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 2,131,514 A→G 54.8% R478R (CGT→CGC)  deaD ← ATP‑dependent RNA helicase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,131,5140AG54.8% 49.1 / 167.6 201R478R (CGT→CGC) deaDATP‑dependent RNA helicase
Reads supporting (aligned to +/- strand):  ref base A (68/23);  new base G (89/21);  total (157/44)
Fisher's exact test for biased strand distribution p-value = 3.08e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.41e-01

Only 100 of 225 total aligned reads displayed.

TTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGCCACGGTCGTTACGATCGCGCGGACCACGGTCAT  >  minE/2131448‑2131581
                                                                  |                                                                   
ttCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCacg                                                                   >  1:402232/1‑69 (MQ=255)
ttCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCacg                                                                   >  1:1182958/1‑69 (MQ=255)
  cAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCacgac                                                                 >  1:1717531/1‑69 (MQ=255)
  cAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCacgac                                                                 >  1:1741076/1‑69 (MQ=255)
  cAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCacgac                                                                 >  1:1965054/1‑69 (MQ=255)
  cAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCacgac                                                                 >  1:3123884/1‑69 (MQ=255)
         atcatcGCTGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACg                                                          <  1:503813/69‑1 (MQ=255)
         atcatcGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACg                                                          >  1:2954214/1‑69 (MQ=255)
         atcatcGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACg                                                          >  1:2759492/1‑69 (MQ=255)
         atcatcGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACg                                                          <  1:1081731/69‑1 (MQ=255)
         atcatcGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACg                                                          >  1:1058196/1‑69 (MQ=255)
          tcatcGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACg                                                          <  1:2853067/68‑1 (MQ=255)
            atcGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATc                                                       >  1:3323398/1‑69 (MQ=255)
            atcGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATc                                                       >  1:1384158/1‑69 (MQ=255)
            atcGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATc                                                       >  1:1436527/1‑69 (MQ=255)
            atcGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATc                                                       >  1:3371239/1‑69 (MQ=255)
            atcGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATc                                                       >  1:2124240/1‑69 (MQ=255)
            atcGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATc                                                       >  1:2060158/1‑69 (MQ=255)
            atcGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATc                                                       >  1:549280/1‑69 (MQ=255)
            atcGCGGCCCACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATc                                                       <  1:898334/69‑1 (MQ=255)
            atcGCGGCCCACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATc                                                       <  1:2878666/69‑1 (MQ=255)
            atcGCGGCCCACTTCAAAACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATc                                                       <  1:1885124/69‑1 (MQ=255)
                cgGCCCACTTCAATGCGGTAGAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGAct                                                          <  1:2152240/62‑2 (MQ=255)
                     cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGt                                               >  1:469296/1‑68 (MQ=255)
                     cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                                              >  1:2723583/1‑69 (MQ=255)
                     cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                                              >  1:2229389/1‑69 (MQ=255)
                     cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                                              >  1:2195745/1‑69 (MQ=255)
                     cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                                              >  1:41779/1‑69 (MQ=255)
                     cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                                              >  1:583208/1‑69 (MQ=255)
                     cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                                              >  1:588052/1‑69 (MQ=255)
                     cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                                              >  1:775405/1‑69 (MQ=255)
                     cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                                              >  1:822780/1‑69 (MQ=255)
                     cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                                              >  1:85258/1‑69 (MQ=255)
                     cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                                              >  1:1793513/1‑69 (MQ=255)
                     cACTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTc                                              >  1:882772/1‑69 (MQ=255)
                       ctacAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                                                     >  1:2184122/4‑60 (MQ=255)
                       cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGCCGCGGACGATCtt                                                     >  1:1487737/1‑60 (MQ=255)
                       cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                                                     >  1:2363160/1‑60 (MQ=255)
                       cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                                                     >  1:308429/1‑60 (MQ=255)
                       cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                                                     >  1:1297345/1‑60 (MQ=255)
                       cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                                                     >  1:1197606/1‑60 (MQ=255)
                       cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                                                     >  1:2447696/1‑60 (MQ=255)
                       cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                                                     >  1:392703/1‑60 (MQ=255)
                       cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                                                     >  1:434587/1‑60 (MQ=255)
                       cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                                                     >  1:2256770/1‑60 (MQ=255)
                       cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                                                     >  1:1136503/1‑60 (MQ=255)
                       cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                                                     >  1:1981186/1‑60 (MQ=255)
                       cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                                                     >  1:650234/1‑60 (MQ=255)
                       cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                                                     >  1:677335/1‑60 (MQ=255)
                       cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                                                     >  1:1914801/1‑60 (MQ=255)
