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 2,891,687 T→C 31.7% I114I (ATT→ATC)  ytfQ → predicted sugar transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,891,6870TC31.7% 127.1 / 78.5 149I114I (ATT→ATC) ytfQpredicted sugar transporter subunit
Reads supporting (aligned to +/- strand):  ref base T (60/41);  new base C (31/16);  total (92/57)
Fisher's exact test for biased strand distribution p-value = 4.74e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 161 total aligned reads displayed.

AAAAGAGGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACATCCTCGAAGGCAAGTTGAT  >  minE/2891636‑2891755
                                                   |                                                                    
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAtc                                                     >  1:1011213/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAtc                                                     >  1:2157915/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAtc                                                     >  1:1451515/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAtc                                                     >  1:278980/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAtc                                                     >  1:3182900/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAtc                                                     >  1:404360/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAt                                                      >  1:1312880/1‑68 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAt                                                      >  1:1916312/1‑68 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAt                                                      >  1:1232104/1‑68 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAAt                                                      >  1:640047/1‑68 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTATTCTTTCTCGATCGTTCCATTGATGTGAAAGACAAAtc                                                     >  1:577194/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAAtc                                                     >  1:394000/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAAtc                                                     >  1:734304/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAAtc                                                     >  1:2058382/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAAtc                                                     >  1:1267536/1‑69 (MQ=255)
aaaaGAGGCGAAAGATGACGAAATCCCGGTATTCTTGCTCGATCGTTCCATAGATGTGAAAGACAAAt                                                      >  1:2915436/1‑68 (MQ=255)
    gagGCGAAAGATGCCGAAATCCCGTTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAAtctctc                                                 <  1:636958/69‑1 (MQ=255)
    gagGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAAtctctc                                                 <  1:2478787/69‑1 (MQ=255)
      ggCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCAtt                                                                      <  1:1898687/46‑1 (MQ=255)
      ggCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCAtt                                                                      <  1:1795354/46‑1 (MQ=255)
      ggCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCAtt                                                                      <  1:2304811/46‑1 (MQ=255)
      ggCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCAtt                                                                      <  1:543908/46‑1 (MQ=255)
      ggCGAAAGATGACGAAATCCCGGTATTCTTGCTCGATCGTTCCAtt                                                                      <  1:3197667/46‑1 (MQ=255)
       gCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCAtt                                                                      <  1:1565902/45‑1 (MQ=255)
               tGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGaccac                                      >  1:1434670/1‑69 (MQ=255)
                gCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGaccacc                                     <  1:2467738/69‑1 (MQ=255)
                gCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGaccacc                                     <  1:2209042/69‑1 (MQ=255)
                gCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGaccacc                                     <  1:884555/69‑1 (MQ=255)
                gCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGaccacc                                     <  1:460890/69‑1 (MQ=255)
                gCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGaccacc                                     <  1:1892750/69‑1 (MQ=255)
                gCCGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGaccacc                                     <  1:1796171/69‑1 (MQ=255)
                gCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAGAGACAAATCTCTCTATATGaccacc                                     >  1:2144617/1‑69 (MQ=255)
                 ccGAAATCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGaccacc                                     <  1:1007700/68‑1 (MQ=255)
                   gAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGt                                   <  1:14747/68‑1 (MQ=255)
                   gAAATCCCGGTATTCTTGCCCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTc                                  <  1:1109030/69‑1 (MQ=255)
                    aaaTCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGACCACCGtta                                 >  1:301449/1‑67 (MQ=255)
                    aaaTCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGACCACCGtta                                 >  1:1063370/1‑67 (MQ=255)
                    aaaTCCCGGTCTTCTTGCTTGACCGTTCCATCGATGTGAAAGACAAATCTCTCTATATGACCACCGtta                                 >  1:2193802/1‑67 (MQ=255)
                            gTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGt                                   <  1:2229149/59‑1 (MQ=255)
                               ttCTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGacaac                      >  1:80789/1‑69 (MQ=255)
                               ttCTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGacaac                      >  1:3126726/1‑69 (MQ=255)
                               ttCTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGacaac                      >  1:2292818/1‑69 (MQ=255)
                               ttCTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGacaac                      >  1:3125140/1‑69 (MQ=255)
