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 2,687,100 A→C 54.9% G393G (GGT→GGG)  pck ← phosphoenolpyruvate carboxykinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,687,1000AC54.9% 30.8 / 82.3 82G393G (GGT→GGG) pckphosphoenolpyruvate carboxykinase
Reads supporting (aligned to +/- strand):  ref base A (10/27);  new base C (28/17);  total (38/44)
Fisher's exact test for biased strand distribution p-value = 1.88e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

CCGCGCCGAAGCAAGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTGATACTGGGTTTGATCGGCAGTCAG  >  minE/2687045‑2687159
                                                       |                                                           
ccGCGCCGAAGCAAGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTgg                                                >  1:1006381/1‑69 (MQ=255)
ccGCGCCGAAGCAAGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTgg                                                >  1:1741838/1‑69 (MQ=255)
ccGCGCCGAAGCAAGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTgg                                                >  1:1972667/1‑69 (MQ=255)
ccGCGCCGAAGCAAGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTgg                                                >  1:20123/1‑69 (MQ=255)
ccGCGCCGAAGCAAGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTgg                                                >  1:3204597/1‑69 (MQ=255)
ccGCGCCGAAGCAAGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTgg                                                >  1:2847925/1‑69 (MQ=255)
ccGCGCCGAAGCAAGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTgg                                                >  1:2346039/1‑69 (MQ=255)
ccGCGCCGAAGCAAGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTgg                                                >  1:2629058/1‑69 (MQ=255)
ccGCGCCGAAGCAAGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTgg                                                >  1:2520655/1‑69 (MQ=255)
ccGCGCCGAAGCAAGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTAAGTACCGGCCAGTTTgg                                                >  1:2108685/1‑69 (MQ=255)
   cgcCGAAGCAGGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCgg                                             <  1:187835/69‑1 (MQ=255)
   cgcCGAAGCAGGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCgg                                             <  1:1112125/69‑1 (MQ=255)
   cgcCGAAGCAGGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCgg                                             <  1:2269584/69‑1 (MQ=255)
   cgcCGAAGCAGGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCgg                                             <  1:2319372/69‑1 (MQ=255)
   cgcCGAAGCAGGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCgg                                             <  1:2539504/69‑1 (MQ=255)
   cgcCGAAGCAGGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCgg                                             <  1:2682988/69‑1 (MQ=255)
   cgcCGAAGCAGGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCgg                                             <  1:3204422/69‑1 (MQ=255)
   cgcCGAAGCAGGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCgg                                             <  1:404465/69‑1 (MQ=255)
   cgcCGAAGCAGGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCgg                                             <  1:408680/69‑1 (MQ=255)
   cgcCGAAGCAGGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCgg                                             <  1:525292/69‑1 (MQ=255)
   cgcCGAAGCAGGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCgg                                             <  1:592355/69‑1 (MQ=255)
   cgcCGAAGCAGGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCgg                                             <  1:750663/69‑1 (MQ=255)
   cgcCGAAGCAGGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCgg                                             <  1:927642/69‑1 (MQ=255)
   cgcCGAAGCAGGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCgg                                             <  1:1441352/69‑1 (MQ=255)
   cgcCGAAGCAGGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCgg                                             <  1:1332438/69‑1 (MQ=255)
   cgcCGAAGCAGGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCgg                                             <  1:130263/69‑1 (MQ=255)
   cgcCGAAGCAGGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCgg                                             <  1:1196351/69‑1 (MQ=255)
           caagcGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCa                                     <  1:917275/69‑1 (MQ=255)
           caagcGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGACa                                     <  1:3042602/69‑1 (MQ=255)
                  agaAGGTTGGCGTCGGTTCGGTTATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGa                              <  1:1365020/69‑1 (MQ=255)
                  agaAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGa                              <  1:1722008/69‑1 (MQ=255)
                  agaAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGa                              <  1:3195769/69‑1 (MQ=255)
                  agaAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGa                              <  1:31129/69‑1 (MQ=255)
                  agaAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGa                              <  1:2286293/69‑1 (MQ=255)
                  agaAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGa                              <  1:1576345/69‑1 (MQ=255)
                  agaAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGa                              <  1:1795151/69‑1 (MQ=255)
                  agaAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGa                              <  1:2551846/69‑1 (MQ=255)
                     aGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGt                           <  1:612137/69‑1 (MQ=255)
                     aGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGt                           <  1:996075/69‑1 (MQ=255)
                     aGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGt                           <  1:816484/69‑1 (MQ=255)
