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 F28 I1 R1 122 92.7 4382561 94.3% 4132755 66.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA minE 2,364,103 A→G W456R (TGG→CGG)  trkH ← potassium transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,364,1030AG99.6% 861.2 / ‑4.6 225W456R (TGG→CGG) trkHpotassium transporter
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base G (115/108);  total (115/110)
Fisher's exact test for biased strand distribution p-value = 4.87e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01

Only 100 of 225 total aligned reads displayed.

AGAGCACCAGCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGCCCTGGCCCCAGGTTA  >  minE/2364043‑2364167
                                                            |                                                                
agagCACCAGCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCAcc                                                        >  1:2438302/1‑71 (MQ=255)
agagCACCAGCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCAcc                                                        >  1:74925/1‑71 (MQ=255)
agagCACCAGCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCAc                                                         >  1:461601/1‑70 (MQ=255)
     aCCAGCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGtt                                                   <  1:3476681/71‑1 (MQ=255)
     aCCAGCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGtt                                                   <  1:3403886/71‑1 (MQ=255)
      ccAGCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGtt                                                   >  1:57370/1‑70 (MQ=255)
      ccAGCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGtt                                                   >  1:3889887/1‑70 (MQ=255)
      ccAGCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGtt                                                   >  1:648411/1‑70 (MQ=255)
      ccAGCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGtt                                                   >  1:3620697/1‑70 (MQ=255)
        aGCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCAt                                                <  1:884380/71‑1 (MQ=255)
         gCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGTATCCGTTTAGCCACCggg                                                     <  1:1948321/65‑1 (MQ=255)
          cAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATa                                               >  1:1318867/1‑70 (MQ=255)
               tAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCggg                                                     <  1:407497/59‑1 (MQ=255)
               tAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCggg                                                     <  1:4225403/59‑1 (MQ=255)
               tAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCggg                                                     <  1:3764280/59‑1 (MQ=255)
               tAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCggg                                                     <  1:3155483/59‑1 (MQ=255)
               tAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCggg                                                     <  1:3211870/59‑1 (MQ=255)
               tAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCggg                                                     <  1:3747314/59‑1 (MQ=255)
               tAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCggg                                                     <  1:673707/59‑1 (MQ=255)
                aaaGACCTCGAGACGACCAAACAGCATGTTGTCAATCAGGATCCGTTTAGCCACCGGGTTCAt                                                >  1:1651891/1‑63 (MQ=255)
                aaaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTc                                                  >  1:209167/1‑61 (MQ=255)
                aaaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATa                                               >  1:2560476/1‑64 (MQ=255)
                aaaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATa                                               >  1:488426/1‑64 (MQ=255)
                aaaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATa                                               >  1:1096737/1‑64 (MQ=255)
                aaaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATa                                               >  1:3465006/1‑64 (MQ=255)
                aaaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATa                                               >  1:3944166/1‑64 (MQ=255)
                aaaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATa                                               >  1:3982442/1‑64 (MQ=255)
                aaaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATa                                               >  1:4239479/1‑64 (MQ=255)
                aaaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATa                                               >  1:2204346/1‑64 (MQ=255)
                 aaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCg                                                       >  1:1150041/1‑55 (MQ=255)
                 aaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCa                                                 >  1:3556420/1‑61 (MQ=255)
                 aaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCa                                                 >  1:2901801/1‑61 (MQ=255)
                 aaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCa                                                 >  1:2351420/1‑61 (MQ=255)
                 aaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCa                                                 >  1:3398156/1‑61 (MQ=255)
                 aaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCa                                                 >  1:2466761/1‑61 (MQ=255)
                 aaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCa                                                 >  1:2219985/1‑61 (MQ=255)
                 aaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCa                                                 >  1:511614/1‑61 (MQ=255)
                 aaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGt                                          >  1:2726103/1‑68 (MQ=255)
                 aaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTaa                                        <  1:2613866/70‑1 (MQ=255)
                 aaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTaa                                        <  1:4268798/70‑1 (MQ=255)
                 aaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTa                                         >  1:1307627/1‑69 (MQ=255)
                 aaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTa                                         >  1:704947/1‑69 (MQ=255)
                 aaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTa                                         >  1:2870101/1‑69 (MQ=255)
                 aaGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTa                                         >  1:545483/1‑69 (MQ=255)
                 aaGACCTCGAGACGACCAAACAGCAAGTAGGCAATCAGCATCCGTTTAGCCAc                                                         >  1:4234857/1‑53 (MQ=255)
                  aGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCAt                                                <  1:2482201/61‑1 (MQ=255)
                  aGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCAt                                                <  1:1406270/61‑1 (MQ=255)
                  aGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCAt                                                <  1:32671/61‑1 (MQ=255)
