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 1,462,113 C→T 20.4% A133A (GCG→GCA)  yfaT ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,462,1130CT20.4% 142.1 / 24.5 97A133A (GCG→GCA) yfaThypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (29/48);  new base T (12/8);  total (41/56)
Fisher's exact test for biased strand distribution p-value = 8.15e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01

Only 100 of 101 total aligned reads displayed.

TAACGCCCCATCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTCACA  >  minE/1462045‑1462176
                                                                    |                                                               
tAACGCCCCATCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAgc                                                                 <  1:1573077/69‑1 (MQ=255)
tAACGCCCCATCCAGACCATTAAGTGCTGGGCATCGACCTGATCGAAAAAAATCATATCGCCAGGCAgc                                                                 <  1:1379457/69‑1 (MQ=255)
     ccccATCCAGACCGTTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGTGCCTg                                                            <  1:2452305/69‑1 (MQ=255)
     ccccATCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGTGCCTg                                                            <  1:2027752/69‑1 (MQ=255)
     ccccATCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGTGCCTg                                                            <  1:10152/69‑1 (MQ=255)
     ccccATCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGTGCCTg                                                            <  1:2220933/69‑1 (MQ=255)
     ccccATCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGTGCCTg                                                            <  1:1605975/69‑1 (MQ=255)
     ccccATCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGTGCCTg                                                            <  1:3337709/69‑1 (MQ=255)
     ccccATCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGTGCCTg                                                            <  1:571408/69‑1 (MQ=255)
     ccccATCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGTGCCTg                                                            <  1:441905/69‑1 (MQ=255)
     ccccATCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTg                                                            >  1:701031/1‑69 (MQ=255)
        cATCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGtt                                                         <  1:951557/69‑1 (MQ=255)
        cATCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGtt                                                         <  1:2346420/69‑1 (MQ=255)
        cATCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGtt                                                         <  1:3070684/69‑1 (MQ=255)
        cATCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGtt                                                         <  1:361825/69‑1 (MQ=255)
        cATCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGtt                                                         <  1:1365334/69‑1 (MQ=255)
        cATCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGtt                                                         <  1:510663/69‑1 (MQ=255)
        cATCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGtt                                                         <  1:1338539/69‑1 (MQ=255)
        cATCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGtt                                                         <  1:67686/69‑1 (MQ=255)
         aTCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGtt                                                         <  1:153704/68‑1 (MQ=255)
            cAGACCATTAAGTGCTGGGCATCGCCCTGATCTAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATg                                                     >  1:3277210/1‑69 (MQ=255)
            cAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAgcgc                                                               >  1:115001/1‑59 (MQ=255)
            cAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAgcg                                                                >  1:2487041/1‑58 (MQ=255)
            cAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTgga                                                          >  1:587006/1‑63 (MQ=255)
            cAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTAt                                                      >  1:693138/1‑68 (MQ=255)
            cAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATg                                                     >  1:1013239/1‑69 (MQ=255)
            cAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATg                                                     >  1:73004/1‑69 (MQ=255)
            cAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATg                                                     <  1:2231765/69‑1 (MQ=255)
            cAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATg                                                     >  1:2243108/1‑69 (MQ=255)
            cAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATg                                                     >  1:2504675/1‑69 (MQ=255)
            cAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATg                                                     >  1:2895877/1‑69 (MQ=255)
            cAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATg                                                     >  1:2916375/1‑69 (MQ=255)
            cAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATg                                                     <  1:2930793/69‑1 (MQ=255)
            cAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATg                                                     >  1:2964559/1‑69 (MQ=255)
            cAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATg                                                     <  1:660269/69‑1 (MQ=255)
            cAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATg                                                     <  1:3323873/69‑1 (MQ=255)
            cAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATg                                                     >  1:1989416/1‑69 (MQ=255)
            cAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATg                                                     >  1:1253872/1‑69 (MQ=255)
            cAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATg                                                     >  1:1513254/1‑69 (MQ=255)
            cAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATg                                                     >  1:1726625/1‑69 (MQ=255)
                 cATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGAAGCGCCTGGTTTATGTCCTg                                                >  1:1690747/1‑69 (MQ=255)
                                  cGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCtgt                               <  1:16442/69‑1 (MQ=255)
                                  cGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCtgt                               <  1:83170/69‑1 (MQ=255)
                                  cGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCtgt                               <  1:595591/69‑1 (MQ=255)
                                  cGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCtgt                               <  1:3163120/69‑1 (MQ=255)
                                  cGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCtgt                               <  1:3275151/69‑1 (MQ=255)
                                   gCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCtgt                               >  1:2595491/1‑68 (MQ=255)
                                   gCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCtgt                               >  1:1566194/1‑68 (MQ=255)
                                   gCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCtgt                               >  1:2599467/1‑68 (MQ=255)
