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 1,629,190 G→A 57.0% T186M (ACG→ATG)  yffH ← predicted NUDIX hydrolase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,629,1900GA57.0% 30.3 / 88.2 113T186M (ACG→ATG) yffHpredicted NUDIX hydrolase
Reads supporting (aligned to +/- strand):  ref base G (23/25);  new base A (27/37);  total (51/62)
Fisher's exact test for biased strand distribution p-value = 5.70e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.86e-01

Only 100 of 115 total aligned reads displayed.

TTTGTCGGATTGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAATAACACCGTCTTACCGTCACGTATCTCGCCGGTTTTGATCATCTCCAGC  >  minE/1629123‑1629258
                                                                   |                                                                    
tttGTCGGATTGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGt                                                                     >  1:1945816/1‑69 (MQ=255)
tttGTCGGATTGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGt                                                                     >  1:1199348/1‑69 (MQ=255)
tttGTCGGATTGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGt                                                                     >  1:1544495/1‑69 (MQ=255)
  tGTCGGATTGAGCGAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:2867453/69‑1 (MQ=255)
  tGTCGGATTGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:2321416/69‑1 (MQ=255)
  tGTCGGATTGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:2726963/69‑1 (MQ=255)
  tGTCGGATTGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:65699/69‑1 (MQ=255)
  tGTCGGATTGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:1552167/69‑1 (MQ=255)
  tGTCGGATTGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:396043/69‑1 (MQ=255)
  tGTCGGATTGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:1995446/69‑1 (MQ=255)
  tGTCGGATTGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:760247/69‑1 (MQ=255)
  tGTCGGATTGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:1369829/69‑1 (MQ=255)
  tGTCGGATTGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:1247850/69‑1 (MQ=255)
  tGTCGGATTGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:3230786/69‑1 (MQ=255)
  tGTCGGATTGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:224747/69‑1 (MQ=255)
  tGTCGGATTGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:3036982/69‑1 (MQ=255)
  tGTCGGATTGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:2268361/69‑1 (MQ=255)
     cGGATTGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCa                                                                >  1:3427653/1‑69 (MQ=255)
     cGGATTGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCa                                                                >  1:1426021/1‑69 (MQ=255)
     cGGATTGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCa                                                                >  1:1720638/1‑69 (MQ=255)
         ttGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:2500894/62‑1 (MQ=255)
         ttGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:2438179/62‑1 (MQ=255)
         ttGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:1871855/62‑1 (MQ=255)
         ttGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:1854957/62‑1 (MQ=255)
         ttGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:1034037/62‑1 (MQ=255)
         ttGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:1708292/62‑1 (MQ=255)
         ttGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:1677613/62‑1 (MQ=255)
         ttGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:414780/62‑1 (MQ=255)
         ttGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:2835725/62‑1 (MQ=255)
         ttGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:3057635/62‑1 (MQ=255)
         ttGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:3019862/62‑1 (MQ=255)
         ttGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTAAGTCCATTAAATGTGACAttt                                                                   <  1:221827/62‑1 (MQ=255)
          tGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:1828913/61‑1 (MQ=255)
          tGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:2086638/61‑1 (MQ=255)
          tGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:3146114/61‑1 (MQ=255)
          tGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACAttt                                                                   <  1:550708/61‑1 (MQ=255)
                   aataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCaa                                                   >  1:1627121/1‑68 (MQ=255)
                   aataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  <  1:503254/69‑1 (MQ=255)
                   aataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  <  1:3075392/69‑1 (MQ=255)
                   aataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  <  1:2889052/69‑1 (MQ=255)
                   aataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  <  1:486440/69‑1 (MQ=255)
                   aataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  <  1:2569125/69‑1 (MQ=255)
                   aataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  <  1:2589304/69‑1 (MQ=255)
                   aataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  <  1:2625333/69‑1 (MQ=255)
                   aataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  >  1:682060/1‑69 (MQ=255)
                   aataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  <  1:1199251/69‑1 (MQ=255)
                   aataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  <  1:1609938/69‑1 (MQ=255)
                   aataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  >  1:1880381/1‑69 (MQ=255)
                   aataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  >  1:526189/1‑69 (MQ=255)