                                 cTTGCTCTATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTc                                  <  1:2587609/55‑1 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAAtctctc                                                 >  1:2758008/1‑40 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTc                                  <  1:2118818/55‑1 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTc                                  <  1:422150/55‑1 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTc                                  <  1:135363/55‑1 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTc                                  <  1:473807/55‑1 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTc                                  <  1:501516/55‑1 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTc                                  <  1:121427/55‑1 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTc                                  <  1:365997/55‑1 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTc                                  <  1:1082434/55‑1 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTc                                  <  1:1529729/55‑1 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTc                                  <  1:61552/55‑1 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTc                                  <  1:2365352/55‑1 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCa                                 >  1:2997748/1‑56 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGacaaca                     >  1:2425988/1‑68 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGacaaca                     >  1:2595487/1‑68 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGacaaca                     >  1:1940302/1‑68 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACAt                    >  1:3412012/1‑69 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACAt                    >  1:3252916/1‑69 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACAt                    >  1:1861163/1‑69 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACAt                    >  1:3207361/1‑69 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACAt                    >  1:512736/1‑69 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACAt                    >  1:1088101/1‑69 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACAt                    >  1:566272/1‑69 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACAt                    >  1:621220/1‑69 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACAt                    >  1:1032570/1‑69 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACAt                    >  1:811947/1‑69 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACAt                    >  1:857306/1‑69 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACAt                    >  1:1997068/1‑69 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACAt                    >  1:2828904/1‑69 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACAt                    >  1:1630022/1‑69 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACAt                    >  1:2008276/1‑69 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCCCTATATGACCACCGTc                                  <  1:3084824/55‑1 (MQ=255)
                                 cTTGCTCGATCGTTCCATTGATATGAAAGACAAATCTCTCTATATGACCACCGTc                                  <  1:109484/55‑1 (MQ=255)
                                        gaccGTTCCATCGATGTGAAAGACAAATCTCTCTATATGACCACCGTTACTGCCGACAACATCCTCGa              >  1:1263351/4‑68 (MQ=255)
                                        gaccGTTCCATCGATGTGAAAGACAAATCTCTCTATATGACCACCGTTACTGCCGACAACATCCTCGa              >  1:3275371/4‑68 (MQ=255)
                                        gaccGTTCCATCGATGTGAAAGACAAATCTCTCTATATGACCACCGTTACTGCCGACAACATCCTCGa              >  1:2263113/4‑68 (MQ=255)
                                        gaccGTTCCATCGATGTGAAAGACAAATCTCTCTATATGACCACCGTTACTGCCGACAACATCCTCGa              >  1:237410/4‑68 (MQ=255)
                                        gaccGTTCCATCGATGTGAAAGACAAATCTCTCTATATGACCACCGTTACTGCCGACAACATCCTCGa              >  1:2575588/4‑68 (MQ=255)
                                        gaccGTTCCATCGATGTGAAAGACAAATCTCTCTATATGACCACCGTTACTGCCGACAACATACt                 >  1:1673815/4‑65 (MQ=255)
                                            gTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACATCCTCGAAGGCa         <  1:1948592/69‑1 (MQ=255)
                                            gTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACATCCTCGAAGGCa         <  1:2979397/69‑1 (MQ=255)
                                            gTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACATCCTCGAAGGCa         <  1:1684803/69‑1 (MQ=255)
                                            gTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGGCACTGCCGACAACATCCTCGAAGGCa         <  1:1408679/69‑1 (MQ=255)
                                               ccATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTc                                  >  1:867261/1‑41 (MQ=255)
                                               ccATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTc                                  >  1:2144183/1‑41 (MQ=255)
                                               ccATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTc                                  >  1:123965/1‑41 (MQ=255)
                                               ccATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTc                                  >  1:704262/1‑41 (MQ=255)
                                               ccATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTc                                  >  1:1053344/1‑41 (MQ=255)
                                               ccATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTc                                  >  1:571222/1‑41 (MQ=255)
                                               ccATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTc                                  >  1:2655424/1‑41 (MQ=255)
                                               ccATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACATCCTCGAAGGCAAg       >  1:663990/1‑68 (MQ=255)
                                               ccATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACATCCTCGAAGGCAAg       >  1:2286558/1‑68 (MQ=255)
                                               ccATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACATCCTCGAAGGCAAg       >  1:795244/1‑68 (MQ=255)
                                               ccATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACATCCTCGAAGGCAAg       >  1:2040595/1‑68 (MQ=255)
                                               ccATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACATCCTCGAAGGCAAg       >  1:2544933/1‑68 (MQ=255)
                                               ccATTGATGTGAAAGACAAATCTCTCTAAATGACCACCGTCACTGCCGACAACATCCTCGAAGGCAAg       >  1:3030830/1‑68 (MQ=255)
                                                   |                                                                    
AAAAGAGGCGAAAGATGCCGAAATCCCGGTATTCTTGCTCGATCGTTCCATTGATGTGAAAGACAAATCTCTCTATATGACCACCGTCACTGCCGACAACATCCTCGAAGGCAAGTTGAT  >  minE/2891636‑2891755

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