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 1,238,281 C→A 31.9% A80A (GCG→GCT)  edd ← 6‑phosphogluconate dehydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,238,2810CA31.9% 150.3 / 80.4 122A80A (GCG→GCT) edd6‑phosphogluconate dehydratase
Reads supporting (aligned to +/- strand):  ref base C (40/43);  new base A (5/34);  total (45/77)
Fisher's exact test for biased strand distribution p-value = 1.21e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

Only 100 of 126 total aligned reads displayed.

CAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACATGCTTTTCAAA  >  minE/1238217‑1238344
                                                                |                                                               
cAACCGTATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGcgcg                                                              <  1:576685/68‑1 (MQ=255)
cAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGcgcg                                                              <  1:573811/68‑1 (MQ=255)
cAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGcgcg                                                              <  1:2537151/68‑1 (MQ=255)
   ccGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgag                                                           >  1:1972625/1‑68 (MQ=255)
   ccGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgag                                                           >  1:198522/1‑68 (MQ=255)
   ccGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgag                                                           >  1:757714/1‑68 (MQ=255)
   ccGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgag                                                           >  1:2017993/1‑68 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGagag                                                         <  1:2495447/69‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGagag                                                         <  1:13539/69‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGagag                                                         <  1:1738456/69‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGagag                                                         <  1:2881044/69‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGagag                                                         <  1:1590675/69‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                                                          <  1:270508/68‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                                                          <  1:2850736/68‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                                                          <  1:3339844/68‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                                                          <  1:3422119/68‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                                                          <  1:2221869/68‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                                                          <  1:2324371/68‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                                                          <  1:2344713/68‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                                                          <  1:780225/68‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                                                          <  1:2852712/68‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                                                          <  1:2911618/68‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                                                          <  1:1484821/68‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                                                          <  1:144446/68‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                                                          <  1:865120/68‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                                                          <  1:1332148/68‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                                                          <  1:878674/68‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                                                          <  1:1136545/68‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                                                          <  1:918180/68‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                                                          <  1:2960656/68‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                                                          <  1:2992245/68‑1 (MQ=255)
    cGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATACTGTTCATAAGGCTGGTGAGCGgaga                                                          <  1:3276460/68‑1 (MQ=255)
     gCATTCGCTTCATGCAGGGCTTTACGAATGATTTCCGGATAGTGTTCATAAGGCTGGTGAGCGgaga                                                          <  1:905957/67‑1 (MQ=255)
          cGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTc                                                   >  1:3142839/1‑69 (MQ=255)
             ttCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGt                                                 <  1:3022383/68‑1 (MQ=255)
             ttCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGt                                                 <  1:2908377/68‑1 (MQ=255)
             ttCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGt                                                 <  1:3206794/68‑1 (MQ=255)
             ttCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGt                                                 <  1:387885/68‑1 (MQ=255)
             ttCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGt                                                 <  1:846842/68‑1 (MQ=255)
             ttCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGt                                                 <  1:1837220/68‑1 (MQ=255)
              tCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTta                                               <  1:3014665/69‑1 (MQ=255)
              tCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTta                                               <  1:777593/69‑1 (MQ=255)
                  gCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATagg                                           <  1:481628/69‑1 (MQ=255)
                     gggCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATaggag                                         <  1:670588/68‑1 (MQ=255)
                      ggCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGt                                       <  1:202350/69‑1 (MQ=255)
                      ggCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGt                                       <  1:2673192/69‑1 (MQ=255)
                      ggCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGt                                       <  1:3235105/69‑1 (MQ=255)
                      ggCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGt                                       <  1:2629456/69‑1 (MQ=255)
                      ggCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGt                                       <  1:3196150/69‑1 (MQ=255)
                       gCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGtg                                      >  1:2164237/1‑69 (MQ=255)
                         tttACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGtgat                                    <  1:1944139/69‑1 (MQ=255)
                         tttACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGtgat                                    <  1:437516/69‑1 (MQ=255)
