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 2,891,666 A→C 43.9% V107V (GTA→GTC)  ytfQ → predicted sugar transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,891,6660AC43.9% 9.7 / 91.1 82V107V (GTA→GTC) ytfQpredicted sugar transporter subunit
Reads supporting (aligned to +/- strand):  ref base A (18/28);  new base C (20/16);  total (38/44)
Fisher's exact test for biased strand distribution p-value = 1.82e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

AAAAGAGGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCA  >  minE/2891636‑2891724
                              |                                                          
aaaaGAGGCGAAAGATGCCGAAATCCCGGTcttctt                                                       >  1:1081365/1‑36 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAtc                      >  1:1011213/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAtc                      >  1:2157915/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAtc                      >  1:2276384/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAtc                      >  1:278980/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAtc                      >  1:1064174/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAtc                      >  1:2809079/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAtc                      >  1:555131/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAtc                      >  1:404360/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAtc                      >  1:1451515/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAtc                      >  1:3182900/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAt                       >  1:1916312/1‑68 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAt                       >  1:1312880/1‑68 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAt                       >  1:1232104/1‑68 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAt                       >  1:640047/1‑68 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTATTCTTTCTCGATCGTTCCATTGATGTGAAAGACAAAtc                      >  1:577194/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTc                                           >  1:3287877/1‑48 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTc                                           >  1:3071453/1‑48 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTc                                           >  1:2833657/1‑48 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTc                                           <  1:632026/48‑1 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTc                                           <  1:857584/48‑1 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTc                                           >  1:920712/1‑48 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAAtc                      >  1:734304/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAAtc                      >  1:394000/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAAtc                      >  1:1176520/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAAtc                      >  1:1267536/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAAtc                      >  1:3155210/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAAtc                      >  1:1088637/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAAtc                      >  1:2058382/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGCTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAtc                      >  1:2142988/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATACCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAAtc                      >  1:1249944/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCAGAAATCCCGGTATTCTTGCTCGAt                                                >  1:3189473/1‑43 (MQ=255)
aaaaGAGGCGAAAGATGACGAAATCCCGGTATTCTTGCTCGATCGTTCCATAGATGTGAAAGACAAAt                       >  1:2915436/1‑68 (MQ=255)
    gagGCGAAAGATGCCGAAATCCCGTTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAAtctctc                  <  1:636958/69‑1 (MQ=255)
    gagGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAAtctctc                  <  1:577110/69‑1 (MQ=255)
    gagGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAAtctctc                  <  1:1884170/69‑1 (MQ=255)
    gagGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAAtctctc                  <  1:1823933/69‑1 (MQ=255)
    gagGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAAtctctc                  <  1:2478787/69‑1 (MQ=255)
      ggCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCAtt                                       <  1:1795354/46‑1 (MQ=255)
      ggCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCAtt                                       <  1:2993751/46‑1 (MQ=255)
      ggCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCAtt                                       <  1:543908/46‑1 (MQ=255)
      ggCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCAtt                                       <  1:2327048/46‑1 (MQ=255)
      ggCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCAtt                                       <  1:2304811/46‑1 (MQ=255)
      ggCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCAtt                                       <  1:1898687/46‑1 (MQ=255)
      ggCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCAtt                                       <  1:685507/46‑1 (MQ=255)
      ggCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCAtt                                       <  1:379015/46‑1 (MQ=255)
      ggCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCAtt                                       <  1:1979599/46‑1 (MQ=255)
      ggCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCAtg                                       <  1:1967305/46‑2 (MQ=255)
      ggCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCta                <  1:1486683/69‑1 (MQ=255)
      ggCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCta                <  1:807931/69‑1 (MQ=255)
      ggCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCta                <  1:488498/69‑1 (MQ=255)
      ggCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCta                <  1:1348079/69‑1 (MQ=255)
      ggCGAAAGATGACGAAATCCCGGTATTCTTGCTCGATCGTTCCAtt                                       <  1:3197667/46‑1 (MQ=255)
       gCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCAtt                                       <  1:1565902/45‑1 (MQ=255)
               tGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGaccac       >  1:1434670/1‑69 (MQ=255)
                gCCGATATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGaccacc      <  1:2289776/69‑1 (MQ=255)
                gCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGaccacc      <  1:460890/69‑1 (MQ=255)
                gCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGaccacc      <  1:433441/69‑1 (MQ=255)
                gCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGaccacc      <  1:3322186/69‑1 (MQ=255)
                gCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGaccacc      <  1:2467738/69‑1 (MQ=255)
                gCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGaccacc      <  1:2581896/69‑1 (MQ=255)
                gCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGaccacc      <  1:105863/69‑1 (MQ=255)
                gCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGaccacc      <  1:2209042/69‑1 (MQ=255)
                gCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGaccacc      <  1:884555/69‑1 (MQ=255)
                gCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGaccacc      <  1:2073244/69‑1 (MQ=255)
                gCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGaccacc      <  1:194618/69‑1 (MQ=255)
                gCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGaccacc      <  1:1631821/69‑1 (MQ=255)
                gCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGaccacc      <  1:1892750/69‑1 (MQ=255)
                gCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGaccacc      <  1:1796171/69‑1 (MQ=255)
                gCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAGAGACAAATCTCTCTATATGaccacc      >  1:2144617/1‑69 (MQ=255)
                gCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGaccacc      >  1:2841016/1‑69 (MQ=255)
                 ccGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGaccacc      <  1:2178567/68‑1 (MQ=255)
                 ccGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGaccacc      <  1:1007700/68‑1 (MQ=255)
                   gAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGt    <  1:14747/68‑1 (MQ=255)
                   gAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGt    <  1:2228744/68‑1 (MQ=255)
                   gAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTc   <  1:1596442/69‑1 (MQ=255)
                   gAAATCCCGGTATTCTTGCCCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTc   <  1:1109030/69‑1 (MQ=255)
                    aaaTCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGACCACCGtta  >  1:50656/1‑67 (MQ=255)
                    aaaTCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGACCACCGtta  >  1:301449/1‑67 (MQ=255)
                    aaaTCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGACCACCGtta  >  1:1063370/1‑67 (MQ=255)
                    aaaTCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGACCACCGtta  >  1:2193802/1‑67 (MQ=255)
                    aaaTCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGACCACCGtta  >  1:1024553/1‑67 (MQ=255)
                            gTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGt    <  1:2229149/59‑1 (MQ=255)
                              |                                                          
AAAAGAGGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCA  >  minE/2891636‑2891724

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A