                  aGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCAt                                                <  1:1618658/61‑1 (MQ=255)
                  aGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCAt                                                <  1:433014/61‑1 (MQ=255)
                  aGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCAt                                                <  1:2043645/61‑1 (MQ=255)
                   gACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGcc                                                           <  1:3110096/49‑1 (MQ=255)
                   gACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGcc                                                           <  1:278083/49‑1 (MQ=255)
                   gACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGcc                                                           <  1:2584783/49‑1 (MQ=255)
                   gACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGcc                                                           <  1:252756/49‑1 (MQ=255)
                   gACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGcc                                                           <  1:1069029/49‑1 (MQ=255)
                    aCCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGt                                     >  1:2966857/1‑70 (MQ=255)
                    aCCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGt                                     >  1:415518/1‑70 (MQ=255)
                    aCCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGt                                     >  1:1464694/1‑70 (MQ=255)
                    aCCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGt                                     >  1:3367047/1‑70 (MQ=255)
                    aCCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGt                                     >  1:840997/1‑70 (MQ=255)
                      cTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTAt                                  >  1:3085013/1‑71 (MQ=255)
                      cTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTAt                                  >  1:783466/1‑71 (MQ=255)
                      cTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTAt                                  >  1:3594617/1‑71 (MQ=255)
                      cTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTAt                                  >  1:1655290/1‑71 (MQ=255)
                      cTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTAt                                  >  1:191102/1‑71 (MQ=255)
                      cTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTAt                                  >  1:1969886/1‑71 (MQ=255)
                      cTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTAt                                  >  1:3466403/1‑71 (MQ=255)
                      cTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTAt                                  >  1:2162528/1‑71 (MQ=255)
                      cTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTAt                                  >  1:2288661/1‑71 (MQ=255)
                         gagaCGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGt                                     <  1:925699/65‑1 (MQ=255)
                         gagaCGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGt                                     <  1:3032971/65‑1 (MQ=255)
                         gagaCGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGt                                     <  1:4063898/65‑1 (MQ=255)
                         gagaCGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACAGGGTTCATACTGGTAAAGt                                     <  1:2329304/65‑1 (MQ=255)
                          agaCGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGc                              <  1:4285461/71‑1 (MQ=255)
                          agaCGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGc                              <  1:10703/71‑1 (MQ=255)
                          agaCGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGc                              <  1:1230507/71‑1 (MQ=255)
                          agaCGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGc                              <  1:1257477/71‑1 (MQ=255)
                          agaCGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGc                              <  1:2101958/71‑1 (MQ=255)
                          agaCGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGc                              <  1:2637049/71‑1 (MQ=255)
                          agaCGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGc                              <  1:2959937/71‑1 (MQ=255)
                          agaCGACCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGc                              <  1:415815/71‑1 (MQ=255)
                           gacgacCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCa                                                          >  1:1341446/1‑42 (MQ=255)
                           gacgacCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTa                                   >  1:1135730/1‑65 (MQ=255)
                           gacgacCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTa                                   >  1:1020997/1‑65 (MQ=255)
                             cgacCAAACAGCATGTTGGCAATCAGGATCCGTTTAGCCGCCGGGTTCATACTGGTAAAGTTATCAGCAAc                           <  1:1709360/71‑1 (MQ=255)
                                        cATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGcc                <  1:578471/71‑1 (MQ=255)
                                        cATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGcc                <  1:372145/71‑1 (MQ=255)
                                        cATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGcc                <  1:3278844/71‑1 (MQ=255)
                                        cATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGcc                <  1:1526379/71‑1 (MQ=255)
                                        cATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGcc                <  1:1791172/71‑1 (MQ=255)
                                        cATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGcc                <  1:3079147/71‑1 (MQ=255)
                                        cATGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGcc                <  1:2815000/71‑1 (MQ=255)
                                          tGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAAc                           <  1:138252/58‑1 (MQ=255)
                                          tGTTGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGCCCt              <  1:712161/71‑1 (MQ=255)
                                            ttGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGCGCTg             <  1:3788801/70‑1 (MQ=255)
                                            ttGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGCCCTg             <  1:1991584/70‑1 (MQ=255)
                                             tGGCAATCAGGATCCGTTTAGCCACCGGGTTCATACTGGTAAAGt                                     <  1:907985/45‑1 (MQ=255)
                                                      ggATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGCCCTGGCCCCAGGTTa  <  1:3812141/71‑1 (MQ=255)
                                                      ggATCCGTTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGCCCTGGCCCCAGGTTa  <  1:3306450/71‑1 (MQ=255)
                                                            |                                                                
AGAGCACCAGCAATGTAAAGACCTCGAGACGACCAAACAGCATGTTGGCAATCAGGATCCATTTAGCCACCGGGTTCATACTGGTAAAGTTATCAGCAACCACGCCAAGCCCTGGCCCCAGGTTA  >  minE/2364043‑2364167

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A