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 F17 I0 R1 71 95.7 2922988 91.7% 2680379 65.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,598,488 C→T 39.9% A60A (GCG→GCA)  yfeT ← predicted DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,598,4880CT39.9% 229.9 / inf 278A60A (GCG→GCA) yfeTpredicted DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (115/52);  new base T (50/61);  total (165/113)
Fisher's exact test for biased strand distribution p-value = 1.04e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 278 total aligned reads displayed.

GCACTGTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGCCATCTG  >  minE/1598441‑1598553
                                               |                                                                 
gCACTGTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAAttt                                            <  1:2301976/71‑1 (MQ=255)
gCACTGTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAAttt                                            <  1:1991898/71‑1 (MQ=255)
gCACTGTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAAttt                                            <  1:1143262/71‑1 (MQ=255)
gCACTGTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAAttt                                            <  1:365714/71‑1 (MQ=255)
gCACTGTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAAttt                                            <  1:239162/71‑1 (MQ=255)
gCACTGTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAAttt                                            <  1:2216505/71‑1 (MQ=255)
gCACTGTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAAttt                                            <  1:1575703/71‑1 (MQ=255)
gCACTGTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAAttt                                            <  1:1551629/71‑1 (MQ=255)
gCACTGTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAAttt                                            <  1:1315067/71‑1 (MQ=255)
gCACTGTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAAttt                                            <  1:1749252/71‑1 (MQ=255)
        ttCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGc                                    >  1:516998/1‑71 (MQ=255)
        ttCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGc                                    >  1:1477695/1‑71 (MQ=255)
        ttCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGc                                    >  1:2222339/1‑71 (MQ=255)
        ttCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGc                                    >  1:2139050/1‑71 (MQ=255)
        ttCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGc                                    >  1:1170589/1‑71 (MQ=255)
                ttAACGCCATACGCAATTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTgg                            <  1:2164720/71‑1 (MQ=255)
                           cGCAATTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAg                 >  1:2800672/1‑71 (MQ=255)
                           cGCAATTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAg                 >  1:2366775/1‑71 (MQ=255)
                           cGCAATTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAg                 >  1:1703686/1‑71 (MQ=255)
                           cGCAATTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAg                 >  1:1891922/1‑71 (MQ=255)
                           cGCAATTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAg                 >  1:132867/1‑71 (MQ=255)
                           cGCAATTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAg                 >  1:2582975/1‑71 (MQ=255)
                           cGCAATTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAg                 >  1:1177718/1‑71 (MQ=255)
                           cGCAATTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAg                 >  1:2019217/1‑71 (MQ=255)
                           cGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGTGCAAATTTCACTATGCTCGACTGGCTAATGCCGAg                 >  1:1349438/1‑71 (MQ=255)
                           cGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAg                 >  1:1872559/1‑71 (MQ=255)
                           cGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAg                 >  1:2485912/1‑71 (MQ=255)
                           cGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAg                 >  1:2109588/1‑71 (MQ=255)
                           cGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAg                 >  1:239821/1‑71 (MQ=255)
                           cGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAg                 >  1:1533127/1‑71 (MQ=255)
                           cGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAg                 >  1:1508268/1‑71 (MQ=255)
                           cGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAg                 >  1:2861720/1‑71 (MQ=255)
                           cGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAg                 >  1:1361469/1‑71 (MQ=255)
                           cGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAg                 >  1:1126561/1‑71 (MQ=255)
                           cGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAg                 >  1:701437/1‑71 (MQ=255)
                             cAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGa                                >  1:2006622/1‑54 (MQ=255)
                             cAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGc                >  1:391191/1‑70 (MQ=255)
                             cAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGc                >  1:2244166/1‑70 (MQ=255)
                             cAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGc                >  1:603995/1‑70 (MQ=255)
                             cAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCt               >  1:278902/1‑71 (MQ=255)
                             cAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCt               >  1:2435109/1‑71 (MQ=255)
                             cAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCt               >  1:2471939/1‑71 (MQ=255)
                             cAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCt               >  1:2607911/1‑71 (MQ=255)
                             cAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCt               >  1:2626173/1‑71 (MQ=255)
                             cAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCt               >  1:2780967/1‑71 (MQ=255)
                             cAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCt               >  1:982511/1‑71 (MQ=255)
                             cAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCt               >  1:298002/1‑71 (MQ=255)
                             cAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCt               >  1:442100/1‑71 (MQ=255)
                             cAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCt               >  1:755341/1‑71 (MQ=255)
                             cAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCt               >  1:79092/1‑71 (MQ=255)
