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 2,173,038 T→G 25.8% R277R (CGT→CGG)  yhbJ → hypothetical protein with nucleoside triphosphate hydrolase domain

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,173,0380TG25.8% 172.5 / 71.4 128R277R (CGT→CGG) yhbJhypothetical protein with nucleoside triphosphate hydrolase domain
Reads supporting (aligned to +/- strand):  ref base T (58/37);  new base G (20/13);  total (78/50)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 128 total aligned reads displayed.

TATTGCAGAGCAACTGGCAGACTACTTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGGCATGCA  >  minE/2172975‑2173105
                                                               |                                                                   
tatTGCAGAGCAACTGGCAGACTACTTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGc                                                                 >  1:1866925/1‑68 (MQ=255)
  ttGCAGAGCAACTGGCAGACTACTTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTg                                                               >  1:2310288/1‑68 (MQ=255)
       gagCAACTGGCAGACTACTTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGaaaaa                                                         <  1:907637/69‑1 (MQ=255)
       gagCAACTGGCAGACTACTTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGaaaaa                                                         <  1:2762255/69‑1 (MQ=255)
       gagCAACTGGCAGACTACTTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGaaaaa                                                         <  1:2361983/69‑1 (MQ=255)
       gagCAACTGGCAGACTACTTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGaaaaa                                                         <  1:3218981/69‑1 (MQ=255)
       gagCAACTGGCAGACTACTTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGaaaaa                                                         <  1:715421/69‑1 (MQ=255)
       gagCAACTGGCAGACTACTTCCGCTCGCGCGGCAAAAACGTCCAGTCACGCCATCGTACGCTGGaaaaa                                                         <  1:3026660/69‑1 (MQ=255)
        agCAACTGGCAGACTACTTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGaaaaa                                                         <  1:516914/68‑1 (MQ=255)
              tGGCAGACTACTTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAAc                                                  <  1:1956620/69‑1 (MQ=255)
              tGGCAGACTACTTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAAc                                                  <  1:603423/69‑1 (MQ=255)
              ctgCAGACTACTTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAAc                                                  <  1:767313/67‑1 (MQ=255)
                     ctactTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCAt                                               >  1:2874542/1‑65 (MQ=255)
                     ctactTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCAt                                               >  1:3224531/1‑65 (MQ=255)
                     ctactTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCAt                                               >  1:343607/1‑65 (MQ=255)
                     ctactTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCAt                                               >  1:3220605/1‑65 (MQ=255)
                     ctactTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCAt                                               >  1:2302880/1‑65 (MQ=255)
                     ctactTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCAt                                               >  1:536801/1‑65 (MQ=255)
                     ctactTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCAt                                               >  1:1364250/1‑65 (MQ=255)
                      tactTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAAc                                                        >  1:511478/1‑55 (MQ=255)
                      tactTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGAcc                                           >  1:1145634/1‑68 (MQ=255)
                      tactTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGAcc                                           >  1:21466/1‑68 (MQ=255)
                      tactTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGAcc                                           >  1:3023013/1‑68 (MQ=255)
                      tactTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGAcc                                           >  1:2807472/1‑68 (MQ=255)
                      tactTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGAcc                                           >  1:2334643/1‑68 (MQ=255)
                      tactTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGAcc                                           >  1:780174/1‑68 (MQ=255)
                      tactTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGAcc                                           >  1:1818846/1‑68 (MQ=255)
                      tactTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGAcc                                           >  1:177211/1‑68 (MQ=255)
                      tactTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGAcc                                           >  1:417222/1‑68 (MQ=255)
                        ctTCCGCTCGCGCGGTAAAAACGTCCAGTCAGGCCATCGTACGCTGGAAAAACGTaaa                                                   >  1:3330980/1‑58 (MQ=255)
