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 2,687,910 A→G 50.6% A123A (GCT→GCC)  pck ← phosphoenolpyruvate carboxykinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,687,9100AG50.6% ‑2.5 / 81.9 89A123A (GCT→GCC) pckphosphoenolpyruvate carboxykinase
Reads supporting (aligned to +/- strand):  ref base A (26/18);  new base G (35/10);  total (61/28)
Fisher's exact test for biased strand distribution p-value = 7.02e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.16e-01

CAGGCCACTTCGGTGATGAAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGCCTTTCAGATG  >  minE/2687851‑2687969
                                                           |                                                           
cAGGCCACTTCGGTGATGAAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGAc                                                     >  1:2084214/1‑68 (MQ=255)
cAGGCCACTTCGGTGATGAAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGAc                                                     >  1:1354092/1‑68 (MQ=255)
cAGGCCACTTCGGTGATGAAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGAc                                                     >  1:194624/1‑68 (MQ=255)
cAGGCCACTTCGGTGATGAAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACa                                                    >  1:2724599/1‑69 (MQ=255)
cAGGCCACTTCGGTGATGAAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACa                                                    >  1:2314554/1‑69 (MQ=255)
cAGGCCACTTCGGTGATGAAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACa                                                    >  1:2014096/1‑69 (MQ=255)
cAGGCCACTTCGGTGATGAAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACa                                                    >  1:2992110/1‑69 (MQ=255)
cAGGCCACTTCGGTGATGAAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACa                                                    >  1:1851355/1‑69 (MQ=255)
cAGGCCACTTCGGTGATGAAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACa                                                    >  1:3084713/1‑69 (MQ=255)
cAGGCCACTTCGGTGATGAAACGGACGGAAAGACGAGTATCCGGGATCGCACCACAGAAGGCGTCGACa                                                    >  1:2472255/1‑69 (MQ=255)
cAGGCCACTTCGGTGATGAAACGGACGGAAAGACGAGTATCCGCGTTCGCACCACAGAAGGCGTCGACa                                                    >  1:1285701/1‑69 (MQ=255)
    ccACTTCGGTGATGAAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAACGa                                                <  1:1105676/69‑1 (MQ=255)
    ccACTTCGGTGATGAAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAACGa                                                <  1:2366600/69‑1 (MQ=255)
    ccACTTCGGTGATGAAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAACGa                                                <  1:3044843/69‑1 (MQ=255)
    ccACTTCGGTGATGAAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAACGa                                                <  1:1699781/69‑1 (MQ=255)
    ccACTTCGGTGATGAAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAACGa                                                <  1:747859/69‑1 (MQ=255)
    ccACTTCGGTGATGAAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAACGa                                                <  1:402127/69‑1 (MQ=255)
     cACTTCGGTGATGAAACGTACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAACGa                                                <  1:1305835/68‑1 (MQ=255)
     cACTTCGGTGATGAAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAACGa                                                <  1:2833296/68‑1 (MQ=255)
     cACTTCGGTGATGAAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAACGa                                                <  1:1799286/68‑1 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:2204809/1‑54 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:1224123/1‑54 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:2099657/1‑54 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:2142837/1‑54 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:2171160/1‑54 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:333354/1‑54 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:2272800/1‑54 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:2300394/1‑54 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:1195437/1‑54 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:784066/1‑54 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:835692/1‑54 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:2677557/1‑54 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:2930888/1‑54 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:1969144/1‑54 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:667129/1‑54 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:663092/1‑54 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:3058742/1‑54 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:1744665/1‑54 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:1710054/1‑54 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:3426915/1‑54 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:3158857/1‑54 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:1522298/1‑54 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:1677033/1‑54 (MQ=255)
                 gaAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAAc                                                  >  1:3347512/1‑54 (MQ=255)
                           aaaaGACGAGTATCCGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGc                         <  1:2858909/68‑1 (MQ=255)
                           aaaaGACGAGTATCCGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGc                         <  1:2405743/68‑1 (MQ=255)
                           aaaaGACGAGTATCCGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGc                         <  1:1148251/68‑1 (MQ=255)
                           aaaaGACGAGTATCCGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGc                         <  1:1000368/68‑1 (MQ=255)
