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 2,183,393 A→G 37.8% E1223E (GAA→GAG)  gltB → glutamate synthase, large subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,183,3930AG37.8% 53.5 / 67.3 103E1223E (GAA→GAG) gltBglutamate synthase, large subunit
Reads supporting (aligned to +/- strand):  ref base A (25/39);  new base G (10/29);  total (35/68)
Fisher's exact test for biased strand distribution p-value = 2.01e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.31e-01

Only 100 of 103 total aligned reads displayed.

AGCTGGACGGTTTCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCACTCTACTGCACCGAAAACAACCCGCCGTTTGATAACGGC  >  minE/2183329‑2183450
                                                                |                                                         
agCTGGACGGTTTCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGc                                                       >  1:970612/1‑69 (MQ=255)
agCTGGACGGTTTCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGc                                                       >  1:1493698/1‑69 (MQ=255)
    ggACGGTTTCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATcc                                                   <  1:3114338/69‑1 (MQ=255)
    ggACGGTTTCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATcc                                                   <  1:211762/69‑1 (MQ=255)
    ggACGGTTTCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATcc                                                   <  1:2043554/69‑1 (MQ=255)
    ggACGGTTTCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATcc                                                   <  1:1887101/69‑1 (MQ=255)
    ggACGGTTTCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATcc                                                   <  1:1396800/69‑1 (MQ=255)
     gACGGTTTCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATcc                                                   <  1:2183287/68‑1 (MQ=255)
          tttCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTaa                                             >  1:966723/1‑69 (MQ=255)
          tttCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTaa                                             >  1:33866/1‑69 (MQ=255)
          tttCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTaa                                             >  1:3252588/1‑69 (MQ=255)
          tttCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTaa                                             >  1:1762374/1‑69 (MQ=255)
          tttCACCGCCAAACAGCAGAAGCTGGCGC‑‑TCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAgg                                           <  1:2496415/69‑1 (MQ=255)
           ttCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTaa                                             >  1:347670/1‑68 (MQ=255)
           ttCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTaa                                             >  1:326778/1‑68 (MQ=255)
           ttCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTaa                                             >  1:1384855/1‑68 (MQ=255)
           ttCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTaa                                             >  1:2125107/1‑68 (MQ=255)
           ttCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGATGGAGACTGCCGAACCGCATCCAGGTa                                              >  1:1230298/1‑67 (MQ=255)
            tCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAgg                                           <  1:3303937/69‑1 (MQ=255)
            tCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAgg                                           <  1:372566/69‑1 (MQ=255)
            tCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAgg                                           <  1:383041/69‑1 (MQ=255)
            tCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAgg                                           <  1:1786114/69‑1 (MQ=255)
            tCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAgg                                           <  1:1267144/69‑1 (MQ=255)
            tCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAgg                                           <  1:2970278/69‑1 (MQ=255)
            tCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAgg                                           <  1:1646759/69‑1 (MQ=255)
            tCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAgg                                           <  1:221899/69‑1 (MQ=255)
            tCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAgg                                           <  1:2875744/69‑1 (MQ=255)
            tCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAgg                                           <  1:2794298/69‑1 (MQ=255)
               ccGCCAAACAGCATAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCATGTAAGGCa                                         <  1:1452186/68‑1 (MQ=255)
               ccGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTATGGCa                                         <  1:3156433/68‑1 (MQ=255)
               ccGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCa                                         <  1:3226835/68‑1 (MQ=255)
               ccGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCa                                         <  1:278398/68‑1 (MQ=255)
               ccGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCa                                         <  1:2512773/68‑1 (MQ=255)
               ccGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCa                                         <  1:3423096/68‑1 (MQ=255)
               ccGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCa                                         <  1:6873/68‑1 (MQ=255)
                cGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCa                                         <  1:424661/67‑1 (MQ=255)
                 gCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCActc                                      <  1:1154114/69‑1 (MQ=255)
                 gCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCActc                                      <  1:2884747/69‑1 (MQ=255)
                 gCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCActc                                      <  1:2383324/69‑1 (MQ=255)
                               gCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCACTCTACTGCACCGaaa                         >  1:2748602/1‑68 (MQ=255)
                               gCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCACTCTACTGCACCGaaa                         >  1:1395957/1‑68 (MQ=255)
                               gCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCACTCTACTGCACCGaaa                         >  1:1550754/1‑68 (MQ=255)
                               gCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCACTCTACTGCACCGaaa                         >  1:1132087/1‑68 (MQ=255)
                               gCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCACTCTACTGCACCGaa                          >  1:3257779/1‑67 (MQ=255)
                                  ggCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCACTCTACTGCACCGAAaacaa                     <  1:1375244/69‑1 (MQ=255)
                                           gAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCActct                                     <  1:914966/44‑1 (MQ=255)
                                           gAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCACTCTACTGCACCGAAAACAACCCGCCGt             >  1:111614/1‑68 (MQ=255)
                                           gAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCACTCTACTGCACCGAAAACAACCCGCCGt             >  1:920822/1‑68 (MQ=255)
                                           gAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCACTCTACTGCACCGAAAACAACCCGCCGt             >  1:918324/1‑68 (MQ=255)
