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 2,481,137 G→C 25.1% Q193E (CAA→GAA)  yidZ ← predicted DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,481,1370GC25.1% 301.2 / 105.3 191Q193E (CAA→GAA) yidZpredicted DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (84/59);  new base C (30/18);  total (114/77)
Fisher's exact test for biased strand distribution p-value = 7.35e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.51e-01

Only 100 of 192 total aligned reads displayed.

GTATCGCTCTGTTCCCAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAGCACTTCATAATC  >  minE/2481070‑2481203
                                                                   |                                                                  
gTATCGCTCTGTTCCCAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGa                                                                   <  1:1119577/69‑1 (MQ=255)
gTATCGCTCTGTTCCCAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGa                                                                   <  1:188926/69‑1 (MQ=255)
gTATCGCTCTGTTCCCAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGa                                                                   <  1:1639581/69‑1 (MQ=255)
  aTCGCTCTGTTCCCAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGa                                                                   >  1:905904/1‑67 (MQ=255)
  aTCGCTCTGTTCCCAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGa                                                                   >  1:835081/1‑67 (MQ=255)
  aTCGCTCTGTTCCCAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGa                                                                   >  1:2546224/1‑67 (MQ=255)
  aTCGCTCTGTTCCCAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGa                                                                   >  1:2436024/1‑67 (MQ=255)
  aTCGCTCTGTTCCCAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGa                                                                   >  1:3362861/1‑67 (MQ=255)
  aTCGCTCTGTTCCCAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGa                                                                   >  1:369387/1‑67 (MQ=255)
   tCGCTCTGTTCGCAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGc                                                                <  1:1072258/69‑1 (MQ=255)
   tCGCTCTGTTCCCAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGc                                                                <  1:2701911/69‑1 (MQ=255)
   tCGCTCTGTTCCCAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGc                                                                <  1:2057420/69‑1 (MQ=255)
   tCGCTCTGTTCCCAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGc                                                                <  1:2109628/69‑1 (MQ=255)
   tCGCTCTGTTCCCAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGc                                                                <  1:3099678/69‑1 (MQ=255)
    cGCTCTGTTCCCAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGCa                                                               >  1:3220808/1‑69 (MQ=255)
    cGCTCTGTTCCCAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGCa                                                               >  1:803509/1‑69 (MQ=255)
        ctGTTCCCAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGc                                                           >  1:2523197/1‑69 (MQ=255)
        ctGTTCCCAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGc                                                           >  1:1902545/1‑69 (MQ=255)
        ctGTTCCCAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGc                                                           >  1:1161030/1‑69 (MQ=255)
        ctGTTCCCAGCAAATGCTGATATGCGGAT‑ACGTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGc                                                           >  1:2930374/1‑68 (MQ=255)
             cccAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGCCGgat                                                      >  1:1593375/1‑69 (MQ=255)
             cccAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGCCGgat                                                      >  1:56272/1‑69 (MQ=255)
             cccAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGCCGgat                                                      >  1:580035/1‑69 (MQ=255)
             cccAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGCCGgat                                                      >  1:2880292/1‑69 (MQ=255)
             cccAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGCCGgat                                                      >  1:2390164/1‑69 (MQ=255)
               cAGCAAATGCTGATATGCGTATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGCCGgatg                                                     <  1:844406/68‑1 (MQ=255)
               cAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGCCGgatg                                                     <  1:1047771/68‑1 (MQ=255)
               cAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGCCGgatg                                                     <  1:1986444/68‑1 (MQ=255)
               cAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGCCGgatg                                                     <  1:47765/68‑1 (MQ=255)
               cAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGCCGgatg                                                     <  1:1293489/68‑1 (MQ=255)
                aGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGc                                                                <  1:1654148/56‑1 (MQ=255)
                                cGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGa                                    <  1:2634017/68‑1 (MQ=255)
                                     aaCGTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAg                               >  1:28078/1‑68 (MQ=255)
                                     aaCGTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAg                               >  1:964826/1‑68 (MQ=255)
                                     aaCGTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAg                               >  1:2318284/1‑68 (MQ=255)
                                     aaCGTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAg                               >  1:2290553/1‑68 (MQ=255)
                                     aaCGTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAg                               >  1:1380655/1‑68 (MQ=255)
                                     aaCGTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAg                               >  1:1964424/1‑68 (MQ=255)
                                        gTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGca                           <  1:2301073/69‑1 (MQ=255)
                                        gTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGca                           <  1:2294087/69‑1 (MQ=255)
                                        gTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGca                           <  1:3206151/69‑1 (MQ=255)
                                                     cAGATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAg              <  1:448088/69‑1 (MQ=255)
                                                     cAGATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAg              >  1:387639/1‑69 (MQ=255)
                                                     cAGATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAg              >  1:513534/1‑69 (MQ=255)
                                                     cAGATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAg              >  1:3240842/1‑69 (MQ=255)
                                                     cAGATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAg              >  1:1562405/1‑69 (MQ=255)
                                                     cAGATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAg              >  1:304445/1‑69 (MQ=255)
                                                     cAGATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAg              >  1:1813124/1‑69 (MQ=255)
                                                     cAGATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAg              <  1:2508112/69‑1 (MQ=255)
                                                       gATTCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAGc             <  1:2199346/68‑1 (MQ=255)
