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 1,287,739 A→G 41.0% E262E (GAA→GAG)  shiA → shikimate transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,287,7390AG41.0% 60.3 / 117.4 156E262E (GAA→GAG) shiAshikimate transporter
Reads supporting (aligned to +/- strand):  ref base A (75/17);  new base G (36/28);  total (111/45)
Fisher's exact test for biased strand distribution p-value = 1.08e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

Only 100 of 157 total aligned reads displayed.

CCGGTTATCGAAGCGCTGTTACGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCTTTGCACTTAATTATTCAA  >  minE/1287671‑1287785
                                                                    |                                              
     tATCGAAGCGCTGTTACGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGc                                            >  1:2951371/1‑68 (MQ=255)
     tATCGAAGCGCTGTTACGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCt                                           >  1:906839/1‑69 (MQ=255)
     tATCGAAGCGCTGTTACGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCt                                           >  1:3408213/1‑69 (MQ=255)
      aTCGAAGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGAC‑‑TGCGAGTTGCTGAc                                        <  1:1323030/69‑1 (MQ=255)
         gAAGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTTAc                                        <  1:1900398/68‑1 (MQ=255)
         gAAGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGAc                                        <  1:2973802/68‑1 (MQ=255)
         gAAGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGAc                                        <  1:1773623/68‑1 (MQ=255)
         gAAGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGAc                                        <  1:2162604/68‑1 (MQ=255)
         gAAGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGAc                                        <  1:2231117/68‑1 (MQ=255)
         gAAGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGAc                                        <  1:2771660/68‑1 (MQ=255)
         gAAGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGAc                                        <  1:3173151/68‑1 (MQ=255)
         gAAGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGAc                                        <  1:3205676/68‑1 (MQ=255)
         gAAGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGAc                                        <  1:1334722/68‑1 (MQ=255)
         gAAGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGAc                                        <  1:952098/68‑1 (MQ=255)
         gAAGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGAc                                        <  1:3395599/68‑1 (MQ=255)
         gAAGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGAc                                        <  1:1356115/68‑1 (MQ=255)
         gAAGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGAc                                        <  1:391628/68‑1 (MQ=255)
          aaGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGAc                                        <  1:2445040/67‑1 (MQ=255)
            gcgcTGTTACGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATg                                    <  1:2737051/69‑1 (MQ=255)
               cTGTTACGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTAc                                 <  1:259119/69‑1 (MQ=255)
                    aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt                            <  1:2848587/69‑1 (MQ=255)
                    aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt                            >  1:2583190/1‑69 (MQ=255)
                    aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt                            >  1:2943252/1‑69 (MQ=255)
                    aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt                            >  1:409177/1‑69 (MQ=255)
                    aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt                            <  1:2200706/69‑1 (MQ=255)
                    aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt                            >  1:567490/1‑69 (MQ=255)
                    aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt                            <  1:1048401/69‑1 (MQ=255)
                    aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt                            >  1:2124456/1‑69 (MQ=255)
                    aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt                            >  1:975906/1‑69 (MQ=255)
                    aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt                            <  1:1649520/69‑1 (MQ=255)
                    aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt                            >  1:1552122/1‑69 (MQ=255)
                    aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt                            >  1:1093778/1‑69 (MQ=255)
                    aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt                            >  1:1675631/1‑69 (MQ=255)
                    aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt                            >  1:1266961/1‑69 (MQ=255)
                    aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt                            >  1:1280083/1‑69 (MQ=255)
                           cccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGcc                     <  1:1011211/69‑1 (MQ=255)
                           cccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGcc                     <  1:1569216/69‑1 (MQ=255)
                           cccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGcc                     <  1:3080065/69‑1 (MQ=255)
                           cccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGcc                     <  1:3095712/69‑1 (MQ=255)
                           cccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGcc                     <  1:564238/69‑1 (MQ=255)
                            ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt                            >  1:1589053/1‑61 (MQ=255)
                            ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGcc                     <  1:1944148/68‑1 (MQ=255)
                            ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGcc                     <  1:921244/68‑1 (MQ=255)
                            ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCt                    >  1:333139/1‑69 (MQ=255)
                            ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCt                    >  1:130385/1‑69 (MQ=255)
                            ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCt                    >  1:1520498/1‑69 (MQ=255)
                            ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCt                    >  1:837580/1‑69 (MQ=255)
                            ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCt                    >  1:266058/1‑69 (MQ=255)
                            ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCt                    >  1:1897395/1‑69 (MQ=255)
                            ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCt                    >  1:205185/1‑69 (MQ=255)
