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 1,728,993 A→C 45.5% E123D (GAA→GAC)  yfhD → predicted transglycosylase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,728,9930AC45.5% 3.8 / 115.0 99E123D (GAA→GAC) yfhDpredicted transglycosylase
Reads supporting (aligned to +/- strand):  ref base A (26/28);  new base C (29/16);  total (55/44)
Fisher's exact test for biased strand distribution p-value = 1.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.35e-01

Only 100 of 101 total aligned reads displayed.

GACGGCGGAGCAACTCACCGTTGCACCGGGTCATGTGGTGGTTAACGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACAAAAAAGGCTCTGCGGAATTAATGGAA  >  minE/1728927‑1729056
                                                                  |                                                               
gACGGCGGAGCAACTCACCGTTGCACCGGGTCATGTGGTGGTTAACGATCTCCAGACCCTGAAAGAAAc                                                               <  1:1041104/69‑1 (MQ=255)
gACGGCGGAGCAACTCACCGTTGCACCGGGTCATGTGGTGGTTAACGATCTCCAGACCCTGAAAGAAAc                                                               <  1:981578/69‑1 (MQ=255)
gACGGCGGAGCAACTCACCGTTGCACCGGGTCATGTGGTGGTTAACGATCTCCAGACCCTGAAAGAAAc                                                               <  1:2409088/69‑1 (MQ=255)
gACGGCGGAGCAACTCACCGTTGCACCGGGTCATGTGGTGGTTAACGATCTCCAGACCCTGAAAGAAAc                                                               <  1:2392170/69‑1 (MQ=255)
   ggcggAGCAACTCACCGTTGCACCGGGTCATGTGGTGGTTAACGATCTCCAGACCCTGAAAGAAACaa                                                             <  1:1244189/68‑1 (MQ=255)
   ggcggAGCAACTCACCGTTGCACCGGGTCATGTGGTGGTTAACGATCTCCAGACCCTGAAAGAAACaa                                                             <  1:3245531/68‑1 (MQ=255)
   ggcggAGCAACTCACCGTTGCACCGGGTCATGTGGTGGTTAACGATCTCCAGACCCTGAAAGAAACaa                                                             <  1:3431322/68‑1 (MQ=255)
   ggcggAGCAACTCACCGTTGCACCGGGTCATGTGGTGGTTAACGATCTCCAGACCCTGAAAGAAACaa                                                             <  1:3419647/68‑1 (MQ=255)
   ggcggAGCAACTCACCGTTGCACCGGGTCATGTGGTGGTTAACGATCTCCAGACCCTGAAAGAAACaa                                                             <  1:1573586/68‑1 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACaaa                                                            >  1:1446914/1‑67 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAAt                                                          >  1:1948824/1‑69 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAAt                                                          >  1:1208336/1‑69 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAAt                                                          >  1:2114776/1‑69 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAAt                                                          >  1:232981/1‑69 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAAt                                                          >  1:1043451/1‑69 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAAt                                                          >  1:2630881/1‑69 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAAt                                                          >  1:264996/1‑69 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAAt                                                          >  1:2889515/1‑69 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAAt                                                          >  1:3199746/1‑69 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAAt                                                          >  1:334345/1‑69 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAAt                                                          >  1:3434446/1‑69 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAAt                                                          >  1:364676/1‑69 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAAt                                                          >  1:42572/1‑69 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAAt                                                          >  1:492085/1‑69 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAAt                                                          >  1:666564/1‑69 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAAt                                                          >  1:669087/1‑69 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAAt                                                          >  1:81847/1‑69 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAAt                                                          >  1:867099/1‑69 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAAt                                                          >  1:871179/1‑69 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAAt                                                          >  1:1301866/1‑69 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAAt                                                          >  1:1596186/1‑69 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAAt                                                          >  1:18404/1‑69 (MQ=255)
     cggAGCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACA‑AAAAtt                                                         >  1:1963717/1‑69 (MQ=255)
         gCAACTCACCGTTGCACCTGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACaaaa                                                           <  1:3094962/64‑1 (MQ=255)
         gCAACTCACCGTTGCACCTGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACaaaa                                                           <  1:1326560/64‑1 (MQ=255)
         gCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACaaaa                                                           <  1:900496/64‑1 (MQ=255)
         gCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACaaaa                                                           <  1:1387091/64‑1 (MQ=255)
         gCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACaaaa                                                           <  1:374186/64‑1 (MQ=255)
         gCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACaaaa                                                           <  1:337295/64‑1 (MQ=255)
         gCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACaaaa                                                           <  1:1917948/64‑1 (MQ=255)
         gCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACaaaa                                                           <  1:1086872/64‑1 (MQ=255)
         gCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACaaaa                                                           <  1:2394630/64‑1 (MQ=255)
         gCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACaaaa                                                           <  1:1823246/64‑1 (MQ=255)
         gCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACaaaa                                                           <  1:1356233/64‑1 (MQ=255)
         gCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACaaaa                                                           <  1:1253586/64‑1 (MQ=255)
         gCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACaaaa                                                           <  1:601818/64‑1 (MQ=255)
         gCAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACaaaa                                                           <  1:2496212/64‑1 (MQ=255)
         gCAACTCACCGTTGCACAGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACaaaa                                                           <  1:569311/64‑1 (MQ=255)
          cAACTCACCGTTGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACaaaa                                                           <  1:3257377/63‑1 (MQ=255)
                    ttGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAATTCCCGGAATTAAGc                                            >  1:2407148/1‑68 (MQ=255)
                    ttGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAATTCCCGGAATTAAGc                                            >  1:785514/1‑68 (MQ=255)