                                                       gATTCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAGc             <  1:3079480/68‑1 (MQ=255)
                                                       gATTCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAGc             <  1:1451641/68‑1 (MQ=255)
                                                       gATTCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAGc             <  1:3436337/68‑1 (MQ=255)
                                                       gATTCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAGc             <  1:2534770/68‑1 (MQ=255)
                                                       gATTCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAGc             <  1:2414469/68‑1 (MQ=255)
                                                       gATTCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAGc             <  1:3327277/68‑1 (MQ=255)
                                                       gATTCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAGc             <  1:1770651/68‑1 (MQ=255)
                                                       gATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACt                    >  1:729629/1‑61 (MQ=255)
                                                       gATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTa                   >  1:1232115/1‑62 (MQ=255)
                                                       gATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTa                   >  1:632351/1‑62 (MQ=255)
                                                       gATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTa                   >  1:278656/1‑62 (MQ=255)
                                                       gATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAGc             <  1:483003/68‑1 (MQ=255)
                                                          tCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCAc                     >  1:2246840/1‑57 (MQ=255)
                                                          tCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCAc                     >  1:1544636/1‑57 (MQ=255)
                                                          tCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCAc                     >  1:375005/1‑57 (MQ=255)
                                                          tCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCAc                     >  1:2323630/1‑57 (MQ=255)
                                                          tCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCAc                     >  1:2082788/1‑57 (MQ=255)
                                                          tCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCAc                     >  1:3188867/1‑57 (MQ=255)
                                                          tCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCAc                     >  1:31484/1‑57 (MQ=255)
                                                          tCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCAc                     >  1:528942/1‑57 (MQ=255)
                                                          tCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCAc                     >  1:2166330/1‑57 (MQ=255)
                                                          tCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCAc                     >  1:589555/1‑57 (MQ=255)
                                                          tCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCAc                     >  1:2954181/1‑57 (MQ=255)
                                                          tCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCAc                     >  1:697838/1‑57 (MQ=255)
                                                          tCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCAc                     >  1:1201463/1‑57 (MQ=255)
                                                          tCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCAc                     >  1:2859114/1‑57 (MQ=255)
                                                          tCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCAc                     >  1:2845182/1‑57 (MQ=255)
                                                          tCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCAc                     >  1:89400/1‑57 (MQ=255)
                                                          tCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCAc                     >  1:2750300/1‑57 (MQ=255)
                                                          tCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCAc                     >  1:1263849/1‑57 (MQ=255)
                                                          tCCATGCTTCATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCAc                     >  1:2688364/1‑57 (MQ=255)
                                                          tCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTGAc                                        >  1:1031557/1‑38 (MQ=255)
                                                          tCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAAc                                        >  1:2897005/1‑38 (MQ=255)
                                                          tCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAAc                                        >  1:2473766/1‑38 (MQ=255)
                                                          tCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAAc                                        >  1:256835/1‑38 (MQ=255)
                                                          tCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAAc                                        >  1:1222513/1‑38 (MQ=255)
                                                          tCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAAc                                        >  1:3132228/1‑38 (MQ=255)
                                                            cACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGCCGCAGGGCACATCACTAAAc                >  1:1475544/1‑60 (MQ=255)
                                                            cACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAGCACTTc        >  1:859638/1‑68 (MQ=255)
                                                            cACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAGCACTTc        >  1:3264047/1‑68 (MQ=255)
                                                            cACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAGCACTTc        >  1:91252/1‑68 (MQ=255)
                                                                 ttGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAGCACTTCATAATc  <  1:3117008/69‑1 (MQ=255)
                                                                 ttGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAGCACTTCATAATc  <  1:1275834/69‑1 (MQ=255)
                                                                 ttGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAGCACTTCATAATc  <  1:161636/69‑1 (MQ=255)
                                                                 ttGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAGCACTTCATAATc  <  1:3062721/69‑1 (MQ=255)
                                                                 ttGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAGCACTTCATAATc  <  1:2902807/69‑1 (MQ=255)
                                                                 ttGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAGCACTTCATAATc  <  1:1994575/69‑1 (MQ=255)
                                                                 ttGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAGCACTTCATAATc  <  1:2605717/69‑1 (MQ=255)
                                                                 ttGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAGCACTTCATAATc  <  1:2143468/69‑1 (MQ=255)
                                                                 ttGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAGCACTTCATAATc  <  1:336775/69‑1 (MQ=255)
                                                                   |                                                                  
GTATCGCTCTGTTCCCAGCAAATGCTGATATGCGGATAACGTAAGAAGGTGTCCAGATTCCACGTTTGATGCAGTGCCGGATGATCTTTGCGTAACCAGACGCAGGGCACATCACTAAACAGCACTTCATAATC  >  minE/2481070‑2481203

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