                       cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                                                     >  1:1811332/1‑60 (MQ=255)
                       cTTCAATACGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                                                     >  1:1693338/1‑60 (MQ=255)
                       cTTCAATACGGTAAAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCtt                                                     >  1:1011348/1‑60 (MQ=255)
                         tCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGAcgcg                                                              <  1:597760/49‑1 (MQ=255)
                         tCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGAcgcg                                                              <  1:2265665/49‑1 (MQ=255)
                         tCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGAcgcg                                                              <  1:2790212/49‑1 (MQ=255)
                            atacGGTACAACTGCATATCGCTAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCAcgc                                       >  1:209339/4‑69 (MQ=255)
                            atacGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCAcgc                                       >  1:1677541/4‑69 (MQ=255)
                            atacGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCAcgc                                       >  1:2607180/4‑69 (MQ=255)
                            atacGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCAcgc                                       >  1:2625988/4‑69 (MQ=255)
                            atacGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCAcgc                                       >  1:2014992/4‑69 (MQ=255)
                            atacGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCAcgc                                       >  1:2293029/4‑69 (MQ=255)
                            atacGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCAcgc                                       >  1:3143286/4‑69 (MQ=255)
                            atacGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCAcgc                                       >  1:1358239/4‑69 (MQ=255)
                            atacGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCAcgc                                       >  1:2945428/4‑69 (MQ=255)
                            atacGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCAcgc                                       >  1:1355634/4‑69 (MQ=255)
                            atacGGTACAACTGCATATCGCCAACATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCAcgc                                       >  1:2336374/4‑69 (MQ=255)
                            atacGGTACAACTGCATATCGCCAACATCACGACGTTCGAGACGCGGACGATCTTCACGGTCGCCAcgc                                       >  1:1885876/4‑69 (MQ=255)
                                 gTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCAcgcg                                      >  1:2517703/1‑65 (MQ=255)
                                 gTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGcc                                  >  1:2462906/1‑69 (MQ=255)
                                 gTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGcc                                  >  1:3014823/1‑69 (MQ=255)
                                 gTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGcc                                  >  1:156328/1‑69 (MQ=255)
                                 gTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGcc                                  >  1:1843613/1‑69 (MQ=255)
                                 gTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGcc                                  >  1:3219501/1‑69 (MQ=255)
                                 gTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGcc                                  >  1:2689184/1‑69 (MQ=255)
                                 gTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGcc                                  >  1:1532445/1‑69 (MQ=255)
                                 gTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGcc                                  >  1:3409820/1‑69 (MQ=255)
                                 gTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGcc                                  >  1:3402429/1‑69 (MQ=255)
                                   aCAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGCCAc                                >  1:2501890/1‑69 (MQ=255)
                                         gCATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGCCACGGTCGt                          >  1:2531174/1‑69 (MQ=255)
                                         gCATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGCCACGGTCGt                          >  1:1100185/1‑69 (MQ=255)
                                          cATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGCCACGGTCGtt                         >  1:2674873/1‑69 (MQ=255)
                                          cATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGCCACGGTCGtt                         >  1:1841395/1‑69 (MQ=255)
                                          cATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGCCACGGTCGtt                         >  1:1547035/1‑69 (MQ=255)
                                          cATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGCCACGGTCGtt                         >  1:1642680/1‑69 (MQ=255)
                                              tCGCCAACATCACGACGTTCACGACGCGGACGCTCTTCACGGTCACCACGCGGGCCACGGTCGTTACGa                     >  1:1126466/1‑69 (MQ=255)
                                              tCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGCCACGGTCGTTACGa                     >  1:789913/1‑69 (MQ=255)
                                              tCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGCCACGGTCGTTACGa                     >  1:460415/1‑69 (MQ=255)
                                              tCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGCCACGGTCGTTACGa                     >  1:2989062/1‑69 (MQ=255)
                                                    aCATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCACGCGGGCCAc                                <  1:2820790/52‑1 (MQ=39)
                                                    aCATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCACGCGGGCCAc                                <  1:159138/52‑1 (MQ=39)
                                                    aCATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCACGCGGGCCAc                                <  1:1928788/52‑1 (MQ=39)
                                                    aCATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCACGCGGGCCAc                                <  1:721049/52‑1 (MQ=39)
                                                    aCATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCACGCGGGCCAc                                <  1:2381557/52‑1 (MQ=39)
                                                    aCATCACGACGTTCGCGACGCGGACGATCTTCACGGTCGCCACGCGGGCCAc                                <  1:2327116/52‑1 (MQ=39)
                                                              gTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGCCACGGTCGTTACGATCGCGCGGACCACGGt     <  1:3261997/69‑1 (MQ=255)
                                                                 cACGACGCGGACGATCTTCACGGTCACCACGCGGGCCACGGTCGTTACGATCGCGCGGACCACGGtcat  >  1:2177136/1‑69 (MQ=255)
                                                                 cACGACGCGGACGATCTTCACGGTCACCACGCGGGCCACGGTCGTTACGATCGCGCGGACCACGGtcat  >  1:2215595/1‑69 (MQ=255)
                                                                 cACGACGCGGACGATCTTCACGGTCACCACGCGGGCCACGGTCGTTACGATCGCGCGGACCACGGtcat  >  1:1293415/1‑69 (MQ=255)
                                                                 cACGACGCGGACGATCTTCACGGTCACCACGCGGGCCACGGTCGTTACGATCGCGCGGACCACGGtcat  >  1:3201788/1‑69 (MQ=255)
                                                                  |                                                                   
TTCAACACCATCATCGCGGCCCACTTCAATGCGGTACAGCTGCATATCGCCAACATCACGACGTTCACGACGCGGACGATCTTCACGGTCACCACGCGGGCCACGGTCGTTACGATCGCGCGGACCACGGTCAT  >  minE/2131448‑2131581

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