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 1,238,257 T→C 28.5% P88P (CCA→CCG)  edd ← 6‑phosphogluconate dehydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,238,2570TC28.5% 121.5 / 52.8 119P88P (CCA→CCG) edd6‑phosphogluconate dehydratase
Reads supporting (aligned to +/- strand):  ref base T (20/65);  new base C (6/28);  total (26/93)
Fisher's exact test for biased strand distribution p-value = 6.25e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.21e-01

Only 100 of 119 total aligned reads displayed.

GAACACCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGAT  >  minE/1238196‑1238310
                                                             |                                                     
gAACACCGCCCGCATCCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAgt                                                <  1:1270605/69‑1 (MQ=255)
gAACACCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAgt                                                <  1:1962003/69‑1 (MQ=255)
gAACACCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAgt                                                <  1:2802441/69‑1 (MQ=255)
gAACACCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAgt                                                <  1:2080477/69‑1 (MQ=255)
gAACACCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAgt                                                <  1:41937/69‑1 (MQ=255)
gAACACCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAgt                                                <  1:505743/69‑1 (MQ=255)
gAACACCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAgt                                                <  1:2007189/69‑1 (MQ=255)
gAACACCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAgt                                                <  1:1982349/69‑1 (MQ=255)
gAACACCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAgt                                                <  1:633320/69‑1 (MQ=255)
gAACACCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAgt                                                <  1:1732077/69‑1 (MQ=255)
gAACACCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAgt                                                <  1:109890/69‑1 (MQ=255)
gAACACCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAgt                                                <  1:1005366/69‑1 (MQ=255)
gAACACCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAgt                                                <  1:1304922/69‑1 (MQ=255)
 aaCACCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCATGGCTTTACGAATGATTTCTGGATAgt                                                <  1:1870584/68‑1 (MQ=255)
   cacCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGtt                                             <  1:1186601/69‑1 (MQ=255)
   cacCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGtt                                             <  1:886811/69‑1 (MQ=255)
   cacCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGtt                                             <  1:2103653/69‑1 (MQ=255)
   cacCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGtt                                             <  1:1940343/69‑1 (MQ=255)
   cacCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGtt                                             <  1:1847129/69‑1 (MQ=255)
   cacCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGtt                                             <  1:2307459/69‑1 (MQ=255)
   cacCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGtt                                             <  1:2495887/69‑1 (MQ=255)
   cacCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGtt                                             <  1:1066527/69‑1 (MQ=255)
    acCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGtt                                             <  1:1613387/68‑1 (MQ=255)
     ccgcccgcAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGtt                                             <  1:1493239/67‑1 (MQ=255)
                     cAACCGTATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGcgcg                            <  1:576685/68‑1 (MQ=255)
                     cAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGcgcg                            <  1:1749767/68‑1 (MQ=255)
                     cAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGcgcg                            <  1:573811/68‑1 (MQ=255)
                     cAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGcgcg                            <  1:2537151/68‑1 (MQ=255)
                        ccGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgag                         >  1:2017993/1‑68 (MQ=255)
                        ccGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgag                         >  1:2116271/1‑68 (MQ=255)
                        ccGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgag                         >  1:1972625/1‑68 (MQ=255)
                        ccGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgag                         >  1:757714/1‑68 (MQ=255)
                        ccGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgag                         >  1:198522/1‑68 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGagag                       <  1:13539/69‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGagag                       <  1:1738456/69‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGagag                       <  1:2495447/69‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:3141759/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:2850736/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:2852712/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:2907323/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:2911618/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:821472/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:2960656/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:780225/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:2992245/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:3339844/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:3373976/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:3422119/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:919740/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:878674/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:918180/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:865120/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:270508/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:1484821/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:2221869/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:144446/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:2324371/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:2344713/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:1136545/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:1332148/68‑1 (MQ=255)
                         cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATACTGTTCATAAGGCTGGTGAGCGgaga                        <  1:3276460/68‑1 (MQ=255)
                          gCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                        <  1:905957/67‑1 (MQ=255)
                               cGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTc                 >  1:3142839/1‑69 (MQ=255)
                                  ttCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGt               <  1:846842/68‑1 (MQ=255)
                                  ttCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGt               <  1:387885/68‑1 (MQ=255)
                                  ttCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGt               <  1:3022383/68‑1 (MQ=255)
                                  ttCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGt               <  1:1837220/68‑1 (MQ=255)
                                  ttCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGt               <  1:2908377/68‑1 (MQ=255)
                                   tCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTta             <  1:194145/69‑1 (MQ=255)
                                       gCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATagg         <  1:481628/69‑1 (MQ=255)
                                          gggCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATaggag       <  1:670588/68‑1 (MQ=255)
                                           ggCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGt     <  1:3196150/69‑1 (MQ=255)
                                           ggCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGt     <  1:202350/69‑1 (MQ=255)
                                           ggCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGt     <  1:3235105/69‑1 (MQ=255)
                                           ggCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGt     <  1:2545786/69‑1 (MQ=255)
                                           ggCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGt     <  1:2629456/69‑1 (MQ=255)
                                           ggCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGt     <  1:2673192/69‑1 (MQ=255)
                                           ggCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGt     <  1:2768684/69‑1 (MQ=255)
                                              tttACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGtgat  <  1:3232347/69‑1 (MQ=255)
                                              tttACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGtgat  <  1:1944139/69‑1 (MQ=255)
                                              tttACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGtgat  <  1:437516/69‑1 (MQ=255)
                                              tttACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGtgat  <  1:321781/69‑1 (MQ=255)
                                              tttACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGtgat  <  1:1105420/69‑1 (MQ=255)
                                               ttACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGtgat  <  1:1581279/68‑1 (MQ=255)
                                                      tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGc                      >  1:2077037/1‑41 (MQ=255)
                                                      tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                  >  1:1086388/1‑45 (MQ=255)
                                                      tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                  >  1:860953/1‑45 (MQ=255)
                                                      tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                  >  1:1111754/1‑45 (MQ=255)
                                                      tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                  >  1:76839/1‑45 (MQ=255)
                                                      tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                  >  1:638834/1‑45 (MQ=255)
                                                      tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                  >  1:487158/1‑45 (MQ=255)
                                                      tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                  >  1:339279/1‑45 (MQ=255)
                                                      tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                  >  1:2444151/1‑45 (MQ=255)
                                                      tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                  >  1:3030286/1‑45 (MQ=255)
                                                      tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                  >  1:2447456/1‑45 (MQ=255)
                                                      tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                  >  1:2965127/1‑45 (MQ=255)
                                                      tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                  >  1:2496521/1‑45 (MQ=255)
                                                      tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                  >  1:2584415/1‑45 (MQ=255)
                                                      tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                  >  1:2620720/1‑45 (MQ=255)
                                                      tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                  >  1:2766285/1‑45 (MQ=255)
                                                             |                                                     
GAACACCGCCCGCAACCTGACCAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGAT  >  minE/1238196‑1238310

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