                                   gCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCtgt                               >  1:2346518/1‑68 (MQ=255)
                                   gCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCtgt                               >  1:191240/1‑68 (MQ=255)
                                   gCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCtgt                               >  1:1828533/1‑68 (MQ=255)
                                   gCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCtgt                               >  1:522507/1‑68 (MQ=255)
                                   gCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCATGGCCAATAAACTGGCtgt                               >  1:2837917/1‑68 (MQ=255)
                                     ccTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCtgttg                             <  1:2409694/68‑1 (MQ=255)
                                     ccTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCtgttg                             <  1:3147646/68‑1 (MQ=255)
                                     ccTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCtgttg                             <  1:1641061/68‑1 (MQ=255)
                                     ccTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCtgttg                             <  1:1739796/68‑1 (MQ=255)
                                     ccTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCtgttg                             <  1:291581/68‑1 (MQ=255)
                                     ccTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCtgttg                             <  1:1310776/68‑1 (MQ=255)
                                          tCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCtgt                               <  1:1532612/61‑1 (MQ=255)
                                                     cATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCtgt                               <  1:1775915/50‑1 (MQ=255)
                                                           gCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAAtt               >  1:1270472/1‑60 (MQ=255)
                                                           gCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAAtt               <  1:1344334/60‑1 (MQ=255)
                                                           gCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAAtt               <  1:3410411/60‑1 (MQ=255)
                                                           gCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAAtt               <  1:1427552/60‑1 (MQ=255)
                                                           gCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAAtt               >  1:3021997/1‑60 (MQ=255)
                                                           gCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAAtt               <  1:2207197/60‑1 (MQ=255)
                                                           gCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAAtt               >  1:1995586/1‑60 (MQ=255)
                                                           gCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAAtt               <  1:2693945/60‑1 (MQ=255)
                                                           gCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAAtt               >  1:2668911/1‑60 (MQ=255)
                                                           gCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAAtt               <  1:1818553/60‑1 (MQ=255)
                                                           gCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAAtt               <  1:2579871/60‑1 (MQ=255)
                                                           gCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAAtt               >  1:2503199/1‑60 (MQ=255)
                                                           gCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGt      <  1:3031432/69‑1 (MQ=255)
                                                           gCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGt      <  1:751066/69‑1 (MQ=255)
                                                           gCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGt      <  1:2036368/69‑1 (MQ=255)
                                                            ccAGGCAGTGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGt      >  1:1837452/1‑68 (MQ=255)
                                                            ccAGGCAGTGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGt      >  1:2449522/1‑68 (MQ=255)
                                                            ccAGGCAGTGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGt      >  1:1190107/1‑68 (MQ=255)
                                                            ccAGGCAGTGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGt      >  1:1348233/1‑68 (MQ=255)
                                                            ccAGGCAGTGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGt      >  1:866794/1‑68 (MQ=255)
                                                            ccAGGCAGTGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGt      >  1:1448019/1‑68 (MQ=255)
                                                            ccAGGCAGTGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGt      >  1:761959/1‑68 (MQ=255)
                                                            ccAGGCAGTGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGt      >  1:2633702/1‑68 (MQ=255)
                                                            ccAGGCAGTGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGt      >  1:2640241/1‑68 (MQ=255)
                                                            ccAGGCAGTGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGt      >  1:2758778/1‑68 (MQ=255)
                                                            ccAGGCAGTGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGt      >  1:85710/1‑68 (MQ=255)
                                                            ccAGGCAGTGCCTGGTTTATGTCCTGGCCAATAAACTGGATGTTGTACTGAATCAAATTAATCGCGGt      >  1:1751105/1‑68 (MQ=255)
                                                               ggCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTcaca  <  1:1045842/69‑1 (MQ=255)
                                                               ggCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTcaca  <  1:100065/69‑1 (MQ=255)
                                                               ggCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTcaca  <  1:668097/69‑1 (MQ=255)
                                                               ggCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTcaca  <  1:582513/69‑1 (MQ=255)
                                                               ggCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTcaca  <  1:1499817/69‑1 (MQ=255)
                                                               ggCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTcaca  <  1:3288737/69‑1 (MQ=255)
                                                               ggCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTcaca  <  1:3027015/69‑1 (MQ=255)
                                                               ggCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTcaca  <  1:1809244/69‑1 (MQ=255)
                                                               ggCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTcaca  <  1:2257852/69‑1 (MQ=255)
                                                                gCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAAtt               <  1:3022641/55‑1 (MQ=255)
                                                                gCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTcaca  <  1:3284879/68‑1 (MQ=255)
                                                                    |                                                               
TAACGCCCCATCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTCACA  >  minE/1462045‑1462176

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