                        ctTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTaaa                                                   >  1:2648483/1‑58 (MQ=255)
                        ctTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAAc                                                  <  1:1902396/59‑1 (MQ=255)
                        ctTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAAc                                                  <  1:2975692/59‑1 (MQ=255)
                        ctTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAAc                                                  <  1:2383308/59‑1 (MQ=255)
                        ctTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAAc                                                  <  1:557012/59‑1 (MQ=255)
                        ctTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAAc                                                  <  1:1305518/59‑1 (MQ=255)
                        ctTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAAc                                                  >  1:1567613/1‑59 (MQ=255)
                        ctTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAAc                                                  >  1:26472/1‑59 (MQ=255)
                        ctTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAAc                                                  >  1:2210950/1‑59 (MQ=255)
                        ctTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAAc                                                  <  1:2161824/59‑1 (MQ=255)
                        ctTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAAc                                                  >  1:3345838/1‑59 (MQ=255)
                        ctTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAAc                                                  >  1:1769874/1‑59 (MQ=255)
                         ttCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAAc                                                  <  1:2990106/58‑1 (MQ=255)
                              cTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCa                                   <  1:1083825/68‑1 (MQ=255)
                              cTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCa                                   <  1:152415/68‑1 (MQ=255)
                              cTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCa                                   <  1:1369090/68‑1 (MQ=255)
                              cTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCa                                   <  1:1602690/68‑1 (MQ=255)
                              cTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCa                                   <  1:2566171/68‑1 (MQ=255)
                              cTCGCGCGGTAAAAACGTCCAGTCACGCCATCGGACGCTGGAAAAACGt                                                      >  1:2972803/1‑49 (MQ=255)
                              cTCGCGCGGTAAAAACGTCCAGTCACGCCATCGGACGCTGGAAAAACGTAAACCATGACCg                                          >  1:673266/1‑61 (MQ=255)
                              cTCGCGCGGTAAAAACGTCCAGTCACGCCATCGGACGCTGGAAAAACGTAAACCATGACCg                                          >  1:1020242/1‑61 (MQ=255)
                              cTCGCGCGGTAAAAACGTCCAGTCACGCCATCGGACGCTGGAAAAACGTAAACCATGACCg                                          >  1:3030002/1‑61 (MQ=255)
                              cTCGCGCGGTAAAAACGTCCAGTCACGCCATCGGACGCTGGAAAAACGTAAACCATGACCg                                          >  1:3242759/1‑61 (MQ=255)
                              cTCGCGCGGTAAAAACGTCCAGTCACGCCATCGGACGCTGGAAAAACGTAAACCATGACCg                                          >  1:3278848/1‑61 (MQ=255)
                              cTCGCGCGGTAAAAACGTCCAGTCACGCCATCGGACGCTGGAAAAACGTAAACCATGACCg                                          >  1:545766/1‑61 (MQ=255)
                              cTCGCGCGGTAAAAACGTCCAGTCACGCCATCGGACGCTGGAAAAACGTAAACCATGACCg                                          >  1:1009079/1‑61 (MQ=255)
                              cTCGCGCGGTAAAAACGTCCAGTCACGCCATCGGACGCTGGAAAAACGTAAACCATGACCg                                          >  1:2652960/1‑61 (MQ=255)
                              cTCGCGCGGTAAAAACGTCCAGTCACGCCATCGGACGCTGGAAAAACGTAAACCATGACCg                                          >  1:1032960/1‑61 (MQ=255)
                              cTCGCGCGGTAAAAACGTCCAGTCACGCCATCGGACGCTGGAAAAACGTAAACCATGACCg                                          >  1:2505261/1‑61 (MQ=255)
                              cTCGCGCGGTAAAAACGTCCAGTCACGCCATCGGACGCTGGAAAAACGTAAACCATGACCg                                          >  1:243266/1‑61 (MQ=255)
                              cTCGCGCGGTAAAAACGTCCAGTCACGCCATCGGACGCTGGAAAAACGTAAACCATGACCg                                          >  1:1725712/1‑61 (MQ=255)
                              cTCGCGCGGTAAAAACGTCCAGTCACGCCATCGGACGCTGGAAAAACGTAAACCATGACCg                                          >  1:224828/1‑61 (MQ=255)
                              cTCGCGCGGTAAAAACGTCCAGTCACGCCATCGGACGCTGGAAAAACGTAAACCATGACCg                                          >  1:2047260/1‑61 (MQ=255)
                              cTCGCGCGGTAAAAACGTCCAGTCACGCCATCGGACGCTGGAAAAACGTAAACCATGACCg                                          >  1:2159609/1‑61 (MQ=255)
                              cTCGCGCGGTAAAAACGTCCAGTCACGCCATCGGACGCTGGAAAAACGTAAAACATGACCg                                          >  1:2865086/1‑61 (MQ=255)
                                cgcgcgGTAAAAACGTTCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAAc                                >  1:1032015/1‑69 (MQ=255)