                             cAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCt               >  1:1829509/1‑71 (MQ=255)
                              aaTTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCAc                                         <  1:2191663/44‑1 (MQ=255)
                              aaTTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCAc                                         <  1:348324/44‑1 (MQ=255)
                              aaTTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCAc                                         <  1:487865/44‑1 (MQ=255)
                              aaTTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCAc                                         <  1:1225333/44‑1 (MQ=255)
                              aaTTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCAc                                         <  1:72427/44‑1 (MQ=255)
                              aaTTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCAc                                         <  1:1034092/44‑1 (MQ=255)
                              aaTTCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCAc                                         <  1:958275/44‑1 (MQ=255)
                                ttCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACt                                        >  1:577530/1‑43 (MQ=255)
                                ttCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTa                                       >  1:1973402/1‑44 (MQ=255)
                                ttCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTa                                       >  1:1091572/1‑44 (MQ=255)
                                ttCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTa                                       >  1:2544639/1‑44 (MQ=255)
                                ttCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTa                                       >  1:1255201/1‑44 (MQ=255)
                                ttCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTa                                       >  1:1465218/1‑44 (MQ=255)
                                ttCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTa                                       >  1:2835554/1‑44 (MQ=255)
                                ttCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTa                                       >  1:2754603/1‑44 (MQ=255)
                                ttCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTa                                       >  1:1621770/1‑44 (MQ=255)
                                ttCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAATTTCACTa                                       >  1:1547420/1‑44 (MQ=255)
                                ttCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTc                                  <  1:2089862/49‑1 (MQ=255)
                                 tCAGTAAATCCTTGTGCGCCGAGTTTTTGGGCAAAttt                                            <  1:630947/38‑1 (MQ=255)
                                  cAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTc          >  1:2407079/1‑71 (MQ=255)
                                  cAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTc          >  1:1909035/1‑71 (MQ=255)
                                    gTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCATTATGCTCGACTGGCTAATGCCGAGCTGTTTCGc        <  1:1000956/71‑1 (MQ=255)
                                    gTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGc        <  1:2740575/71‑1 (MQ=255)
                                    gTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGc        <  1:2052704/71‑1 (MQ=255)
                                    gTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGc        <  1:768363/71‑1 (MQ=255)
                                    gTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGc        <  1:1057768/71‑1 (MQ=255)
                                    gTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGc        <  1:2466519/71‑1 (MQ=255)
                                    gTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGc        <  1:1957632/71‑1 (MQ=255)
                                    gTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGc        <  1:682908/71‑1 (MQ=255)
                                    gTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGc        <  1:622436/71‑1 (MQ=255)
                                    gTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGc        <  1:2551834/71‑1 (MQ=255)
                                    gTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGc        <  1:532007/71‑1 (MQ=255)
                                    gTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGc        <  1:1603286/71‑1 (MQ=255)
                                    gTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGc        <  1:2599132/71‑1 (MQ=255)
                                    gTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGc        <  1:2845024/71‑1 (MQ=255)
                                    gTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGc        <  1:402703/71‑1 (MQ=255)
                                    gTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGc        <  1:503365/71‑1 (MQ=255)
                                    gTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGc        <  1:2695144/71‑1 (MQ=255)
                                    gTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGc        <  1:2713537/71‑1 (MQ=255)
                                    gTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGc        <  1:1407941/71‑1 (MQ=255)
                                     tAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGc        <  1:1735067/70‑1 (MQ=255)
                                          ccTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGCCATCTg  >  1:1382578/1‑71 (MQ=255)
                                          ccTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGCCATCTg  >  1:947179/1‑71 (MQ=255)
                                          ccTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGCCATCTg  >  1:841464/1‑71 (MQ=255)
                                          ccTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGCCATCTg  >  1:325982/1‑71 (MQ=255)
                                          ccTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGCCATCTg  >  1:1275620/1‑71 (MQ=255)
                                          ccTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGCCATCTg  >  1:64934/1‑71 (MQ=255)
                                          ccTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGCCATCTg  >  1:1195589/1‑71 (MQ=255)
                                          ccTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGCCATCTg  >  1:544358/1‑71 (MQ=255)
                                               |                                                                 
GCACTGTATTCGCCTATTAACGCCATACGCAATTCAGTAAATCCTTGCGCGCCGAGTTTTTGGGCAAATTTCACTATGCTCGACTGGCTAATGCCGAGCTGTTTCGCCATCTG  >  minE/1598441‑1598553

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A