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 2,647,670 A→G 48.9% G26G (GGA→GGG)  glgB → 1,4‑alpha‑glucan branching enzyme

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,647,6700AG48.9% ‑4.1 / 67.4 75G26G (GGA→GGG) glgB1,4‑alpha‑glucan branching enzyme
Reads supporting (aligned to +/- strand):  ref base A (20/18);  new base G (18/18);  total (38/37)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCGATAGAGACGTGATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTCCGTGCCCTTTTACCCGACGCTACCGATG  >  minE/2647605‑2647728
                                                                 |                                                          
aTCGATAGAGACGTGATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAAt                                                          >  1:2465173/1‑68 (MQ=255)
aTCGATAGAGACGTGATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATg                                                         >  1:307301/1‑69 (MQ=255)
aTCGATAGAGACGTGATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATg                                                         >  1:1853042/1‑69 (MQ=255)
aTCGATAGAGACGTGATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATg                                                         >  1:136901/1‑69 (MQ=255)
aTCGATAGAGACGTGATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATg                                                         >  1:545941/1‑69 (MQ=255)
aTCGATAGAGACGTGATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATg                                                         >  1:161898/1‑69 (MQ=255)
 tCGATAGAGACGTGATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATg                                                         >  1:2600702/1‑68 (MQ=255)
 tCGATAGAGACGTGATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATg                                                         >  1:3390972/1‑68 (MQ=255)
      agagACGTGATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATaaa                                                   >  1:137330/1‑69 (MQ=255)
      agagACGTGATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATaaa                                                   >  1:354479/1‑69 (MQ=255)
         gaCGTGATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAac                                                 <  1:867179/68‑1 (MQ=255)
         gaCGTGATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAac                                                 <  1:1590051/68‑1 (MQ=255)
         gaCGTGATTAACGCGCTAATTGCAGGCCATATTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAac                                                 <  1:418938/68‑1 (MQ=255)
              gATTAACGCGCTAATTGCAGTCCATTTTGCGGATCCTTTTTCCGTACTGGGGATGCATAAAACCACcgc                                           <  1:805636/69‑1 (MQ=255)
              gATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGTATGCATAAAACCACcgc                                           <  1:3373143/69‑1 (MQ=255)
              gATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGATGCATAAAACCACcgc                                           <  1:2603630/69‑1 (MQ=255)
              gATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGATGCATAAAACCACcgc                                           <  1:2427372/69‑1 (MQ=255)
              gATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGATGCATAAAACCACcgc                                           <  1:2799898/69‑1 (MQ=255)
              gATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGATGCATAAAACCACcgc                                           <  1:1305298/69‑1 (MQ=255)
              gATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGATGCATAAAACCACcgc                                           <  1:3117170/69‑1 (MQ=255)
              gATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGATGCATAAAACCACcgc                                           <  1:372814/69‑1 (MQ=255)
              gATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGATGCATAAAACCACcgc                                           <  1:533825/69‑1 (MQ=255)
              gATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGATGCATAAAACCACcgc                                           <  1:77551/69‑1 (MQ=255)
              gATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGATGCATAAAACCACcgc                                           <  1:870074/69‑1 (MQ=255)
              gATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGATGCATAAAACCACcgc                                           <  1:1132045/69‑1 (MQ=255)
              gATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGATGCATAAAACCACcgc                                           <  1:1308059/69‑1 (MQ=255)
              gATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGATGCATAAAACCACcgc                                           <  1:187058/69‑1 (MQ=255)
              gATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGATGCATAAAACCACcgc                                           <  1:1390434/69‑1 (MQ=255)
              gATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAACCACcgc                                           >  1:486/1‑69 (MQ=255)
              gATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAACCACcgc                                           >  1:2747944/1‑69 (MQ=255)
               aTTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGAt                                                          >  1:2929890/1‑53 (MQ=255)
               aTTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGAt                                                          >  1:1631558/1‑53 (MQ=255)
               aTTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGAt                                                          >  1:1617883/1‑53 (MQ=255)
               aTTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGAt                                                          >  1:1688278/1‑53 (MQ=255)
               aTTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGAt                                                          >  1:1701232/1‑53 (MQ=255)
               aTTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGAt                                                          >  1:486489/1‑53 (MQ=255)
               aTTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGAt                                                          >  1:3132815/1‑53 (MQ=255)
               aTTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGAt                                                          >  1:1409872/1‑53 (MQ=255)
               aTTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGAt                                                          >  1:1864464/1‑53 (MQ=255)
               aTTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGAt                                                          >  1:600308/1‑53 (MQ=255)
               aTTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGAt                                                          >  1:2712756/1‑53 (MQ=255)
               aTTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGAt                                                          >  1:81460/1‑53 (MQ=255)
               aTTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGAt                                                          >  1:2025620/1‑53 (MQ=255)
               aTTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGAt                                                          >  1:2561194/1‑53 (MQ=255)
               aTTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGAt                                                          >  1:932093/1‑53 (MQ=255)
               aTTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGAt                                                          >  1:2409839/1‑53 (MQ=255)
               aTTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGAt                                                          >  1:2365432/1‑53 (MQ=255)
               aTTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGAt                                                          >  1:2330010/1‑53 (MQ=255)
                  aaCGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAACCACCGCGGGa                                       >  1:2159239/1‑69 (MQ=255)
                   aCGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGATGCATAAAACCACcgc                                           <  1:390560/64‑1 (MQ=255)
                        cTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGATGCATAAAACCACcgc                                           <  1:2475345/59‑1 (MQ=255)
                           aTTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGATGCATAAAACCACcgc                                           <  1:3392003/56‑1 (MQ=255)
                             tGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGGATGCATAAAACCACcgc                                           <  1:2967283/54‑1 (MQ=255)
                             tGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTc                              <  1:1559658/67‑1 (MQ=255)
                             tGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTc                              <  1:2584480/67‑1 (MQ=255)
                             tGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTc                              <  1:553228/67‑1 (MQ=255)
                             tGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTc                              <  1:2140804/67‑1 (MQ=255)
                             tGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTc                              <  1:701847/67‑1 (MQ=255)
                              gCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTc                              >  1:350614/1‑66 (MQ=255)
                              gCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTc                              >  1:3279580/1‑66 (MQ=255)
                              gCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTc                              >  1:3265115/1‑66 (MQ=255)
                              gCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTc                              >  1:751580/1‑66 (MQ=255)
                              gCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTCCg                            >  1:389007/1‑68 (MQ=255)
                              gCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTCCGt                           >  1:878376/1‑69 (MQ=255)
                              gCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTCCGt                           >  1:1788108/1‑69 (MQ=255)
                                 ggCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTCCGTGc                         <  1:2065169/68‑1 (MQ=255)
                                 ggCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTCCGTGc                         <  1:1365140/68‑1 (MQ=255)
                                 ggCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTCCGTGc                         <  1:581735/68‑1 (MQ=255)
                                 ggCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTCCGTGc                         <  1:154103/68‑1 (MQ=255)
                                       tttGCGGATCCTTTTTCCGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTCCGTGCCCTTTTa                  <  1:3171100/69‑1 (MQ=255)
                                                ccTTTTTCCGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTCCGTGCCCTTTTACCCGACGCt         <  1:965209/69‑1 (MQ=255)
                                                ccTTTTTCCGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTCCGTGCCCTTTTACCCGACGCt         <  1:377055/69‑1 (MQ=255)
                                                ccTTTTTCCGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTCCGTGCCCTTTTACCCGACGCt         <  1:869130/69‑1 (MQ=255)
                                                        cGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTCCGTGCCCTTTTACCCGACGCTACCGAtg  <  1:2025329/68‑1 (MQ=255)
                                                        cGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTCCGTGCCCTTTTACCCGACGCTACCGAtg  <  1:3002493/68‑1 (MQ=255)
                                                                 |                                                          
ATCGATAGAGACGTGATTAACGCGCTAATTGCAGGCCATTTTGCGGATCCTTTTTCCGTACTGGGAATGCATAAAACCACCGCGGGACTGGAAGTCCGTGCCCTTTTACCCGACGCTACCGATG  >  minE/2647605‑2647728

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