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 2,604,047 T→C 50.0% P208P (CCA→CCG)  yhiP ← predicted transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,604,0470TC50.0% ‑3.2 / 138.8 146P208P (CCA→CCG) yhiPpredicted transporter
Reads supporting (aligned to +/- strand):  ref base T (43/30);  new base C (45/28);  total (88/58)
Fisher's exact test for biased strand distribution p-value = 8.66e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.47e-01

Only 100 of 146 total aligned reads displayed.

CGCATACGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGTAAACCAGT  >  minE/2603986‑2604110
                                                             |                                                               
cgcATACGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGa                                                          >  1:3227864/1‑69 (MQ=255)
cgcATACGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGa                                                          >  1:3349374/1‑69 (MQ=255)
 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCTGCCGGaa                                                         <  1:27614/69‑1 (MQ=255)
 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                         <  1:2536681/69‑1 (MQ=255)
 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                         <  1:1832805/69‑1 (MQ=255)
 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                         <  1:1804689/69‑1 (MQ=255)
 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                         <  1:1765088/69‑1 (MQ=255)
 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                         <  1:3249134/69‑1 (MQ=255)
 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                         <  1:2782675/69‑1 (MQ=255)
 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                         <  1:1673443/69‑1 (MQ=255)
 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                         <  1:2794484/69‑1 (MQ=255)
 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                         <  1:3390598/69‑1 (MQ=255)
 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                         <  1:2027669/69‑1 (MQ=255)
 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                         <  1:1452294/69‑1 (MQ=255)
 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                         <  1:2462364/69‑1 (MQ=255)
 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                         <  1:1311349/69‑1 (MQ=255)
 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                         <  1:2815567/69‑1 (MQ=255)
 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                         <  1:2877215/69‑1 (MQ=255)
 gcAGACGAAGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGaa                                                         <  1:490707/69‑1 (MQ=255)
      cGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCgg                                                    >  1:3096504/1‑69 (MQ=255)
      cGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCgg                                                    >  1:585701/1‑69 (MQ=255)
      cGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCgg                                                    >  1:1650696/1‑69 (MQ=255)
         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGACGCTCATCGGCCGGAAGTCggg                                                   >  1:2494773/1‑67 (MQ=255)
         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                                   >  1:512508/1‑67 (MQ=255)
         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                                   >  1:2329265/1‑67 (MQ=255)
         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                                   >  1:669173/1‑67 (MQ=255)
         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                                   >  1:2684238/1‑67 (MQ=255)
         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                                   >  1:74710/1‑67 (MQ=255)
         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                                   >  1:2527930/1‑67 (MQ=255)
         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                                   >  1:2898475/1‑67 (MQ=255)
         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                                   >  1:2036763/1‑67 (MQ=255)
         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                                   >  1:2031786/1‑67 (MQ=255)
         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                                   >  1:2003828/1‑67 (MQ=255)
         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                                   >  1:77133/1‑67 (MQ=255)
         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                                   >  1:157579/1‑67 (MQ=255)
         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                                   >  1:3415106/1‑67 (MQ=255)
         aGATCATCACCACGCTGCCAAGTAATACGTACAACAGTTTACTGAAGCTCATCGGCCGGAAGTCggg                                                   >  1:1363849/1‑67 (MQ=255)
            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAg                                                        >  1:2313551/1‑59 (MQ=255)
            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                              <  1:3407919/69‑1 (MQ=255)
            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                              <  1:2652171/69‑1 (MQ=255)
            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                              >  1:1088840/1‑69 (MQ=255)
            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                              >  1:1091199/1‑69 (MQ=255)
            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                              >  1:529219/1‑69 (MQ=255)
            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                              >  1:364648/1‑69 (MQ=255)
            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                              >  1:3177810/1‑69 (MQ=255)
            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                              <  1:588055/69‑1 (MQ=255)
            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                              <  1:592337/69‑1 (MQ=255)
            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                              <  1:2904647/69‑1 (MQ=255)
            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                              >  1:1839790/1‑69 (MQ=255)
            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                              >  1:2441616/1‑69 (MQ=255)
            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                              >  1:1924493/1‑69 (MQ=255)
            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                              >  1:1981055/1‑69 (MQ=255)
            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                              >  1:2230142/1‑69 (MQ=255)
            tcatcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                              <  1:2058425/69‑1 (MQ=255)
            tcaacaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAg                                              >  1:3158687/1‑69 (MQ=255)
             catcaCCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGa                                             >  1:1763008/1‑69 (MQ=255)
                 accacGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAAcc                                          >  1:2639867/1‑68 (MQ=255)
                 accacGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAAcc                                          >  1:793193/1‑68 (MQ=255)
                 accacGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAAcc                                          >  1:3089130/1‑68 (MQ=255)
                 accacGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAAcc                                          >  1:2136413/1‑68 (MQ=255)
                 accacGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAAcc                                          >  1:1252040/1‑68 (MQ=255)
                 accacGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAAcc                                          >  1:1132375/1‑68 (MQ=255)
                            aaGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCAc                              <  1:1194971/69‑1 (MQ=255)
                               tAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCa                            >  1:2133343/1‑68 (MQ=255)
                               tAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCa                            >  1:3012687/1‑68 (MQ=255)
                               tAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCAt                           >  1:276671/1‑69 (MQ=255)
                               tAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCAt                           >  1:3246523/1‑69 (MQ=255)
                                aaCACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCAt                           >  1:1612754/1‑68 (MQ=255)
                                aaCACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCAt                           >  1:2429779/1‑68 (MQ=255)
                                                tGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGt          <  1:881956/69‑1 (MQ=255)
                                                tGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGt          <  1:405043/69‑1 (MQ=255)
                                                  cTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGTa         <  1:520726/68‑1 (MQ=255)
                                                  cTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGTa         <  1:2718139/68‑1 (MQ=255)
                                                  cTGAAGCTCATCGGCCGGAAGTCGGGTTCAGAACCa                                         >  1:1870893/1‑36 (MQ=255)
                                                  cTGAAGCTCATCGGCCGGAAGTCGGGTTCAGAACCAATGt                                     >  1:823264/1‑40 (MQ=255)
                                                  cTGAAGCTCATCGGCCGGAAGTCGGGTTCAGAACCAATGt                                     >  1:2946913/1‑40 (MQ=255)
                                                  cTGAAGCTCATCGGCCGGAAGTCGGGTTCAGAACCAATGt                                     >  1:208404/1‑40 (MQ=255)
                                                  cTGAAGCTCATCGGCCGGAAGTCGGGTTCAGAACCAATGt                                     >  1:2149152/1‑40 (MQ=255)
                                                  cTGAAGCTCATCGGCCGGAAGTCGGGTTCAGAACCAATGt                                     >  1:529617/1‑40 (MQ=255)
                                                  cTGAAGCTCATCGGCCGGAAGTCGGGTTCAGAACCAATGt                                     >  1:2303909/1‑40 (MQ=255)
                                                  cTGAAGCTCATCGGCCGGAAGTCGGGTTCAGAACCAATGt                                     >  1:453889/1‑40 (MQ=255)
                                                  cTGAAGCTCATCGGCCGGAAGTCGGGTTCAGAACCAATGt                                     >  1:2618387/1‑40 (MQ=255)
                                                       gCTCATCGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGTAAAc      >  1:642645/1‑66 (MQ=255)
                                                       gCTCATCGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGTAAACCa    >  1:896449/1‑68 (MQ=255)
                                                       gCTCATCGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGTAAACCa    >  1:2681071/1‑68 (MQ=255)
                                                       gCTCATCGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGTAAACCa    >  1:417431/1‑68 (MQ=255)
                                                       gCTCATCGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGTAAACCa    >  1:366372/1‑68 (MQ=255)
                                                       gCTCATCGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGTAAACCa    >  1:331181/1‑68 (MQ=255)
                                                       gCTCATCGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGTAAACCa    >  1:215058/1‑68 (MQ=255)
                                                       gCTCATCGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGTAAACCa    >  1:2085399/1‑68 (MQ=255)
                                                       gCTCATCGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGTAAACCa    >  1:169773/1‑68 (MQ=255)
                                                        cTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGTAAACCAGt  <  1:3118979/69‑1 (MQ=255)
                                                        cTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGTAAACCAGt  <  1:296824/69‑1 (MQ=255)
                                                        cTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGTAAACCAGt  <  1:2561177/69‑1 (MQ=255)
                                                        cTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGTAAACCAGt  <  1:2201313/69‑1 (MQ=255)
                                                        cTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGTAAACCAGt  <  1:731337/69‑1 (MQ=255)
                                                        cTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGTAAACCAGt  <  1:1584741/69‑1 (MQ=255)
                                                        cTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGTAAACCAGt  <  1:1506933/69‑1 (MQ=255)
                                                        cTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGTAAACCAGt  <  1:939543/69‑1 (MQ=255)
                                                           aTTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCa                       >  1:1727014/1‑45 (MQ=255)
                                                             |                                                               
CGCATACGAAGATCATCACCACGCTGCCAAGTAACACGTACAACAGTTTGCTGAAGCTCATTGGCCGGAAGTCGGGTTCAGAACCAATGTCTTTCACCATTCCACGACAGGCGATGTAAACCAGT  >  minE/2603986‑2604110

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