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 1,287,709 C→T 36.8% F252F (TTC→TTT)  shiA → shikimate transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,287,7090CT36.8% 99.1 / 92.9 149F252F (TTC→TTT) shiAshikimate transporter
Reads supporting (aligned to +/- strand):  ref base C (67/27);  new base T (35/20);  total (102/47)
Fisher's exact test for biased strand distribution p-value = 3.64e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.15e-01

Only 100 of 153 total aligned reads displayed.

TTATCAAGCTGCCGCGAAAAAACGCATCCCGGTTATCGAAGCGCTGTTACGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCTTTGCA  >  minE/1287643‑1287772
                                                                  |                                                               
ttATCAAGCTGCCGCGAAAAAACGCATCCCGGTTATCGAAGCGCTGTTACGACATCCCGGTGCTTTcc                                                                >  1:1612242/1‑68 (MQ=255)
       gCTGCCGCGAAAAAACGCATCCCGGTTATCGAAGCGCTGTTACGACATCCCGGTGCTTTCCTGAAGatt                                                        <  1:1301665/69‑1 (MQ=255)
       gCTGCCGCGAAAAAACGCATCCCGGTTATCGAAGCGCTGTTACGACATCCCGGTGCTTTCCTGAAGatt                                                        <  1:3426271/69‑1 (MQ=255)
       gCTGCCGCGAAAAAACGCATCCCGGTTATCGAAGCGCTGTTACGACATCCCGGTGCTTTCCTGAAGat                                                         <  1:736508/68‑1 (MQ=255)
        cTGCCGCGAAAAAACGCATCCCGGTTATCGAAGCGCTGTTACGACATCCCGGTGCTTTCCTGAAGatta                                                       >  1:2242627/1‑69 (MQ=255)
        cTGCCGCGAAAAAACGCATCCCGGTTATCGAAGCGCTGTTACGACATCCCGGTGCTTTCCTGAAGatta                                                       >  1:1249961/1‑69 (MQ=255)
        cTGCCGCGAAAAAACGCATCCCGGTTATCGAAGCGCTGTTACGACATCCCGGTGCTTTCCTGAAGatta                                                       >  1:3156613/1‑69 (MQ=255)
        cTGCCGCGAAAAAACGCATCCCGGTTATCGAAGCGCTGTTACGACATCCCGGTGCTTTCCTGAAGatta                                                       >  1:1537986/1‑69 (MQ=255)
                          tCCCGGTTATCGAAGCGCTGTTACGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCg                                     <  1:3008057/69‑1 (MQ=255)
                          tCCCGGTTATCGAAGCGCTGTTACGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCg                                     <  1:324475/69‑1 (MQ=255)
                                 tATCGAAGCGCTGTTACGACATCCCGGTGCTTTcc                                                                >  1:1377600/1‑35 (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                           <  1:2908378/68‑1 (MQ=255)
                                     gAAGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGAc                           <  1:2973802/68‑1 (MQ=255)
                                     gAAGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGAc                           <  1:1706394/68‑1 (MQ=255)
                                     gAAGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGAc                           <  1:3205676/68‑1 (MQ=255)
                                     gAAGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGAc                           <  1:2771660/68‑1 (MQ=255)
                                     gAAGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGAc                           <  1:2162604/68‑1 (MQ=255)
                                     gAAGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGAc                           <  1:3173151/68‑1 (MQ=255)
                                     gAAGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGAc                           <  1:391628/68‑1 (MQ=255)
                                     gAAGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGAc                           <  1:1334722/68‑1 (MQ=255)
                                     gAAGCTCTGTTACGACATCCCGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGAc                           <  1:952098/68‑1 (MQ=255)
                                           cTGTTACGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTAc                    <  1:259119/69‑1 (MQ=255)
                                            tGTTACGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTAc                    <  1:497562/68‑1 (MQ=255)
                                                aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt               <  1:1048401/69‑1 (MQ=255)
                                                aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt               >  1:409177/1‑69 (MQ=255)
                                                aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt               >  1:2943252/1‑69 (MQ=255)
                                                aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt               <  1:2848587/69‑1 (MQ=255)
                                                aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt               >  1:567490/1‑69 (MQ=255)
                                                aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt               >  1:2583190/1‑69 (MQ=255)
                                                aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt               >  1:2373768/1‑69 (MQ=255)
                                                aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt               <  1:2200706/69‑1 (MQ=255)
                                                aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt               >  1:975906/1‑69 (MQ=255)
                                                aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt               >  1:1734952/1‑69 (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)
                                                aCGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGt               <  1:1649520/69‑1 (MQ=255)
                                                       cccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGcc        <  1:1011211/69‑1 (MQ=255)
                                                       cccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGcc        <  1:3095712/69‑1 (MQ=255)
                                                       cccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGcc        <  1:1569216/69‑1 (MQ=255)
                                                       cccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGcc        <  1:1968092/69‑1 (MQ=255)
                                                        ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGcc        <  1:921244/68‑1 (MQ=255)
                                                        ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCt       >  1:333139/1‑69 (MQ=255)
                                                        ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCt       >  1:1520498/1‑69 (MQ=255)
                                                        ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCt       >  1:1582824/1‑69 (MQ=255)
                                                        ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCt       >  1:1623339/1‑69 (MQ=255)
                                                        ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCt       >  1:53956/1‑69 (MQ=255)
                                                        ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCt       >  1:3052068/1‑69 (MQ=255)
