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 2,109,353 C→T 36.1% L33L (CTG→TTG)  agaB → N‑acetylgalactosamine‑specific enzyme IIB component of PTS

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,109,3530CT36.1% 87.1 / 77.1 127L33L (CTG→TTG) agaBN‑acetylgalactosamine‑specific enzyme IIB component of PTS
Reads supporting (aligned to +/- strand):  ref base C (32/49);  new base T (28/18);  total (60/67)
Fisher's exact test for biased strand distribution p-value = 2.66e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.84e-01

Only 100 of 132 total aligned reads displayed.

TATTGATAACCGTCTGGTTCACGGTCAGGTTGGCGTGACCTGGACATCCACCATCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTATTACC  >  minE/2109286‑2109415
                                                                   |                                                              
tATTGATAACCGTCTGGTTCACGGTCAGGTTGGCGTGACCTGGACATCCACCATCGGTGCAAATctgct                                                               <  1:1665399/69‑1 (MQ=255)
tATTGATAACCGTCTGGTTCACGGTCAGGTTGGCGTGACCTGGACATCCACCATCGGTGCAAATctgct                                                               <  1:2930320/69‑1 (MQ=255)
tATTGATAACCGTCTGGTTCACGGTCAGGTTGGCGTGACCTGGACATCCACCATCGGTGCAAATctgct                                                               <  1:1137463/69‑1 (MQ=255)
tATTGATAACCGTCTGGTTCACGGTCAGGTTGGCGTGACCTGGACATCCACCATCGGTGCAAATctgct                                                               <  1:1930075/69‑1 (MQ=255)
tATTGATAACCGTCTGGTTCACGGTCAGGTTGGCGTGACCTGGACATCCACCATCGGTGCAAATctgct                                                               <  1:2050945/69‑1 (MQ=255)
       aaCCGTCTGGTTCACGGTCAGGTTGGCGTGACCTGGACATCCACCATCGGTGCAAATCTGCTGGTAGTc                                                        >  1:2711243/1‑69 (MQ=255)
       aaCCGTCTGGTTCACGGTCAGGTTGGCGTGACCTGGACATCCACCATCGGTGCAAATCTGCTGGTAGTc                                                        >  1:1681139/1‑69 (MQ=255)
                              tGGCGTGACCTGGACATCCACCATCGGTGCGAATCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACga                                 <  1:357365/69‑1 (MQ=255)
                              tGGCGTGACCTGGACATCCACCATCGGTGCGAATCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACga                                 <  1:1640613/69‑1 (MQ=255)
                              tGGCGTGACCTGGACATCCACCATCGGTGCGAATCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACga                                 <  1:1650269/69‑1 (MQ=255)
                              tGGCGTGACCTGGACATCCACCATCGGTGCGAATCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACga                                 <  1:1526788/69‑1 (MQ=255)
                              tGGCGTGACCTGGACATCCACCATCGGTGCGAATCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACga                                 <  1:188172/69‑1 (MQ=255)
                              tGGCGTGACCTGGACATCCACCATCGGTGCGAATCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACga                                 <  1:2345360/69‑1 (MQ=255)
                              tGGCGTGACCTGGACATCCACCATCGGTGCGAATCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACga                                 <  1:2552782/69‑1 (MQ=255)
                              tGGCGTGACCTGGACATCCACCATCGGTGCGAATCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACga                                 <  1:2674793/69‑1 (MQ=255)
                              tGGCGTGACCTGGACATCCACCATCGGTGCGAATCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACga                                 <  1:2954598/69‑1 (MQ=255)
                              tGGCGTGACCTGGACATCCACCATCGGTGCGAATCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACga                                 <  1:3116342/69‑1 (MQ=255)
                              tGGCGTGACCTGGACATCCACCATCGGTGCGAATCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACga                                 <  1:3210288/69‑1 (MQ=255)
                              tGGCGTGACCTGGACATCCACCATCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACga                                 <  1:1837837/69‑1 (MQ=255)
                              tGGCGTGACCTGGACATCCACCATCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACg                                  >  1:545143/1‑68 (MQ=255)
                               ggCGTGACCTGGACATCCACCATCGGTGCGAATCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACga                                 <  1:1006211/68‑1 (MQ=255)
                                   tGACCTGGACATCCACCATCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGata                            <  1:1946782/69‑1 (MQ=255)
                                   tGACCTGGACATCCACCATCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGata                            <  1:2483610/69‑1 (MQ=255)
                                   tGACCTGGACATCCACCATCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGata                            <  1:826021/69‑1 (MQ=255)
                                   tGACCTGGACATCCACCATCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGata                            <  1:750021/69‑1 (MQ=255)
                                   tGACCTGGACATCCACCATCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGata                            <  1:3428553/69‑1 (MQ=255)
                                   tGACCTGGACATCCACCATCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGata                            <  1:1361802/69‑1 (MQ=255)
                                   tGACCTGGACATCCACCATCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGata                            <  1:1493742/69‑1 (MQ=255)
                                   tGACCTGGACATCCACCATCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGata                            <  1:1582216/69‑1 (MQ=255)
                                   tGACCTGGACATCCACCATCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGata                            <  1:3138044/69‑1 (MQ=255)
                                    gACCTGGACATCCACCATCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGata                            <  1:1406355/68‑1 (MQ=255)
                                           aCATCCACCATCGGTGCGAATCTGTTGGTAGTCGt                                                      >  1:3093093/1‑35 (MQ=38)
                                           aCATCCACCATCGGTGCGAATCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAAc                      >  1:584601/1‑67 (MQ=255)
                                           aCATCCACCATCGGTGCGAATCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACa                     >  1:3032756/1‑68 (MQ=255)
                                           aCATCCACCATCGGTGCGAATCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACa                     >  1:2293396/1‑68 (MQ=255)
                                           aCATCCACCATCGGTGCGAATCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACa                     >  1:1239909/1‑68 (MQ=255)
                                           aCATCCACCATCGGTGCGAATCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACa                     >  1:1872601/1‑68 (MQ=255)
                                           aCATCCACCATCGGTGCGAATCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACa                     >  1:3357987/1‑68 (MQ=255)
                                           aCATCCACCATCGGTGCGAATCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACa                     >  1:1933706/1‑68 (MQ=255)
                                           aCATCCACCATCGGTGCGAATCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACa                     >  1:299400/1‑68 (MQ=255)
                                           aCATCCACCATCGGTGCGAATCTGTTGGTAGTCGTGGATGATGTTGTCGATAACGATGATATTCAACa                     >  1:3132790/1‑68 (MQ=255)
                                                caccaTCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               <  1:278368/69‑1 (MQ=255)
                                                caccaTCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               >  1:876594/1‑69 (MQ=255)
                                                caccaTCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               <  1:2945506/69‑1 (MQ=255)
                                                caccaTCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               >  1:1150215/1‑69 (MQ=255)
                                                caccaTCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               >  1:1092075/1‑69 (MQ=255)
                                                caccaTCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               <  1:2560531/69‑1 (MQ=255)
                                                caccaTCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               <  1:2387164/69‑1 (MQ=255)
                                                caccaTCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               >  1:2509342/1‑69 (MQ=255)
                                                caccaTCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               <  1:3301617/69‑1 (MQ=255)
                                                caccaTCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               >  1:1567976/1‑69 (MQ=255)
                                                caccaTCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               >  1:226765/1‑69 (MQ=255)
                                                caccaTCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               <  1:1769722/69‑1 (MQ=255)
                                                caccaTCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               >  1:2109057/1‑69 (MQ=255)
                                                caccaTCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               <  1:2074857/69‑1 (MQ=255)
                                                caccaTCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               <  1:1870036/69‑1 (MQ=255)
                                                caccaTCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               >  1:520381/1‑69 (MQ=255)
                                                caccaTCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAt                >  1:1145697/1‑68 (MQ=255)
                                                 accaTCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               <  1:3283160/68‑1 (MQ=255)
                                                    aTCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATTATATTCAACAGAAATTAATg           <  1:498460/69‑1 (MQ=255)
                                                       ggTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCt                                      <  1:2241569/39‑1 (MQ=255)
                                                       ggTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCt                                      <  1:2636695/39‑1 (MQ=255)
                                                       ggTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCt                                      <  1:3420882/39‑1 (MQ=255)
                                                       ggTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCt                                      <  1:735786/39‑1 (MQ=255)
                                                       ggTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               <  1:355800/62‑1 (MQ=255)