                                           gAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCACTCTACTGCACCGAAAACAACCCGCCGt             >  1:703498/1‑68 (MQ=255)
                                           gAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCACTCTACTGCACCGAAAACAACCCGCCGt             >  1:393442/1‑68 (MQ=255)
                                           gAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCACTCTACTGCACCGAAAACAACCCGCCGt             >  1:1894726/1‑68 (MQ=255)
                                           gAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCACTCTACTGCACCGAAAACAACCCGCCGt             >  1:1500274/1‑68 (MQ=255)
                                           gAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCACTCTACTGCACCGAAAACAACCCGCCGt             >  1:2191679/1‑68 (MQ=255)
                                           gAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCACTCTACTGCACCGAAAACAACCCGCCGt             >  1:1735917/1‑68 (MQ=255)
                                           gAAGCTGCTGGAAACTGCCGAGCCACATGCAGGTAAGTCACTCTACTGTACCGAAAACAACccgccg              <  1:2639378/67‑1 (MQ=255)
                                           gAAGCTGCTGGAAACTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACccgccg              <  1:330133/67‑1 (MQ=255)
                                           gAAGCTGCTGGAAACTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACccgccg              <  1:2082570/67‑1 (MQ=255)
                                           gAAGCTGCTGGAAACTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACccgccg              <  1:357386/67‑1 (MQ=255)
                                           gAAGCTGCTGGAAACTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACccgccg              <  1:1834479/67‑1 (MQ=255)
                                           gAAGCTGCTGGAAACTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACccgccg              <  1:2941575/67‑1 (MQ=255)
                                           gAAGCTGCTGGAAACTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACccgccg              <  1:2393067/67‑1 (MQ=255)
                                            aaGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCActct                                     <  1:2112899/43‑1 (MQ=255)
                                               ctgctgGAGACTGCCGAACCGCATCCAGGTAAGGCACTCTACTGCACCGAAAACAACCCGCCGTTTGAt        <  1:580048/69‑1 (MQ=255)
                                               ctgctgGAGACTGCCGAACCGCATCCAGGTAAGGCACTCTACTGCACCGAAAACAACCCGCCGTTTGAt        <  1:1719534/69‑1 (MQ=255)
                                               ctgctgGAGACTGCCGAACCGCATCCAGGTAAGGCACTCTACTGCACCGAAAACAACCCGCCGTTTGAt        <  1:3082223/69‑1 (MQ=255)
                                               ctgctgGAGACTGCCGAACCGCATCCAGGTAAGGCACTCTACTGCACCGAAAACAACCCGCCGTTTGAt        <  1:1058424/69‑1 (MQ=255)
                                               ctgctgGAGACTGCCGAACCGCATCCAGGTAAGGCACTCTACTGCACCGAAAACAACCCGCCGTTTGAt        <  1:2610036/69‑1 (MQ=255)
                                                  ctgGAAACTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAaaca                      >  1:1240965/1‑52 (MQ=25)
                                                  ctgGAAACTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAAc     >  1:514371/1‑69 (MQ=255)
                                                  ctgGAAACTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAAc     >  1:1784893/1‑69 (MQ=255)
                                                  ctgGAAACTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAAc     >  1:1856091/1‑69 (MQ=255)
                                                  ctgGAAACTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAAc     >  1:1505580/1‑69 (MQ=255)
                                                  ctgGAAACTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAAc     >  1:1345464/1‑69 (MQ=255)
                                                  ctgGAAACTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAAc     >  1:1395242/1‑69 (MQ=255)
                                                  ctgGAAACTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAAc     >  1:261281/1‑69 (MQ=255)
                                                  ctgGAAACTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAAc     >  1:232890/1‑69 (MQ=255)
                                                  ctgGAAACTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAAc     >  1:225756/1‑69 (MQ=255)
                                                      attcTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATACCGGc  <  1:3412125/65‑1 (MQ=255)
                                                      attcTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAACGGc  <  1:460401/65‑1 (MQ=255)
                                                      attcTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAACGGc  <  1:2464838/65‑1 (MQ=255)
                                                      attcTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAACGGc  <  1:2780988/65‑1 (MQ=255)
                                                      attcTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAACGGc  <  1:1679624/65‑1 (MQ=255)
                                                      attcTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAACGGc  <  1:2360141/65‑1 (MQ=255)
                                                      attcTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAACGGc  <  1:1720395/65‑1 (MQ=255)
                                                      attcTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAACGGc  <  1:2843336/65‑1 (MQ=255)
                                                      attcTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAACGGc  <  1:589507/65‑1 (MQ=255)
                                                      attcTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAACGGc  <  1:49821/65‑1 (MQ=255)
                                                      attcTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAACGGc  <  1:2043713/65‑1 (MQ=255)
                                                      attcTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAACGGc  <  1:3009857/65‑1 (MQ=255)
                                                      attcTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAACGGc  <  1:407125/65‑1 (MQ=255)
                                                      attcTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAACGGc  <  1:1831284/65‑1 (MQ=255)
                                                      attcTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAACGGc  <  1:3146145/65‑1 (MQ=255)
                                                      attcTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAACGGc  <  1:2160520/65‑1 (MQ=255)
                                                      attcTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAACGGc  <  1:3232499/65‑1 (MQ=255)
                                                      attcTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAACGGc  <  1:351995/65‑1 (MQ=255)
                                                      attcTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAACGGc  <  1:1206617/65‑1 (MQ=255)
                                                      attcTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAACGGc  <  1:1924626/65‑1 (MQ=255)
                                                      attcTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAACGGc  <  1:1993824/65‑1 (MQ=255)
                                                       ttcTGCCGAGCCACATGCAGGTAAGGCACTCTACTGTACCGAAAACAACCCGCCGTTTGATAACGGc  <  1:790923/65‑1 (MQ=255)
                                                                |                                                         
AGCTGGACGGTTTCACCGCCAAACAGCAGAAGCTGGCGCTGTCGAAGCTGCTGGAGACTGCCGAACCGCATCCAGGTAAGGCACTCTACTGCACCGAAAACAACCCGCCGTTTGATAACGGC  >  minE/2183329‑2183450

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A