                                cgcgcgGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAAc                                >  1:2371270/1‑69 (MQ=255)
                                               tCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCacaa                  >  1:1904059/1‑68 (MQ=255)
                                               tCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCacaa                  >  1:3304693/1‑68 (MQ=255)
                                               tCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCacaa                  >  1:3243589/1‑68 (MQ=255)
                                               tCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCacaa                  >  1:3127251/1‑68 (MQ=255)
                                               tCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCacaa                  >  1:2232523/1‑68 (MQ=255)
                                               tCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCacaa                  >  1:1136029/1‑68 (MQ=255)
                                                        gCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTggg        <  1:139701/69‑1 (MQ=255)
                                                        gCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTggg        <  1:156636/69‑1 (MQ=255)
                                                        gCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTggg        <  1:486895/69‑1 (MQ=255)
                                                        gCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTggg        <  1:62244/69‑1 (MQ=255)
                                                        gCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTggg        <  1:334640/69‑1 (MQ=255)
                                                        gCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTggg        <  1:3319979/69‑1 (MQ=255)
                                                        gCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTggg        <  1:2759354/69‑1 (MQ=255)
                                                        gCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTggg        <  1:2767903/69‑1 (MQ=255)
                                                        gCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTggg        <  1:2984128/69‑1 (MQ=255)
                                                        gCCATCGGACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTgg         <  1:1673122/68‑1 (MQ=255)
                                                        gCCATCGGACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTgg         <  1:166910/68‑1 (MQ=255)
                                                        gCCATCGGACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTgg         <  1:1134862/68‑1 (MQ=255)
                                                        gCCATCGGACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTgg         <  1:1617334/68‑1 (MQ=255)
                                                        gCCATCGGACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTgg         <  1:1220875/68‑1 (MQ=255)
                                                           aTCGGACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTgg         <  1:516989/65‑1 (MQ=255)
                                                              gTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGgcatgca  >  1:2670792/1‑69 (MQ=255)
                                                              gTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGgcatgca  >  1:2623363/1‑69 (MQ=255)
                                                              gTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGgcatgca  >  1:1237553/1‑69 (MQ=255)
                                                              gTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGgcatgca  >  1:1294562/1‑69 (MQ=255)
                                                              gTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGgcatgca  >  1:2190889/1‑69 (MQ=255)
                                                              gTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGgcatgca  >  1:2068844/1‑69 (MQ=255)
                                                              gTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGgcatgca  >  1:2001994/1‑69 (MQ=255)
                                                              gTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGgcatgca  >  1:46370/1‑69 (MQ=255)
                                                              gTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGgcatgca  >  1:3350682/1‑69 (MQ=255)
                                                              gTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGgcatgca  >  1:335014/1‑69 (MQ=255)
                                                              gTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGgcatgca  >  1:3309530/1‑69 (MQ=255)
                                                              gTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCAAAAACAAGCTGGgcatgca  >  1:2304512/1‑69 (MQ=255)
                                                               |                                                                   
TATTGCAGAGCAACTGGCAGACTACTTCCGCTCGCGCGGTAAAAACGTCCAGTCACGCCATCGTACGCTGGAAAAACGTAAACCATGACCGTCAAGCAAACTGTTGAAATCACAAACAAGCTGGGCATGCA  >  minE/2172975‑2173105

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