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 2,619,680 G→A 39.7% I353I (ATC→ATT)  zntA ← zinc, cobalt and lead efflux system

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,619,6800GA39.7% 46.5 / 62.0 93I353I (ATC→ATT) zntAzinc, cobalt and lead efflux system
Reads supporting (aligned to +/- strand):  ref base G (27/29);  new base A (31/6);  total (58/35)
Fisher's exact test for biased strand distribution p-value = 5.14e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.02e-01

Only 100 of 101 total aligned reads displayed.

TGGCGGCAAACAGCAGCGGTGGCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGTT  >  minE/2619613‑2619747
                                                                   |                                                                   
tGGCGGCAAACAGCAGCGGTGGCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGa                                                                    >  1:940490/1‑69 (MQ=255)
tGGCGGCAAACAGCAGCGGTGGCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGa                                                                    >  1:19884/1‑69 (MQ=255)
tGGCGGCAAACAGCAGCGGTGGCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGa                                                                    >  1:846274/1‑69 (MQ=255)
tGGCGGCAAACAGCAGCGGTGGCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGa                                                                    <  1:2211539/69‑1 (MQ=255)
tGGCGGCAAACAGCAGCGGTGGCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGa                                                                    >  1:1174669/1‑69 (MQ=255)
tGGCGGCAAACAGCAGCGGTGGCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGa                                                                    <  1:2207471/69‑1 (MQ=255)
                     gCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGATACGGCTGAAACGGTCGATaa                                               <  1:1277104/69‑1 (MQ=255)
                     gCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGATACGGCTGAAACGGTCGATaa                                               <  1:2815054/69‑1 (MQ=255)
                     gCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGATACGGCTGAAACGGTCGATaa                                               <  1:3213286/69‑1 (MQ=255)
                     gCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGATACGGCTGAAACGGTCGATaa                                               <  1:3202302/69‑1 (MQ=255)
                     gCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGATACGGCTGAAACGGTCGATaa                                               <  1:135403/69‑1 (MQ=255)
                     gCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGATACGGCTGAAACGGTCGATaa                                               <  1:592156/69‑1 (MQ=255)
                     gCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGATACGGCTGAAACGGTCGATaa                                               <  1:1607366/69‑1 (MQ=255)
                      cACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGATACGGCTGAAACGGTCGATaa                                               <  1:209127/68‑1 (MQ=255)
                         cAGCGTTACCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCg                                           <  1:2481791/69‑1 (MQ=255)
                         cAGCGTTACCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCg                                           <  1:3069154/69‑1 (MQ=255)
                         cAGCGTTACCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCg                                           <  1:1094997/69‑1 (MQ=255)
                         cAGCGTTACCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCg                                           <  1:1403107/69‑1 (MQ=255)
                         cAGCGTTACCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCg                                           <  1:913888/69‑1 (MQ=255)
                         cAGCGTTACCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCg                                           <  1:2477753/69‑1 (MQ=255)
                          aGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGa                                                                    <  1:3066179/43‑1 (MQ=255)
                          aGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGa                                                                    <  1:153234/43‑1 (MQ=255)
                          aGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGa                                                                    <  1:1396610/43‑1 (MQ=255)
                          aGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGa                                                                    <  1:1995341/43‑1 (MQ=255)
                          aGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGa                                                                    <  1:2458816/43‑1 (MQ=255)
                              ttaCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTc                                        >  1:2763744/3‑67 (MQ=255)
                              ttaCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTc                                        >  1:2478615/3‑67 (MQ=255)
                              ttaCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTc                                        >  1:2321372/3‑67 (MQ=255)
                              ttaCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTc                                        >  1:327510/3‑67 (MQ=255)
                              ttaCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTc                                        >  1:2358850/3‑67 (MQ=255)
                              ttaCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTc                                        >  1:2345198/3‑67 (MQ=255)
                              ttaCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTc                                        >  1:2181769/3‑67 (MQ=255)
                              ttaCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTc                                        >  1:1274166/3‑67 (MQ=255)
                              ttaCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTc                                        >  1:1068341/3‑67 (MQ=255)
                               taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCaa                                      >  1:2386833/2‑68 (MQ=255)
                               taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt                                     >  1:240914/2‑69 (MQ=255)
                               taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt                                     >  1:239925/2‑69 (MQ=255)
                               taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt                                     >  1:3102736/2‑69 (MQ=255)
                               taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt                                     >  1:2562213/2‑69 (MQ=255)
                               taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt                                     >  1:2904186/2‑69 (MQ=255)
                               taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt                                     >  1:2985705/2‑69 (MQ=255)
