                          cAATTACATGTTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAACCGCGCa          >  1:2953675/1‑71 (MQ=255)
                                                          cAATTACATGTTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAACCGCGCa          >  1:239791/1‑71 (MQ=255)
                                                          cAATTACATGTTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAACCGCGCa          >  1:2363349/1‑71 (MQ=255)
                                                          cAATTACATGTTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAACCGCGCa          >  1:1634601/1‑71 (MQ=255)
                                                           aaTTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAACCGCGCAc         <  1:2263484/71‑1 (MQ=255)
                                                           aaTTACATGCTGCCGGAGCAGTTATCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAACCGCGCAc         <  1:646641/71‑1 (MQ=255)
                                                            aTTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAACCGCGCAc         >  1:1296737/1‑70 (MQ=255)
                                                            aTTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAACCGCGCAc         <  1:592060/70‑1 (MQ=255)
                                                            aTTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAACCGCGCACt        <  1:1094668/71‑1 (MQ=255)
                                                            aTTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAACCGCGCACt        <  1:1592055/71‑1 (MQ=255)
                                                            aTTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAACCGCGCACt        <  1:622815/71‑1 (MQ=255)
                                                            aTTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAACCGCGCACt        <  1:508832/71‑1 (MQ=255)
                                                              tACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTa                     >  1:1518905/1‑56 (MQ=255)
                                                                   gctgcCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGaa                 >  1:541696/1‑55 (MQ=255)
                                                                   gctgcCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAAc                >  1:406101/1‑56 (MQ=255)
                                                                   gctgcCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAAc                >  1:1244759/1‑56 (MQ=255)
                                                                   gctgcCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAAc                >  1:3196177/1‑56 (MQ=255)
                                                                   gctgcCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAACcg              <  1:1845191/58‑1 (MQ=255)
                                                                   gctgcCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAACCGCGCACTATTCAc  >  1:3508668/1‑70 (MQ=255)
                                                                   gctgcAGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGaa                 >  1:1673720/1‑55 (MQ=255)
                                                                    |                                                                    
ATTCACGCGCAGAAGTGAACGAGATGCAGATCCTCAAACAAGCTGATGTGGTGATGCTCAATTACATGCTGCCGGAGCAGTTCTCAGCGGCATCGTGTCTTGCCAATCTGCAATTTTATGAACCGCGCACTATTCAC  >  minE/909505‑909641

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