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
A6 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,015,211 A→G 29.8% G286G (GGT→GGC)  fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,015,2110AG29.8% 79.2 / 41.8 57G286G (GGT→GGC) fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base A (21/19);  new base G (7/10);  total (28/29)
Fisher's exact test for biased strand distribution p-value = 5.65e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.74e-01

AGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCG  >  minE/1015141‑1015280
                                                                      |                                                                     
aGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCa                                                                       >  1:2787290/1‑71 (MQ=255)
    tGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCa                                                                   <  1:2837449/71‑1 (MQ=255)
      cgcCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGa                                                                 >  1:2380973/1‑71 (MQ=255)
        ccGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCa                                                                       <  1:472444/63‑1 (MQ=255)
        ccGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGAcc                                                               <  1:2259648/71‑1 (MQ=255)
        ccGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGAcc                                                               <  1:322860/71‑1 (MQ=255)
        ccGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGAc                                                                >  1:3107929/1‑70 (MQ=255)
         cGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGAcc                                                               >  1:73788/1‑70 (MQ=255)
         cGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGAcc                                                               >  1:2369732/1‑70 (MQ=255)
         cGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGAcc                                                               <  1:2094105/70‑1 (MQ=255)
               gTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAttt                                                        >  1:1204794/1‑71 (MQ=255)
                tGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGtttct                                                       <  1:3538794/71‑3 (MQ=255)
                  gCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTgg                                                     >  1:3748278/1‑70 (MQ=255)
                  gCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTgg                                                     >  1:197621/1‑70 (MQ=255)
                    aGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTg                                                      <  1:2654428/68‑1 (MQ=255)
                    aGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTg                                                      <  1:1729927/68‑1 (MQ=255)
                      gCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCAcc                                                                     >  1:3176725/1‑51 (MQ=255)
                        gAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCAcc                                                                     <  1:2672173/49‑1 (MQ=255)
                         aaTCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGa                                              <  1:2636938/71‑1 (MQ=255)
                         aaTCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCGTCGa                                              <  1:1510792/71‑1 (MQ=255)
                          aTCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGAt                                             >  1:2149742/1‑71 (MQ=255)
                           tCACGCGGATGTCGTGAGCGAAGTATTTACCACCTAACTGCGCACCCAGACCAAGATTTTGCGCTTCGAt                                             >  1:1224255/1‑70 (MQ=255)
                                cgGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTc                                                >  1:255338/1‑62 (MQ=255)
                                    tGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCt                                   <  1:2850582/71‑1 (MQ=255)
                                      tCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCttt                                 <  1:123056/71‑1 (MQ=255)
                                         tGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCg                                               <  1:2444911/54‑1 (MQ=255)
                                          gAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTc                              >  1:1434402/1‑70 (MQ=255)
                                            gCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAg                           <  1:761127/71‑1 (MQ=255)
                                               aaGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTgggc                                                   >  1:1193010/1‑44 (MQ=12)
                                               aaGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTc                        >  1:1230023/1‑71 (MQ=255)
                                                aGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTcc                       <  1:1825202/71‑1 (MQ=255)
                                                  tATTTACCGCCAAACTGCGCGCCAAGACCGAGtttc                                                        <  1:1917897/36‑2 (MQ=12)
                                                  tATTTACCGCCAAACTGCGCGCCAAGACCGAGtttc                                                        <  1:3255009/36‑2 (MQ=12)
                                                  tATTTACCGCCAAACTGCGCGCCAAGACCGAGtttc                                                        <  1:45772/36‑2 (MQ=12)
                                                  tATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCTCTTCGATCAGCAATTCTTTTTcc                             <  1:3576004/63‑1 (MQ=255)
                                                  tATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCcac                     <  1:3951433/71‑1 (MQ=255)
                                                   aTTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCcaca                    >  1:1578601/1‑71 (MQ=255)
                                                   aTTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCcaca                    >  1:2323110/1‑71 (MQ=255)
                                                    tttACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCtt                                  <  1:3916735/56‑1 (MQ=255)
                                                      tACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCa                            >  1:3248751/1‑60 (MQ=255)
                                                      tACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATcg                 >  1:1425660/1‑71 (MQ=255)
                                                          gccaAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAgc                          <  1:38180/57‑2 (MQ=255)
                                                           ccaAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCttttt                               >  1:3846029/1‑52 (MQ=255)
                                                           ccaAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCttttt                               >  1:933603/1‑52 (MQ=255)
                                                             aaaCTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAGCTGGACATCGCGGAACg          >  1:3231890/1‑71 (MQ=255)
                                                             aaaCTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAGCTGGACATCGCGGAACg          <  1:1363336/71‑1 (MQ=255)
                                                             aaaCTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCt                                   >  1:924361/1‑46 (MQ=255)
                                                              aaCTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAGCTGGACATCGCGGAACGc         >  1:2134061/1‑71 (MQ=255)
                                                               aCTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGcc        >  1:772568/1‑71 (MQ=255)
                                                                cTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTc                        >  1:1734605/1‑54 (MQ=255)
                                                                cTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACAt                   <  1:3433633/59‑1 (MQ=255)
                                                                cTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACAt                   <  1:572389/59‑1 (MQ=255)
                                                                cTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCt       >  1:1216288/1‑71 (MQ=255)
                                                                 tGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAGCTGGACATCGCGGAACGCCt       >  1:31996/1‑70 (MQ=255)
                                                                  gcgcACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCttt                                 >  1:2006461/1‑43 (MQ=255)
                                                                    gcACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGAcc   <  1:151129/71‑1 (MQ=255)
                                                                    gcACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGAcc   <  1:164936/71‑1 (MQ=255)
                                                                     cACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCg  <  1:3950693/71‑1 (MQ=255)
                                                                     cACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCg  <  1:2768556/71‑1 (MQ=255)
                                                                      aCCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACAt                   <  1:3234393/53‑1 (MQ=255)
                                                                      |                                                                     
AGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCGCTTCGATCAGCAATTCTTTTTCCAGTTCCACATCGCGGAACGCCTGACCG  >  minE/1015141‑1015280

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