                                                        ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCt       >  1:2764276/1‑69 (MQ=255)
                                                        ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCt       >  1:1947461/1‑69 (MQ=255)
                                                        ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCt       >  1:2657403/1‑69 (MQ=255)
                                                        ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCt       >  1:205185/1‑69 (MQ=255)
                                                        ccGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCt       >  1:2077835/1‑69 (MQ=255)
                                                        ccGGTGCGTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGcc        >  1:3305034/1‑68 (MQ=255)
                                                         cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGGTGACGATGTACAtt                 >  1:3345395/1‑57 (MQ=255)
                                                         cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                 >  1:142723/1‑57 (MQ=255)
                                                         cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                 >  1:1492438/1‑57 (MQ=255)
                                                         cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                 >  1:2488035/1‑57 (MQ=255)
                                                         cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                 >  1:130898/1‑57 (MQ=255)
                                                         cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                 >  1:509596/1‑57 (MQ=255)
                                                         cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                 >  1:2489473/1‑57 (MQ=255)
                                                         cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                 >  1:2545051/1‑57 (MQ=255)
                                                         cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                 >  1:2334657/1‑57 (MQ=255)
                                                         cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                 >  1:2564224/1‑57 (MQ=255)
                                                         cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                 >  1:1603228/1‑57 (MQ=255)
                                                         cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                 >  1:3091864/1‑57 (MQ=255)
                                                         cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                 >  1:719055/1‑57 (MQ=255)
                                                         cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                 >  1:1909335/1‑57 (MQ=255)
                                                         cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                 >  1:2119371/1‑57 (MQ=255)
                                                         cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                 >  1:2028207/1‑57 (MQ=255)
                                                         cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                 >  1:2973716/1‑57 (MQ=255)
                                                         cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                 >  1:2912251/1‑57 (MQ=255)
                                                         cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                 >  1:1769085/1‑57 (MQ=255)
                                                         cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                 >  1:2886202/1‑57 (MQ=255)
                                                         cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                 >  1:2815498/1‑57 (MQ=255)
                                                         cGGTGCTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACAtt                 >  1:2795705/1‑57 (MQ=255)
                                                           gTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATg                       >  1:666939/1‑50 (MQ=255)
                                                           gTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATg                       >  1:2252376/1‑50 (MQ=255)
                                                            tGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCTTTGc   <  1:1773871/69‑1 (MQ=255)
                                                             gCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg          >  1:212019/1‑61 (MQ=255)
                                                             gCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg          >  1:727298/1‑61 (MQ=255)
                                                             gCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg          >  1:743834/1‑61 (MQ=255)
                                                             gCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg          >  1:861515/1‑61 (MQ=255)
                                                             gCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg          >  1:574781/1‑61 (MQ=255)
                                                             gCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg          >  1:31071/1‑61 (MQ=255)
                                                             gCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg          >  1:3079129/1‑61 (MQ=255)
                                                             gCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg          >  1:2952281/1‑61 (MQ=255)
                                                             gCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg          >  1:2951651/1‑61 (MQ=255)
                                                             gCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg          >  1:2717853/1‑61 (MQ=255)
                                                             gCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg          >  1:2923293/1‑61 (MQ=255)
                                                              cTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACATTGTTACTGCCTTTGCa  >  1:1345579/1‑68 (MQ=255)
                                                              cTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACATTGTTACTGCCTTTGCa  >  1:2673759/1‑68 (MQ=255)
                                                              cTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACATTGTTACTGCCTTTGCa  >  1:1100525/1‑68 (MQ=255)
                                                              cTTTTCTGAAGATTATTGCACTACGACTGTGCGAGTTGCTGACGATGTACATTGTTACTGCCTTTGCa  >  1:1779681/1‑68 (MQ=255)
                                                              cTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTg          >  1:671357/1‑60 (MQ=255)
                                                                  |                                                               
TTATCAAGCTGCCGCGAAAAAACGCATCCCGGTTATCGAAGCGCTGTTACGACATCCCGGTGCTTTCCTGAAGATTATTGCGCTACGACTGTGCGAATTGCTGACGATGTACATCGTTACTGCCTTTGCA  >  minE/1287643‑1287772

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