                    ttGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAATTCCCGGAATTAAGc                                            >  1:301046/1‑68 (MQ=255)
                    ttGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAATTCCCGGAATTAAGc                                            >  1:2236635/1‑68 (MQ=255)
                    ttGCACCGGGTCACGTGGTGGTTAACGATCTCCAGACCCTGAAAGACACAAAATTCCCGGAATTAAGc                                            >  1:133171/1‑68 (MQ=255)
                      gCACCGGGTCATGTGGTGGTTAACGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTgg                                         <  1:884501/69‑1 (MQ=255)
                                aTGTGGTGGTTAACGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAgac                                >  1:1516671/1‑68 (MQ=255)
                                aTGTGGTGGTTAACGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAgac                                >  1:2158353/1‑68 (MQ=255)
                                        gtTAACGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACaaaaaa                       >  1:1577203/1‑69 (MQ=255)
                                        gtTAACGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACaaaaaa                       >  1:2727530/1‑69 (MQ=255)
                                        gtTAACGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACaaaaaa                       >  1:3054452/1‑69 (MQ=255)
                                        gtTAACGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACaaaaaa                       >  1:1805051/1‑69 (MQ=255)
                                        gtTAACGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACaaaaaa                       >  1:827329/1‑69 (MQ=255)
                                        gtTAACGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACaaaaa                        >  1:2896833/1‑68 (MQ=255)
                                        gtTAACGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACaaaaa                        >  1:2858661/1‑68 (MQ=255)
                                        gtTAACGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACaa                           >  1:1251548/1‑65 (MQ=255)
                                        gtTAACGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACa                            >  1:837390/1‑64 (MQ=255)
                                          tAACGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACAAAAAAgg                     >  1:1012179/1‑69 (MQ=255)
                                          tAACGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACAAAAAAgg                     >  1:683558/1‑69 (MQ=255)
                                          tAACGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACAAAAAAgg                     >  1:2062370/1‑69 (MQ=255)
                                          tAACGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACAAAAAAgg                     >  1:2231065/1‑69 (MQ=255)
                                          tAACGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACAAAAAAgg                     >  1:534030/1‑69 (MQ=255)
                                          tAACGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACAAAAAAgg                     >  1:2424718/1‑69 (MQ=255)
                                          tAACGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACAAAAAAgg                     >  1:3243801/1‑69 (MQ=255)
                                          tAACGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACAAAAAAg                      >  1:2428646/1‑68 (MQ=255)
                                          tAACGATCTCCAGACCCTGAAAGAAACAAAATTCACGGAATTAAGCTGGAAGGTAGACGACAAAAAAgg                     >  1:2260723/1‑69 (MQ=255)
                                          tAACGATCTACAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACAAAAAAgg                     >  1:190973/1‑69 (MQ=255)
                                           aaCGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTTGAAGGTAGACGACaa                           <  1:1851262/62‑1 (MQ=255)
                                           aaCGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACaa                           <  1:85059/62‑1 (MQ=255)
                                           aaCGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACaa                           <  1:3070512/62‑1 (MQ=255)
                                           aaCGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACaa                           <  1:229287/62‑1 (MQ=255)
                                           aaCGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACaa                           <  1:2534335/62‑1 (MQ=255)
                                           aaCGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACaa                           <  1:1447335/62‑1 (MQ=255)
                                           aaCGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACaa                           <  1:2567546/62‑1 (MQ=255)
                                           aaCGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACaa                           <  1:2117119/62‑1 (MQ=255)
                                           aaCGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACaa                           <  1:2916472/62‑1 (MQ=255)
                                           aaCGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACaa                           <  1:2852374/62‑1 (MQ=255)
                                           aaCGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACaa                           <  1:462457/62‑1 (MQ=255)
                                           aaCGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACAAAAAAGGc                    <  1:2901974/69‑1 (MQ=255)
                                           aaCGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACAAAAAAGGc                    <  1:183419/69‑1 (MQ=255)
                                           aaCGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACAAAAAAGGc                    <  1:712963/69‑1 (MQ=255)
                                           aaCGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACAAAAAAGGc                    <  1:32362/69‑1 (MQ=255)
                                            aCGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACAAAAAAGGc                    <  1:13949/68‑1 (MQ=255)
                                                 ctcCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTATACGACAAAAAAGGCTCTGc               >  1:1897091/1‑68 (MQ=255)
                                                 ctcCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACAAAAAAGGCTCTGc               >  1:749388/1‑68 (MQ=255)
                                                 ctcCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACAAAAAAGGCTCTGc               >  1:1144494/1‑68 (MQ=255)
                                                 ctcCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACAAAAAAGGCTCTGc               >  1:194250/1‑68 (MQ=255)
                                                 ctcCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACAAAAAAGGCTCTGc               >  1:2959488/1‑68 (MQ=255)
                                                      gACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACAAAAAAGGCTCTGCgg             <  1:1353283/65‑1 (MQ=255)
                                                               agaaaCAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACAAAAAAGGCTCTGCGGAATTAATGGaa  <  1:2458641/67‑1 (MQ=255)
                                                               agaaaCAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACAAAAAAGGCTCTGCGGAATTAATGGaa  <  1:609454/67‑1 (MQ=255)
                                                                  |                                                               
GACGGCGGAGCAACTCACCGTTGCACCGGGTCATGTGGTGGTTAACGATCTCCAGACCCTGAAAGAAACAAAATTCCCGGAATTAAGCTGGAAGGTAGACGACAAAAAAGGCTCTGCGGAATTAATGGAA  >  minE/1728927‑1729056

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