                               taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt                                     >  1:2225678/2‑69 (MQ=255)
                               taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt                                     >  1:378010/2‑69 (MQ=255)
                               taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt                                     >  1:468730/2‑69 (MQ=255)
                               taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt                                     >  1:534268/2‑69 (MQ=255)
                               taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt                                     >  1:578750/2‑69 (MQ=255)
                               taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt                                     >  1:71371/2‑69 (MQ=255)
                               taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt                                     >  1:814914/2‑69 (MQ=255)
                               taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt                                     >  1:958432/2‑69 (MQ=255)
                               taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt                                     >  1:1142794/2‑69 (MQ=255)
                               taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt                                     >  1:22133/2‑69 (MQ=255)
                               taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt                                     >  1:1324010/2‑69 (MQ=255)
                               taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt                                     >  1:1379873/2‑69 (MQ=255)
                               taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt                                     >  1:1559124/2‑69 (MQ=255)
                               taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt                                     >  1:1747421/2‑69 (MQ=255)
                                                     aTCGCGGGCGTATAGATACTGCTGAAACGGTCGATAAACCGCTCAATGGCAg                                >  1:2145346/1‑52 (MQ=255)
                                                     aTCGCGGGCGTATAGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGc                        >  1:3402567/1‑60 (MQ=255)
                                                     aTCGCGGGCGTATAGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGc                        >  1:1946408/1‑60 (MQ=255)
                                                     aTCGCGGGCGTATAGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGc                        >  1:2592990/1‑60 (MQ=255)
                                                     aTCGCGGGCGTATAGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGc                        >  1:1066069/1‑60 (MQ=255)
                                                     aTCGCGGGCGTATAGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGct               >  1:2494269/1‑69 (MQ=255)
                                                     aTCGCGGGCGTATAGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGc                >  1:1045715/1‑68 (MQ=255)
                                                     aTCGAGGGCGTATAGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGc                        >  1:2217670/1‑60 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGGGCGACGCTCTTCGGCTTCTTCGATCAGt   >  1:1399189/1‑69 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCTCGACGCTCTTCGGCTTCTTCGATc      <  1:1085747/66‑1 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATc      <  1:515307/66‑1 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATc      <  1:2053452/66‑1 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATc      <  1:3232107/66‑1 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATc      <  1:2376719/66‑1 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATc      <  1:2054912/66‑1 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAg    >  1:1478339/1‑68 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAg    >  1:1585597/1‑68 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   >  1:606678/1‑69 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   <  1:1356699/69‑1 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   >  1:3269856/1‑69 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   <  1:131902/69‑1 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   <  1:333638/69‑1 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   >  1:74540/1‑69 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   >  1:809476/1‑69 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   <  1:1534725/69‑1 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   >  1:3262884/1‑69 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   >  1:1560508/1‑69 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   >  1:1596296/1‑69 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   <  1:2134562/69‑1 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   >  1:2977207/1‑69 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   >  1:1878254/1‑69 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   >  1:1935434/1‑69 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   <  1:2108503/69‑1 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   >  1:263052/1‑69 (MQ=255)
                                                                 taGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   >  1:2074063/1‑69 (MQ=255)
                                                                 taGATACGGCTGAAACGGGCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATc      <  1:217469/66‑1 (MQ=255)
                                                                  aGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   <  1:1663742/68‑1 (MQ=255)
                                                                   gATACGGCTGAAACGGTCGATAACCCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGtt  >  1:942242/1‑68 (MQ=255)
                                                                   gATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAg    >  1:2372738/1‑66 (MQ=255)
                                                                   gATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   >  1:1045135/1‑67 (MQ=255)
                                                                   gATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   >  1:689790/1‑67 (MQ=255)
                                                                   gATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   >  1:2038740/1‑67 (MQ=255)
                                                                   gATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   >  1:2045592/1‑67 (MQ=255)
                                                                   gATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   >  1:2146700/1‑67 (MQ=255)
                                                                   gATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGt   >  1:102329/1‑67 (MQ=255)
                                                                   |                                                                   
TGGCGGCAAACAGCAGCGGTGGCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCTTCTTCGATCAGTT  >  minE/2619613‑2619747

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