                            ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCt                    >  1:1947461/1‑69 (MQ=255)
                            ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCt                    >  1:1623339/1‑69 (MQ=255)
                            ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCt                    >  1:1707719/1‑69 (MQ=255)
                            ccGGTGCGTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGcc                     >  1:3305034/1‑68 (MQ=255)
                             cGGTGCTTTTCTGAAGATTCTTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                              >  1:2904804/1‑57 (MQ=255)
                             cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                              >  1:2564224/1‑57 (MQ=255)
                             cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                              >  1:643894/1‑57 (MQ=255)
                             cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                              >  1:509596/1‑57 (MQ=255)
                             cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                              >  1:466848/1‑57 (MQ=255)
                             cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                              >  1:2119371/1‑57 (MQ=255)
                             cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                              >  1:2028207/1‑57 (MQ=255)
                             cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                              >  1:1769085/1‑57 (MQ=255)
                             cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                              >  1:142723/1‑57 (MQ=255)
                             cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                              >  1:2304281/1‑57 (MQ=255)
                             cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                              >  1:1492438/1‑57 (MQ=255)
                             cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                              >  1:2973716/1‑57 (MQ=255)
                             cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                              >  1:2334657/1‑57 (MQ=255)
                             cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                              >  1:2488035/1‑57 (MQ=255)
                             cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                              >  1:1603228/1‑57 (MQ=255)
                             cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                              >  1:2545051/1‑57 (MQ=255)
                             cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                              >  1:2815498/1‑57 (MQ=255)
                             cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                              >  1:2912251/1‑57 (MQ=255)
                             cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                              >  1:2832889/1‑57 (MQ=255)
                             cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                              >  1:2489473/1‑57 (MQ=255)
                                 gCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg                       >  1:743834/1‑61 (MQ=255)
                                 gCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg                       >  1:727298/1‑61 (MQ=255)
                                 gCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg                       >  1:676849/1‑61 (MQ=255)
                                 gCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg                       >  1:1194297/1‑61 (MQ=255)
                                 gCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg                       >  1:2717853/1‑61 (MQ=255)
                                 gCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg                       >  1:2919905/1‑61 (MQ=255)
                                 gCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg                       >  1:31071/1‑61 (MQ=255)
                                 gCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg                       >  1:3079129/1‑61 (MQ=255)
                                 gCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg                       >  1:3050114/1‑61 (MQ=255)
                                 gCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg                       >  1:300348/1‑61 (MQ=255)
                                 gCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg                       >  1:2952281/1‑61 (MQ=255)
                                  cTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACATTGTTACTGCCTTTGCa               >  1:1779681/1‑68 (MQ=255)
                                  cTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg                       >  1:671357/1‑60 (MQ=255)
                                            gATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACATTGTTACTGCCTTTGCACTTAattat      <  1:1709085/67‑1 (MQ=255)
                                            gATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACATTGTTACTGCCTTTGCACTTAattat      <  1:2795478/67‑1 (MQ=255)
                                            gATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACATTGTTACTGCCTTTGCACTTAattat      <  1:424617/67‑1 (MQ=255)
                                            gATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACATTGTTACTGCCTTTGCACTTAattat      <  1:577707/67‑1 (MQ=255)
                                               tattGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCTTTGCACTTAATTATTCaa  >  1:1804552/1‑68 (MQ=255)
                                               tattGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCTTTGCACTTAATTATTCaa  >  1:1067760/1‑68 (MQ=255)
                                               tattGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCTTTGCACTTAATTATTCaa  >  1:1861026/1‑68 (MQ=255)
                                               tattGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCTTTGCACTTAATTATTCaa  >  1:385875/1‑68 (MQ=255)
                                               tattGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCTTTGCACTTAATTATTCaa  >  1:132421/1‑68 (MQ=255)
                                               tattGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCTTTGCACTTAATTATTCaa  >  1:1490488/1‑68 (MQ=255)
                                               tattGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCTTTGCACTTAATTATTCaa  >  1:3115415/1‑68 (MQ=255)
                                               tattGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCTTTGCACTTAATTATTCaa  >  1:2890132/1‑68 (MQ=255)
                                               tattGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTACCTTTGCACTTAATTATTCaa  >  1:878134/1‑68 (MQ=255)
                                                                    |                                              
CCGGTTATCGAAGCGCTGTTACGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCTTTGCACTTAATTATTCAA  >  minE/1287671‑1287785

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