                               gACGAGTATCCGGGTTCGCACCACAGAAGGCGTCGACAACGa                                                <  1:1152348/42‑1 (MQ=255)
                                       tCCGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAgg             >  1:2611764/1‑69 (MQ=255)
                                       tCCGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAgg             >  1:832812/1‑69 (MQ=255)
                                       tCCGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAgg             >  1:3355435/1‑69 (MQ=255)
                                       tCCGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAgg             >  1:1649637/1‑69 (MQ=255)
                                       tCCGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAgg             >  1:329757/1‑69 (MQ=255)
                                       tCCGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAgg             >  1:1773067/1‑69 (MQ=255)
                                       tCCGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAgg             >  1:1879521/1‑69 (MQ=255)
                                       tCCGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAgg             >  1:296733/1‑69 (MQ=255)
                                       tCCGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAgg             >  1:2917073/1‑69 (MQ=255)
                                       tCCGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCAGAAAGCTGCCTGGTCACCAgg             >  1:365490/1‑69 (MQ=255)
                                         cGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGcc           >  1:382985/1‑69 (MQ=255)
                                         cGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGcc           >  1:63046/1‑69 (MQ=255)
                                         cGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGcc           >  1:1889547/1‑69 (MQ=255)
                                         cGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGcc           >  1:3421211/1‑69 (MQ=255)
                                         cGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGcc           >  1:1391352/1‑69 (MQ=255)
                                         cGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGcc           >  1:2318901/1‑69 (MQ=255)
                                         cGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGcc           >  1:1641168/1‑69 (MQ=255)
                                         cGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGcc           >  1:2310219/1‑69 (MQ=255)
                                         cGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGcc           >  1:3291530/1‑69 (MQ=255)
                                         cGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGcc           >  1:701146/1‑69 (MQ=255)
                                         cGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGcc           >  1:2387735/1‑69 (MQ=255)
                                         cGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGcc           >  1:853476/1‑69 (MQ=255)
                                         cGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGcc           >  1:3039576/1‑69 (MQ=255)
                                             ttCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGCCt          >  1:2992839/1‑66 (MQ=255)
                                              tCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGCCTTTCa      <  1:1378157/69‑1 (MQ=255)
                                              tCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGCCTTTCa      <  1:3089280/69‑1 (MQ=255)
                                               cGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTGACCAGGCCTTTCAg     <  1:1486792/69‑1 (MQ=255)
                                               cGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGCCTTTCAg     <  1:1474270/69‑1 (MQ=255)
                                               cGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGCCTTTCAg     <  1:436172/69‑1 (MQ=255)
                                               cGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGCCTTTCAg     <  1:367289/69‑1 (MQ=255)
                                               cGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGCCTTTCAg     <  1:1433818/69‑1 (MQ=255)
                                               cGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGCCTTTCAg     <  1:3418002/69‑1 (MQ=255)
                                               cGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGCCTTTCAg     <  1:3230360/69‑1 (MQ=255)
                                               cGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGCCTTTCAg     <  1:1708641/69‑1 (MQ=255)
                                               cGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGCCTTTCAg     <  1:2639058/69‑1 (MQ=255)
                                               cGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGCCTTTCAg     <  1:1974629/69‑1 (MQ=255)
                                               cGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGCCTTTCAg     <  1:904341/69‑1 (MQ=255)
                                                 caccacAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGCCTTTCAGa    <  1:170797/68‑1 (MQ=255)
                                                  accacAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGCCTTTCAGAtg  >  1:531601/1‑69 (MQ=255)
                                                  accacAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGCCTTTCAGAt   >  1:254464/1‑68 (MQ=255)
                                                           |                                                           
CAGGCCACTTCGGTGATGAAACGGACGGAAAGACGAGTATCCGGGTTCGCACCACAGAAAGCGTCGACAACGAACAGACGTTTGCCGGAAAGCTGCCTGGTCACCAGGCCTTTCAGATG  >  minE/2687851‑2687969

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