                   aataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  <  1:579685/69‑1 (MQ=255)
                   aataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  <  1:1997756/69‑1 (MQ=255)
                   aataaACAACGAAATATTAT‑‑TTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  <  1:1183943/67‑1 (MQ=255)
                    ataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCaa                                                   >  1:649456/1‑67 (MQ=255)
                    ataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  >  1:307010/1‑68 (MQ=255)
                    ataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  >  1:3205389/1‑68 (MQ=255)
                    ataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  >  1:1210784/1‑68 (MQ=255)
                    ataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  <  1:883831/68‑1 (MQ=255)
                    ataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  >  1:2983942/1‑68 (MQ=255)
                    ataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  >  1:1276058/1‑68 (MQ=255)
                    ataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  >  1:712240/1‑68 (MQ=255)
                    ataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  >  1:2149891/1‑68 (MQ=255)
                    ataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  >  1:445033/1‑68 (MQ=255)
                    ataaACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAAt                                                  >  1:2583652/1‑68 (MQ=255)
                              aaaTATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAATAACACCGTCtt                                       <  1:82386/69‑1 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACTTTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:2332145/1‑69 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:930570/1‑69 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:987051/1‑69 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:330485/1‑69 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:3366623/1‑69 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:768285/1‑69 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:609405/1‑69 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:302042/1‑69 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:1138760/1‑69 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:1233928/1‑69 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:1343361/1‑69 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:1402953/1‑69 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:1420649/1‑69 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:1488226/1‑69 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:1804127/1‑69 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:2138644/1‑69 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:2207772/1‑69 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:2409093/1‑69 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:2642529/1‑69 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:2821458/1‑69 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:2828784/1‑69 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:2875402/1‑69 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:2993049/1‑69 (MQ=255)
                                atatTATTGTTATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTTAAGCAATAACACCGTCTTAc                                     >  1:2935872/1‑69 (MQ=255)
                                atatTATTGTAATTTTTCAGTCCATTAAATGTGACATTTGCAAATAGTAAAGCAATaa                                                >  1:3323998/1‑58 (MQ=255)
                                   ttattGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAATAACACCGTCTTACCGt                                  >  1:1578019/1‑69 (MQ=255)
                                   ttattGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAATAACACCGTCTTACCGt                                  >  1:2901321/1‑69 (MQ=255)
                                        gTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAATAACACCGTCTTACCGTCACGt                             <  1:3042265/69‑1 (MQ=255)
                                        gTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAATAACACCGTCTTACCGTCACGt                             <  1:1160476/69‑1 (MQ=255)
                                        gTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAATAACACCGTCTTACCGTCACGt                             <  1:1486296/69‑1 (MQ=255)
                                        gTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAATAACACCGTCTTACCGTCACGt                             <  1:1731277/69‑1 (MQ=255)
                                        gTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAATAACACCGTCTTACCGTCACGt                             <  1:341232/69‑1 (MQ=255)
                                        gTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAATAACACCGTCTTACCGTCACGt                             <  1:2309391/69‑1 (MQ=255)
                                        gTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAATAACACCGTCTTACCGTCACGt                             <  1:2543336/69‑1 (MQ=255)
                                         ttATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAATAACACCGTCTTACCGTCACGt                             <  1:3311078/68‑1 (MQ=255)
                                                                   gTTTGCAAATAGTTAAGCAATAACACCGTCTTACCGTCACGTATCTCGCCGGTTTTGATCATCTCCAgc  >  1:858189/1‑69 (MQ=255)
                                                                   |                                                                    
TTTGTCGGATTGAGCCAATAATAAACAACGAAATATTATTGTTATTTTTCAGTCCATTAAATGTGACGTTTGCAAATAGTTAAGCAATAACACCGTCTTACCGTCACGTATCTCGCCGGTTTTGATCATCTCCAGC  >  minE/1629123‑1629258

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A