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 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,509,118 G→A 74.4% A728T (GCG→ACG)  yicI → predicted alpha‑glucosidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,509,1180GA74.4% 153.0 / 51.6 133A728T (GCG→ACG) yicIpredicted alpha‑glucosidase
Reads supporting (aligned to +/- strand):  ref base G (2/32);  new base A (80/18);  total (82/51)
Fisher's exact test for biased strand distribution p-value = 1.51e-15
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.19e-01

Only 100 of 133 total aligned reads displayed.

GGTGATCTTTACTTTAAAAGCAGCACGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCGAAGAACTGGACACTGTGCCTGCGCAATGTTGTGAAAGTAAATGGTC  >  minE/2509063‑2509175
                                                       |                                                         
ggTGATCTTTACTTTAAAAGCAGCACGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCgaa                                              <  1:3228909/69‑1 (MQ=255)
ggTGATCTTTACTTTAAAAGCAGCACGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCgaa                                              <  1:1161290/69‑1 (MQ=255)
ggTGATCTTTACTTTAAAAGCAGCACGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCgaa                                              <  1:3200667/69‑1 (MQ=255)
ggTGATCTTTACTTTAAAAGCAGCACGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCgaa                                              <  1:2811435/69‑1 (MQ=255)
ggTGATCTTTACTTTAAAAGCAGCACGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCgaa                                              <  1:2657935/69‑1 (MQ=255)
ggTGATCTTTACTTTAAAAGCAGCACGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCgaa                                              <  1:2542128/69‑1 (MQ=255)
ggTGATCTTTACTTTAAAAGCAGCACGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCgaa                                              <  1:1733699/69‑1 (MQ=255)
ggTGATCTTTACTTTAAAAGCAGCACGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCgaa                                              <  1:1602197/69‑1 (MQ=255)
   gATCTTTACTTTAAAAGCAGCACGTACTGGCAACACGATTACTGTGACTGGTTCGGGCGAGGCgaagaa                                           <  1:959978/69‑1 (MQ=255)
   gATCTTTACTTTAAAAGCAGCACGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCgaagaa                                           <  1:1933023/69‑1 (MQ=255)
   gATCTTTACTTTAAAAGCAGCACGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCgaagaa                                           <  1:3267078/69‑1 (MQ=255)
   gATCTTTACTTTAAAAGCAGCACGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCgaagaa                                           <  1:1982901/69‑1 (MQ=255)
   gATCTTTACTTTAAAAGCAGCACGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCgaagaa                                           <  1:1516957/69‑1 (MQ=255)
   gATCTTTACTTTAAAAGCAGCACGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCgaagaa                                           <  1:1382827/69‑1 (MQ=255)
   gATCTTTACTTTAAAAGCAGCACGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCgaagaa                                           <  1:795311/69‑1 (MQ=255)
    aTCTTTACTTTAAAAGCAGCACGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCGAAGAAc                                          >  1:2687211/1‑69 (MQ=255)
            tttaAAAGCAGCACGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCGAAGAACTGGacac                                   <  1:276577/68‑1 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCgaag                                             >  1:642816/1‑55 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCgaag                                             >  1:357375/1‑55 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCgaag                                             >  1:390378/1‑55 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCgaag                                             >  1:2329920/1‑55 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCgaag                                             >  1:3353654/1‑55 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCgaag                                             >  1:3331511/1‑55 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCgaag                                             >  1:1246937/1‑55 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCgaag                                             >  1:1216340/1‑55 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCgaag                                             >  1:2857515/1‑55 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCgaag                                             >  1:693923/1‑55 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCgaag                                             >  1:1689674/1‑55 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCgaag                                             >  1:886462/1‑55 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCgaag                                             >  1:703189/1‑55 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCgaag                                             >  1:764494/1‑55 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCgaag                                             >  1:3011329/1‑55 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCgaag                                             >  1:910065/1‑55 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCgaag                                             >  1:771151/1‑55 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACtgtg                               >  1:1428667/1‑69 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACtgtg                               >  1:2905701/1‑69 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACtgtg                               >  1:2911637/1‑69 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACtgtg                               >  1:1262082/1‑69 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACtgtg                               >  1:2573657/1‑69 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACtgtg                               >  1:2390915/1‑69 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACtgtg                               >  1:3013372/1‑69 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACtgtg                               >  1:207388/1‑69 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACtgtg                               >  1:1439711/1‑69 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACtgtg                               >  1:1339469/1‑69 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACtgtg                               >  1:1634474/1‑69 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACtgtg                               >  1:1657280/1‑69 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACtgtg                               >  1:3172198/1‑69 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACtgtg                               >  1:1864744/1‑69 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACtgtg                               >  1:2008899/1‑69 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACtgtg                               >  1:541883/1‑69 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACtgt                                >  1:1273461/1‑68 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACtgt                                >  1:2361662/1‑68 (MQ=255)