                         tttACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGtgat                                    <  1:965337/69‑1 (MQ=255)
                         tttACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGtgat                                    <  1:1105420/69‑1 (MQ=255)
                         tttACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGtgat                                    <  1:2556546/69‑1 (MQ=255)
                         tttACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGtgat                                    <  1:321781/69‑1 (MQ=255)
                          ttACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGtgat                                    <  1:1581279/68‑1 (MQ=255)
                                 tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGc                                                        >  1:2077037/1‑41 (MQ=255)
                                 tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                                                    >  1:860953/1‑45 (MQ=255)
                                 tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                                                    >  1:339279/1‑45 (MQ=255)
                                 tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                                                    >  1:638834/1‑45 (MQ=255)
                                 tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                                                    >  1:1086388/1‑45 (MQ=255)
                                 tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                                                    >  1:2766285/1‑45 (MQ=255)
                                 tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                                                    >  1:3030286/1‑45 (MQ=255)
                                 tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                                                    >  1:1111754/1‑45 (MQ=255)
                                 tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                                                    >  1:2444151/1‑45 (MQ=255)
                                 tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                                                    >  1:2584415/1‑45 (MQ=255)
                                 tGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGt                                                    >  1:2496521/1‑45 (MQ=255)
                                              gtgtTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCaa               <  1:818304/69‑1 (MQ=255)
                                                gtTCATAAGGCTTGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGatat                         <  1:542900/57‑1 (MQ=255)
                                                 ttCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGatat                         <  1:812577/56‑1 (MQ=255)
                                                 ttCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACAt            >  1:433916/1‑69 (MQ=255)
                                                 ttCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACAt            >  1:716532/1‑69 (MQ=255)
                                                 ttCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACAt            >  1:2277907/1‑69 (MQ=255)
                                                 ttCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACAt            >  1:1604253/1‑69 (MQ=255)
                                                 ttCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACAt            >  1:2502241/1‑69 (MQ=255)
                                                 ttCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACAt            >  1:888683/1‑69 (MQ=255)
                                                 ttCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACAt            >  1:2619761/1‑69 (MQ=255)
                                                 ttCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACAt            >  1:1121757/1‑69 (MQ=255)
                                                 ttCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACAt            >  1:1026222/1‑69 (MQ=255)
                                                 ttCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACAt            >  1:2919136/1‑69 (MQ=255)
                                                   cATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACATga          >  1:2252103/1‑68 (MQ=255)
                                                   cATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACATGc          >  1:970349/1‑69 (MQ=255)
                                                       aGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTgatgat                                 >  1:2683842/1‑42 (MQ=255)
                                                       aGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACATGCttt       >  1:2254219/1‑68 (MQ=255)
                                                       aGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACATGCttt       >  1:1353802/1‑68 (MQ=255)
                                                       aGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACATGCttt       >  1:190477/1‑68 (MQ=255)
                                                       aGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACATGCttt       >  1:2082423/1‑68 (MQ=255)
                                                       aGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACATGCttt       >  1:2632781/1‑68 (MQ=255)
                                                       aGGCTGGTGAGCGGAGAGCATGTCGTTATAGGAGGtgatg                                   <  1:846771/40‑1 (MQ=255)
                                                       aGGCTGGTGAGCGGAGAGCATGTCGTTATAGGAGGtgatg                                   <  1:538256/40‑1 (MQ=255)
                                                       aGGCTGGTGAGCGGAGAGCATGTCGTTATAGGAGGtgatg                                   <  1:358565/40‑1 (MQ=255)
                                                       aGGCTGGTGAGCGGAGAGCATGTCGTTATAGGAGGtgatg                                   <  1:3274895/40‑1 (MQ=255)
                                                       aGGCTGGTGAGCGGAGAGCATGTCGTTATAGGAGGtgatg                                   <  1:2885588/40‑1 (MQ=255)
                                                       aGGCTGGTGAGCGGAGAGCATGTCGTTATAGGAGGtgatg                                   <  1:97112/40‑1 (MQ=255)
                                                           tGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACATGCTTTTCaaa  <  1:1878965/69‑1 (MQ=255)
                                                           tGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACATGCTTTTCaaa  <  1:1765993/69‑1 (MQ=255)
                                                           tGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACATGCTTTTCaaa  <  1:2586079/69‑1 (MQ=255)
                                                           tGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACATGCTTTTCaaa  <  1:2631154/69‑1 (MQ=255)
                                                            ggTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACATGCTTTTCaaa  <  1:1262766/68‑1 (MQ=255)
                                                                |                                                               
CAACCGCATTCGCTTCATGCAGGGCTTTACGAATGATTTCTGGATAGTGTTCATAAGGCTGGTGCGCGGAGAGCATGTCGTTATAGGAGGTGATGATGGCGATATTGTTACGCAACATGCTTTTCAAA  >  minE/1238217‑1238344

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A