                                                       ggTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               <  1:3102823/62‑1 (MQ=255)
                                                       ggTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               <  1:196435/62‑1 (MQ=255)
                                                       ggTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               <  1:1970279/62‑1 (MQ=255)
                                                       ggTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               <  1:1105177/62‑1 (MQ=255)
                                                       ggTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               <  1:1628504/62‑1 (MQ=255)
                                                       ggTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAAtt               <  1:2473083/62‑1 (MQ=255)
                                                       ggTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGt        >  1:478679/1‑69 (MQ=255)
                                                       ggTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGt        >  1:2185644/1‑69 (MQ=255)
                                                       ggTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGt        >  1:1717614/1‑69 (MQ=255)
                                                       ggTGCAAATCTGCTGGTAGTCGT‑GATGATGTTGTCGCt                                      <  1:3237649/38‑1 (MQ=38)
                                                          gCAAATCTGCTTGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTAtt     <  1:2973792/69‑1 (MQ=255)
                                                          gCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTaa                                    >  1:556318/1‑38 (MQ=255)
                                                          gCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTAtt     >  1:1011797/1‑69 (MQ=255)
                                                          gCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTAtt     >  1:3223638/1‑69 (MQ=255)
                                                          gCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTAtt     >  1:2760872/1‑69 (MQ=255)
                                                          gCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTAtt     <  1:2625414/69‑1 (MQ=255)
                                                          gCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTAtt     <  1:1549925/69‑1 (MQ=255)
                                                          gCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTAtt     >  1:1994394/1‑69 (MQ=255)
                                                          gCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTAtt     >  1:1776286/1‑69 (MQ=255)
                                                           cAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGa                   >  1:3431608/1‑54 (MQ=255)
                                                           cAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAAAAGAAATTAATGGGTATTa    >  1:1356759/1‑69 (MQ=255)
                                                             aaTCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTATTAcc  >  1:337106/1‑69 (MQ=255)
                                                             aaTCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTATTAcc  >  1:2735155/1‑69 (MQ=255)
                                                             aaTCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTATTAcc  >  1:1427021/1‑69 (MQ=255)
                                                             aaTCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTATTAcc  >  1:2108418/1‑69 (MQ=255)
                                                             aaTCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTATTAc   >  1:945906/1‑68 (MQ=255)
                                                              aTCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTATTAc   >  1:1784906/1‑67 (MQ=255)
                                                              aTCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTATTAc   >  1:1904302/1‑67 (MQ=255)
                                                              aTCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTATTAc   >  1:368807/1‑67 (MQ=255)
                                                              aTCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTATTAc   >  1:728558/1‑67 (MQ=255)
                                                              aTCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTATTAc   >  1:2119945/1‑67 (MQ=255)
                                                              aTCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTATTAc   >  1:2480637/1‑67 (MQ=255)
                                                              aTCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTATTAc   >  1:1253088/1‑67 (MQ=255)
                                                              aTCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTATTAc   >  1:1032625/1‑67 (MQ=255)
                                                              aTCTGTTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTATTAc   >  1:3172809/1‑67 (MQ=255)
                                                                   |                                                              
TATTGATAACCGTCTGGTTCACGGTCAGGTTGGCGTGACCTGGACATCCACCATCGGTGCAAATCTGCTGGTAGTCGTGGATGATGTTGTCGCTAACGATGATATTCAACAGAAATTAATGGGTATTACC  >  minE/2109286‑2109415

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