                     aGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGt                           <  1:2892639/69‑1 (MQ=255)
                     aGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGt                           <  1:1495646/69‑1 (MQ=255)
                     aGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGt                           <  1:1839280/69‑1 (MQ=255)
                     aGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGt                           <  1:1986813/69‑1 (MQ=255)
                      ggTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGt                           <  1:2584023/68‑1 (MQ=255)
                      ggTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGt                           <  1:1165443/68‑1 (MQ=255)
                        ttGGCGTCGGTTTGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTggt                        >  1:2975358/1‑67 (MQ=255)
                        ttGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCa                                                      >  1:247538/1‑39 (MQ=255)
                        ttGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTggt                        >  1:2063052/1‑67 (MQ=255)
                        ttGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTggt                        >  1:444035/1‑67 (MQ=255)
                        ttGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTggt                        >  1:1282676/1‑67 (MQ=255)
                        ttGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTggt                        >  1:3408821/1‑67 (MQ=255)
                        ttGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTggt                        >  1:339459/1‑67 (MQ=255)
                        ttGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTggt                        >  1:1673002/1‑67 (MQ=255)
                        ttGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTggt                        >  1:2233174/1‑67 (MQ=255)
                        ttGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTggt                        >  1:1579002/1‑67 (MQ=255)
                        ttGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTggt                        >  1:1563094/1‑67 (MQ=255)
                        ttGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTggt                        >  1:1960403/1‑67 (MQ=255)
                        ttGGCGTCGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTggt                        >  1:1466992/1‑67 (MQ=255)
                        ttGGCGTAGGTTCGGTGATGCCACGCTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTggt                        >  1:555114/1‑67 (MQ=255)
                                  ttcggtGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTGATACTGGGTTTg              <  1:843258/69‑1 (MQ=255)
                                  ttcggtGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTGATACTGGGTTTg              <  1:1288455/69‑1 (MQ=255)
                                  ttcggtGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTGATACTGGGTTTg              <  1:391921/69‑1 (MQ=255)
                                  ttcggtGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTGATACTGGGTTTg              <  1:2790294/69‑1 (MQ=255)
                                  ttcggtGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTGATACTGGGTTTg              <  1:284359/69‑1 (MQ=255)
                                  ttcggtGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTGATACTGGGTTTg              <  1:2219351/69‑1 (MQ=255)
                                   tcggtGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTGATACTGGGTTTg              <  1:777632/68‑1 (MQ=255)
                                   tcggtGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTGATACTGGGTTTg              <  1:773572/68‑1 (MQ=255)
                                                 cTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTGGTACTGGGTTTGATCGGCAGTCAg  >  1:431679/1‑66 (MQ=255)
                                                 cTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTGGTACTGGGTTTGATCGGCAGTCAg  >  1:974170/1‑66 (MQ=255)
                                                 cTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTGGTACTGGGTTTGATCGGCAGTCAg  >  1:1160254/1‑66 (MQ=255)
                                                 cTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTGGTACTGGGTTTGATCGGCAGTCAg  >  1:1445220/1‑66 (MQ=255)
                                                 cTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTGGTACTGGGTTTGATCGGCAGTCAg  >  1:757411/1‑66 (MQ=255)
                                                 cTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTGGTACTGGGTTTGATCGGCAGTCAg  >  1:2279472/1‑66 (MQ=255)
                                                 cTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTGGTACTGGGTTTGATCGGCAGTCAg  >  1:664948/1‑66 (MQ=255)
                                                 cTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTGGTACTGGGTTTGATCGGCAGTCAg  >  1:630517/1‑66 (MQ=255)
                                                 cTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTGGTACTGGGTTTGATCGGCAGTCAg  >  1:2190601/1‑66 (MQ=255)
                                                 cTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTGGTACTGGGTTTGATCGGCAGTCAg  >  1:1642348/1‑66 (MQ=255)
                                                 cTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTGGTACTGGGTTTGATCGGCAGTCAg  >  1:360623/1‑66 (MQ=255)
                                                 cTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTGGTACTGGGTTTGATCGGCAGTCAg  >  1:49210/1‑66 (MQ=255)
                                                 cTCAGTCCCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTGGTACTGGGTTTGATCGGCAGTCAg  >  1:1500956/1‑66 (MQ=255)
                                                 cTCAGTCCCGGACAGTTTGGCGGTGAAGCCAGAGAGGAAGTGGTACTGGGTTTGATCGGCAGTCAg  >  1:1815230/1‑66 (MQ=255)
                                                       |                                                           
CCGCGCCGAAGCAAGCGGAGAAGGTTGGCGTCGGTTCGGTGATGCCACGCTCAGTACCGGCCAGTTTGGCGGTGAAGCCAGAGAGGAAGTGATACTGGGTTTGATCGGCAGTCAG  >  minE/2687045‑2687159

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