               aaaaGCAGCACGTACTGGCAACACGACTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACtgtg                               >  1:3034065/1‑69 (MQ=255)
               aaaaGCAGAACGTACTGGCAACACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACtgtg                               >  1:1816212/1‑69 (MQ=255)
                 aaGCAGCACGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCGAAGAACTGGACACtgt                                <  1:3423155/66‑1 (MQ=255)
                  agcagcACGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCgaagaa                                           <  1:2404248/54‑1 (MQ=255)
                      gcaCGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCGAAGAACTGGACACTGTGCCTgcgc                        <  1:1504965/69‑1 (MQ=255)
                       caCGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCGAAGAACTGGACACTGTGCCTGCGCa                       <  1:1849430/69‑1 (MQ=255)
                        aCGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCGAAGAACTGGACACTGTGCCTGCGCaa                      <  1:3097848/69‑1 (MQ=255)
                        aCGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCGAAGAACTGGACACTGTGCCTGCGCaa                      <  1:3053889/69‑1 (MQ=255)
                        aCGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCGAAGAACTGGACACTGTGCCTGCGCaa                      <  1:2505033/69‑1 (MQ=255)
                         cGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCGAAGAACTGGACACTGTGCCTGCGCaa                      <  1:1481837/68‑1 (MQ=255)
                         cGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCGAAGAACTGGACACTGTGCCTGCGCAAt                     >  1:2037247/1‑69 (MQ=255)
                                  aaCACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAATATTGTGa              <  1:316369/67‑1 (MQ=255)
                                  aaCACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAATATTGTGa              <  1:1080776/67‑1 (MQ=255)
                                  aaCACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAATATTGTGa              <  1:3326869/67‑1 (MQ=255)
                                  aaCACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAATATTGTGa              <  1:3422663/67‑1 (MQ=255)
                                  aaCACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAATATTGTGa              <  1:595979/67‑1 (MQ=255)
                                  aaCACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAATATTGTGa              <  1:600391/67‑1 (MQ=255)
                                  aaCACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAATATTGTGa              <  1:853037/67‑1 (MQ=255)
                                  aaCACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAATATTGTGa              <  1:2070728/67‑1 (MQ=255)
                                  aaCACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAATATTGTGa              <  1:1044409/67‑1 (MQ=255)
                                  aaCACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAATATTGTGa              <  1:1092534/67‑1 (MQ=255)
                                  aaCACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAATATTGTGa              <  1:2035368/67‑1 (MQ=255)
                                  aaCACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAATATTGTGa              <  1:2197650/67‑1 (MQ=255)
                                  aaCACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAATATTGTGa              <  1:2278484/67‑1 (MQ=255)
                                  aaCACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAATATTGTGa              <  1:2734777/67‑1 (MQ=255)
                                  aaCACGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAATATTGTGa              <  1:2738803/67‑1 (MQ=255)
                                    cacGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAAtattg                 >  1:620845/1‑62 (MQ=255)
                                    cacGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAAtattg                 >  1:3101167/1‑62 (MQ=255)
                                    cacGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAAtattg                 >  1:3049378/1‑62 (MQ=255)
                                    cacGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAAtattg                 >  1:120970/1‑62 (MQ=255)
                                    cacGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAAtattg                 >  1:1264489/1‑62 (MQ=255)
                                    cacGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAAtattg                 >  1:1265991/1‑62 (MQ=255)
                                    cacGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAAtattg                 >  1:1399222/1‑62 (MQ=255)
                                    cacGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAAtattg                 >  1:157086/1‑62 (MQ=255)
                                    cacGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAAtattg                 >  1:72634/1‑62 (MQ=255)
                                    cacGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAAtattg                 >  1:1579935/1‑62 (MQ=255)
                                    cacGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAAtattg                 >  1:1705050/1‑62 (MQ=255)
                                    cacGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAAtattg                 >  1:183170/1‑62 (MQ=255)
                                    cacGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAAtattg                 >  1:409378/1‑62 (MQ=255)
                                    cacGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAAtattg                 >  1:398036/1‑62 (MQ=255)
                                    cacGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAAtattg                 >  1:3253052/1‑62 (MQ=255)
                                    cacGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAAtattg                 >  1:2995227/1‑62 (MQ=255)
                                    cacGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAAtattg                 >  1:2303844/1‑62 (MQ=255)
                                    cacGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAAtattg                 >  1:2674164/1‑62 (MQ=255)
                                    cacGATTACTGTGACTGGTACGGGCGAGGCGAAGAACTGGACACTGTGCTTGCGCAAtattg                 >  1:2846957/1‑62 (MQ=255)
                                     acGATTACTGTGACTGGTGCGGGCGAGGCGAAGAACTGGACACTGTGCCTGCGCAATGTTGTGAAAGTa         <  1:1735739/69‑1 (MQ=255)
                                     acGATTACTGTGACTGGTGCGGGCGAGGCGAAGAACTGGACACTGTGCCTGCGCAATGTTGTGAAAGTa         <  1:3012197/69‑1 (MQ=255)
                                        aTTACTGTGACTGGTGCGGGCGAGGCGAAGAACTGGACACTGTGCCTGCGCaa                      <  1:3133712/53‑1 (MQ=255)
                                                       |                                                         
GGTGATCTTTACTTTAAAAGCAGCACGTACTGGCAACACGATTACTGTGACTGGTGCGGGCGAGGCGAAGAACTGGACACTGTGCCTGCGCAATGTTGTGAAAGTAAATGGTC  >  minE/2509063‑2509175

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